Starting phenix.real_space_refine on Tue Mar 19 07:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/03_2024/4uy8_2773_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.183 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 143 5.21 5 S 91 5.16 5 C 46104 2.51 5 N 17191 2.21 5 O 26408 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92995 Number of models: 1 Model: "" Number of chains: 47 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1117 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "6" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 227 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "7" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 170 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "8" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 61274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2854, 61274 Classifications: {'RNA': 2854} Modifications used: {'rna2p_pur': 268, 'rna2p_pyr': 143, 'rna3p_pur': 1380, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 411, 'rna3p': 2442} Chain breaks: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1649 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p': 1, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 65} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Classifications: {'peptide': 2} Modifications used: {'COO': 2, 'NH2NOTPRO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Unusual residues: {' MG': 135} Classifications: {'undetermined': 135} Link IDs: {None: 134} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 416 Classifications: {'water': 416} Link IDs: {None: 415} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1819 SG CYS 4 11 117.787 76.424 177.464 1.00 27.97 S ATOM 1844 SG CYS 4 14 116.976 77.821 176.178 1.00 12.31 S ATOM 1947 SG CYS 4 27 118.821 78.134 177.054 1.00 25.55 S Time building chain proxies: 36.50, per 1000 atoms: 0.39 Number of scatterers: 92995 At special positions: 0 Unit cell: (201.3, 210.1, 258.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 3049 15.00 Mg 143 11.99 O 26408 8.00 N 17191 7.00 C 46104 6.00 H 8 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 89763 O4' C V 56 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.02 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 102 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 102 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 14 " Number of angles added : 3 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 41 sheets defined 24.4% alpha, 10.6% beta 985 base pairs and 1495 stacking pairs defined. Time for finding SS restraints: 40.63 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 removed outlier: 4.721A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 23 Processing helix chain '2' and resid 25 through 36 Processing helix chain '3' and resid 7 through 10 No H-bonds generated for 'chain '3' and resid 7 through 10' Processing helix chain '3' and resid 37 through 43 Processing helix chain '3' and resid 54 through 60 Processing helix chain '4' and resid 31 through 33 No H-bonds generated for 'chain '4' and resid 31 through 33' Processing helix chain '5' and resid 4 through 7 No H-bonds generated for 'chain '5' and resid 4 through 7' Processing helix chain '5' and resid 9 through 18 removed outlier: 3.708A pdb=" N SER 5 16 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 46 removed outlier: 3.584A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '5' and resid 95 through 103 removed outlier: 3.664A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 137 Processing helix chain '5' and resid 140 through 147 removed outlier: 3.790A pdb=" N GLU 5 145 " --> pdb=" O ALA 5 141 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 6 No H-bonds generated for 'chain '6' and resid 4 through 6' Processing helix chain '6' and resid 16 through 19 No H-bonds generated for 'chain '6' and resid 16 through 19' Processing helix chain '6' and resid 25 through 28 No H-bonds generated for 'chain '6' and resid 25 through 28' Processing helix chain '8' and resid 14 through 23 Processing helix chain '8' and resid 44 through 52 Processing helix chain '8' and resid 54 through 58 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.503A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.592A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.546A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.583A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.600A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 removed outlier: 3.672A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 104 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.578A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 12 No H-bonds generated for 'chain 'H' and resid 10 through 12' Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'I' and resid 24 through 27 removed outlier: 3.621A pdb=" N LEU I 27 " --> pdb=" O GLY I 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 27' Processing helix chain 'I' and resid 34 through 36 No H-bonds generated for 'chain 'I' and resid 34 through 36' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 107 through 115 removed outlier: 4.480A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 132 removed outlier: 3.929A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 27 through 37 removed outlier: 3.893A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 106 removed outlier: 3.940A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.573A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 57 removed outlier: 3.873A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.651A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.527A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 81 removed outlier: 4.466A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 5 through 21 removed outlier: 4.274A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'O' and resid 68 through 85 removed outlier: 3.551A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 112 removed outlier: 5.067A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 11 removed outlier: 3.687A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.968A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 31 through 70 removed outlier: 4.149A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 94 through 100 removed outlier: 3.591A pdb=" N PHE Q 100 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.602A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 23 No H-bonds generated for 'chain 'S' and resid 21 through 23' Processing helix chain 'S' and resid 29 through 38 removed outlier: 3.645A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 Processing helix chain 'T' and resid 18 through 23 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.599A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'X' and resid 54 through 61 Processing helix chain 'X' and resid 63 through 71 removed outlier: 3.958A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.617A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 33 Processing helix chain 'Y' and resid 40 through 58 removed outlier: 3.985A pdb=" N GLN Y 45 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU Y 56 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU Y 57 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN Y 58 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing sheet with id= A, first strand: chain '0' and resid 27 through 29 Processing sheet with id= B, first strand: chain '1' and resid 6 through 11 Processing sheet with id= C, first strand: chain '1' and resid 35 through 39 Processing sheet with id= D, first strand: chain '4' and resid 17 through 19 Processing sheet with id= E, first strand: chain '8' and resid 62 through 65 removed outlier: 7.994A pdb=" N ASN 8 5 " --> pdb=" O ASP 8 43 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP 8 43 " --> pdb=" O ASN 8 5 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE 8 89 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL 8 92 " --> pdb=" O ALA 8 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA 8 74 " --> pdb=" O VAL 8 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= G, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.731A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.712A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'D' and resid 12 through 15 Processing sheet with id= K, first strand: chain 'D' and resid 25 through 28 Processing sheet with id= L, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.355A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.828A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= O, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= P, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= Q, first strand: chain 'J' and resid 17 through 19 removed outlier: 6.415A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'J' and resid 75 through 77 Processing sheet with id= S, first strand: chain 'K' and resid 5 through 9 removed outlier: 3.509A pdb=" N CYS K 21 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET K 7 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL K 19 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.282A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.630A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.693A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= X, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= Y, first strand: chain 'O' and resid 91 through 93 removed outlier: 3.647A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 37 through 43 removed outlier: 3.779A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 70 through 74 removed outlier: 3.772A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.686A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 20 through 23 Processing sheet with id= AD, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= AE, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.212A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'S' and resid 4 through 7 removed outlier: 6.577A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 61 through 63 removed outlier: 3.837A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.627A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= AJ, first strand: chain 'U' and resid 40 through 45 Processing sheet with id= AK, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AL, first strand: chain 'U' and resid 24 through 27 removed outlier: 6.883A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 12 through 14 Processing sheet with id= AN, first strand: chain 'X' and resid 35 through 38 Processing sheet with id= AO, first strand: chain 'Z' and resid 35 through 37 607 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2477 hydrogen bonds 3952 hydrogen bond angles 0 basepair planarities 985 basepair parallelities 1495 stacking parallelities Total time for adding SS restraints: 171.40 Time building geometry restraints manager: 45.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 8 1.06 - 1.26: 7257 1.26 - 1.46: 52856 1.46 - 1.67: 40333 1.67 - 1.87: 168 Bond restraints: 100622 Sorted by residual: bond pdb=" C4 5MU V 54 " pdb=" C5 5MU V 54 " ideal model delta sigma weight residual 1.802 1.441 0.361 2.00e-02 2.50e+03 3.27e+02 bond pdb=" N1 5MU V 54 " pdb=" C6 5MU V 54 " ideal model delta sigma weight residual 1.635 1.382 0.253 2.00e-02 2.50e+03 1.59e+02 bond pdb=" CA ARG S 88 " pdb=" C ARG S 88 " ideal model delta sigma weight residual 1.523 1.374 0.149 1.25e-02 6.40e+03 1.42e+02 bond pdb=" N3 5MU V 54 " pdb=" C4 5MU V 54 " ideal model delta sigma weight residual 1.182 1.404 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CA MET S 86 " pdb=" C MET S 86 " ideal model delta sigma weight residual 1.524 1.388 0.135 1.26e-02 6.30e+03 1.15e+02 ... (remaining 100617 not shown) Histogram of bond angle deviations from ideal: 54.48 - 74.61: 2 74.61 - 94.75: 12 94.75 - 114.88: 83896 114.88 - 135.02: 67032 135.02 - 155.15: 30 Bond angle restraints: 150972 Sorted by residual: angle pdb=" O ARG 7 23 " pdb=" C ARG 7 23 " pdb=" N PRO 7 24 " ideal model delta sigma weight residual 121.32 147.82 -26.50 1.15e+00 7.56e-01 5.31e+02 angle pdb=" C4' U A2585 " pdb=" C3' U A2585 " pdb=" O3' U A2585 " ideal model delta sigma weight residual 113.00 83.11 29.89 1.50e+00 4.44e-01 3.97e+02 angle pdb=" C4' G A2608 " pdb=" C3' G A2608 " pdb=" O3' G A2608 " ideal model delta sigma weight residual 113.00 141.42 -28.42 1.50e+00 4.44e-01 3.59e+02 angle pdb=" N ASN 7 14 " pdb=" CA ASN 7 14 " pdb=" CB ASN 7 14 " ideal model delta sigma weight residual 111.01 138.91 -27.90 1.56e+00 4.11e-01 3.20e+02 angle pdb=" CA ARG 7 23 " pdb=" C ARG 7 23 " pdb=" N PRO 7 24 " ideal model delta sigma weight residual 118.44 90.93 27.51 1.59e+00 3.96e-01 2.99e+02 ... (remaining 150967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 56291 35.26 - 70.53: 7307 70.53 - 105.79: 841 105.79 - 141.06: 17 141.06 - 176.32: 20 Dihedral angle restraints: 64476 sinusoidal: 54640 harmonic: 9836 Sorted by residual: dihedral pdb=" N ASP 7 16 " pdb=" C ASP 7 16 " pdb=" CA ASP 7 16 " pdb=" CB ASP 7 16 " ideal model delta harmonic sigma weight residual 122.80 94.77 28.03 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" CA ASP 7 21 " pdb=" C ASP 7 21 " pdb=" N HIS 7 22 " pdb=" CA HIS 7 22 " ideal model delta harmonic sigma weight residual 180.00 126.30 53.70 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" O4' U A 546 " pdb=" C1' U A 546 " pdb=" N1 U A 546 " pdb=" C2 U A 546 " ideal model delta sinusoidal sigma weight residual 200.00 28.34 171.66 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 64473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 19315 0.352 - 0.704: 34 0.704 - 1.056: 2 1.056 - 1.408: 2 1.408 - 1.761: 6 Chirality restraints: 19359 Sorted by residual: chirality pdb=" CB VAL 5 27 " pdb=" CA VAL 5 27 " pdb=" CG1 VAL 5 27 " pdb=" CG2 VAL 5 27 " both_signs ideal model delta sigma weight residual False -2.63 -0.87 -1.76 2.00e-01 2.50e+01 7.75e+01 chirality pdb=" CG LEU 5 81 " pdb=" CB LEU 5 81 " pdb=" CD1 LEU 5 81 " pdb=" CD2 LEU 5 81 " both_signs ideal model delta sigma weight residual False -2.59 -0.91 -1.68 2.00e-01 2.50e+01 7.02e+01 chirality pdb=" CB ILE 5 123 " pdb=" CA ILE 5 123 " pdb=" CG1 ILE 5 123 " pdb=" CG2 ILE 5 123 " both_signs ideal model delta sigma weight residual False 2.64 1.03 1.61 2.00e-01 2.50e+01 6.50e+01 ... (remaining 19356 not shown) Planarity restraints: 7768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU V 54 " 0.006 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 5MU V 54 " 0.421 2.00e-02 2.50e+03 pdb=" O4' 5MU V 54 " 0.666 2.00e-02 2.50e+03 pdb=" C3' 5MU V 54 " -0.622 2.00e-02 2.50e+03 pdb=" O3' 5MU V 54 " -0.563 2.00e-02 2.50e+03 pdb=" C2' 5MU V 54 " -0.190 2.00e-02 2.50e+03 pdb=" O2' 5MU V 54 " 0.918 2.00e-02 2.50e+03 pdb=" C1' 5MU V 54 " 0.229 2.00e-02 2.50e+03 pdb=" N1 5MU V 54 " -0.865 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 39 " -0.183 2.00e-02 2.50e+03 1.75e-01 9.16e+02 pdb=" N9 G V 39 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G V 39 " 0.261 2.00e-02 2.50e+03 pdb=" N7 G V 39 " 0.189 2.00e-02 2.50e+03 pdb=" C5 G V 39 " 0.055 2.00e-02 2.50e+03 pdb=" C6 G V 39 " -0.084 2.00e-02 2.50e+03 pdb=" O6 G V 39 " -0.211 2.00e-02 2.50e+03 pdb=" N1 G V 39 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G V 39 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G V 39 " 0.308 2.00e-02 2.50e+03 pdb=" N3 G V 39 " -0.262 2.00e-02 2.50e+03 pdb=" C4 G V 39 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C V 4 " -0.305 2.00e-02 2.50e+03 1.69e-01 6.44e+02 pdb=" N1 C V 4 " 0.015 2.00e-02 2.50e+03 pdb=" C2 C V 4 " 0.071 2.00e-02 2.50e+03 pdb=" O2 C V 4 " 0.089 2.00e-02 2.50e+03 pdb=" N3 C V 4 " 0.025 2.00e-02 2.50e+03 pdb=" C4 C V 4 " 0.039 2.00e-02 2.50e+03 pdb=" N4 C V 4 " -0.290 2.00e-02 2.50e+03 pdb=" C5 C V 4 " 0.208 2.00e-02 2.50e+03 pdb=" C6 C V 4 " 0.149 2.00e-02 2.50e+03 ... (remaining 7765 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 7 1.62 - 2.37: 915 2.37 - 3.11: 70847 3.11 - 3.86: 248127 3.86 - 4.60: 370834 Warning: very small nonbonded interaction distances. Nonbonded interactions: 690730 Sorted by model distance: nonbonded pdb=" NH1 ARG F 79 " pdb=" C1' C V 56 " model vdw 0.879 3.250 nonbonded pdb=" O PRO 7 24 " pdb=" O2' A V 76 " model vdw 1.043 2.200 nonbonded pdb=" NH1 ARG F 79 " pdb=" O4' C V 56 " model vdw 1.237 2.350 nonbonded pdb=" OP1 A A2602 " pdb=" OP1 C V 75 " model vdw 1.395 2.800 nonbonded pdb=" O2' G A2061 " pdb=" N4 C A2063 " model vdw 1.396 2.350 ... (remaining 690725 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=0.89 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.220 Extract box with map and model: 13.680 Check model and map are aligned: 1.050 Set scattering table: 0.660 Process input model: 363.880 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 387.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 : 0.010 0.361 100614 Z= 0.617 Angle : 1.501 70.523 150960 Z= 0.794 Chirality : 0.070 1.761 19359 Planarity : 0.012 0.578 7768 Dihedral : 23.514 176.323 58134 Min Nonbonded Distance : 0.879 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 6.82 % Allowed : 16.31 % Favored : 76.87 % Rotamer: Outliers : 11.16 % Allowed : 12.91 % Favored : 75.94 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.88 % Twisted General : 0.27 % 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: -5.04 (0.12), residues: 3402 helix: -3.74 (0.11), residues: 854 sheet: -2.86 (0.21), residues: 532 loop : -3.44 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP R 92 HIS 0.018 0.003 HIS S 7 PHE 0.038 0.004 PHE D 118 TYR 0.029 0.004 TYR J 75 ARG 0.026 0.002 ARG Q 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1034 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 HIS cc_start: 0.5234 (OUTLIER) cc_final: 0.4813 (p-80) REVERT: 5 43 LYS cc_start: 0.3182 (OUTLIER) cc_final: 0.2963 (ttpt) REVERT: 5 125 ARG cc_start: -0.0324 (OUTLIER) cc_final: -0.2645 (ptt180) REVERT: 5 143 MET cc_start: 0.0587 (tmt) cc_final: 0.0076 (mmp) REVERT: 6 26 MET cc_start: 0.3694 (OUTLIER) cc_final: 0.0491 (ppp) REVERT: C 144 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6198 (mt-10) REVERT: C 166 ARG cc_start: 0.4829 (OUTLIER) cc_final: 0.3942 (ptm160) REVERT: F 46 LYS cc_start: 0.0349 (OUTLIER) cc_final: -0.0513 (mmmt) REVERT: G 151 ARG cc_start: 0.4091 (OUTLIER) cc_final: 0.3676 (mpt90) REVERT: L 40 SER cc_start: 0.7276 (p) cc_final: 0.7037 (t) REVERT: N 106 ASP cc_start: 0.4991 (p0) cc_final: 0.4479 (p0) REVERT: Q 50 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6874 (mmt-90) REVERT: Q 63 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7013 (ptt90) REVERT: S 4 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7909 (pt) REVERT: S 60 HIS cc_start: 0.7157 (t-90) cc_final: 0.6930 (t-170) REVERT: Y 8 GLU cc_start: 0.6780 (tp30) cc_final: 0.6191 (tp30) REVERT: Y 29 ARG cc_start: 0.6604 (mtm-85) cc_final: 0.6319 (ttm170) REVERT: Z 2 LYS cc_start: 0.2797 (OUTLIER) cc_final: 0.1018 (mmtp) outliers start: 313 outliers final: 93 residues processed: 1232 average time/residue: 1.0641 time to fit residues: 2108.6700 Evaluate side-chains 833 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 729 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 5 residue 43 LYS Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 125 ARG Chi-restraints excluded: chain 6 residue 26 MET Chi-restraints excluded: chain 7 residue 11 LYS Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 18 LYS Chi-restraints excluded: chain 7 residue 21 ASP Chi-restraints excluded: chain 8 residue 65 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 50 ARG Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 0.0470 chunk 482 optimal weight: 2.9990 chunk 267 optimal weight: 10.9990 chunk 164 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 499 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 578 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 57 ASN 7 17 ASN 7 22 HIS 8 44 HIS 8 87 GLN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 152 GLN C 162 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 185 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN H 20 ASN H 43 ASN J 80 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN O 100 HIS O 104 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN R 18 GLN R 66 HIS ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Z 33 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 100614 Z= 0.202 Angle : 0.669 15.229 150960 Z= 0.349 Chirality : 0.035 0.284 19359 Planarity : 0.006 0.125 7768 Dihedral : 23.721 179.383 51592 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 42.07 Ramachandran Plot: Outliers : 3.06 % Allowed : 12.43 % Favored : 84.51 % Rotamer: Outliers : 8.91 % Allowed : 22.96 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.13), residues: 3402 helix: -1.82 (0.16), residues: 873 sheet: -2.47 (0.21), residues: 537 loop : -2.92 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 38 HIS 0.018 0.002 HIS N 16 PHE 0.020 0.002 PHE X 28 TYR 0.021 0.002 TYR F 127 ARG 0.017 0.001 ARG N 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 832 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 24 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7565 (mmt90) REVERT: 5 143 MET cc_start: -0.0238 (OUTLIER) cc_final: -0.0553 (ptm) REVERT: 6 17 MET cc_start: 0.2281 (ppp) cc_final: -0.1179 (mmt) REVERT: 6 26 MET cc_start: 0.3738 (OUTLIER) cc_final: 0.0300 (ppp) REVERT: D 68 PHE cc_start: 0.7105 (m-80) cc_final: 0.6863 (m-80) REVERT: D 70 LYS cc_start: 0.6622 (mmmt) cc_final: 0.6328 (mttm) REVERT: F 46 LYS cc_start: 0.0731 (OUTLIER) cc_final: -0.0907 (mmmt) REVERT: G 151 ARG cc_start: 0.5359 (OUTLIER) cc_final: 0.5131 (ttt90) REVERT: G 159 LYS cc_start: 0.4013 (mtpt) cc_final: 0.3032 (mtpt) REVERT: J 16 TYR cc_start: 0.6939 (m-80) cc_final: 0.6730 (m-10) REVERT: K 82 ASN cc_start: 0.5783 (m-40) cc_final: 0.5566 (m-40) REVERT: N 94 TYR cc_start: 0.6808 (m-80) cc_final: 0.6465 (m-80) REVERT: N 106 ASP cc_start: 0.5113 (p0) cc_final: 0.4813 (p0) REVERT: Q 55 GLN cc_start: 0.7156 (mp10) cc_final: 0.6887 (mp10) REVERT: Q 63 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7029 (ptt90) REVERT: R 53 PHE cc_start: 0.5594 (m-80) cc_final: 0.5368 (m-80) REVERT: R 89 HIS cc_start: 0.6942 (t-90) cc_final: 0.6548 (t-90) REVERT: S 88 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7928 (mtp85) REVERT: U 4 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7218 (mm) REVERT: U 20 LYS cc_start: 0.4881 (mmtm) cc_final: 0.4553 (mmtm) REVERT: Y 8 GLU cc_start: 0.6744 (tp30) cc_final: 0.5525 (tp30) REVERT: Y 27 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7880 (t0) REVERT: Z 2 LYS cc_start: 0.3350 (OUTLIER) cc_final: 0.1731 (mmtp) outliers start: 250 outliers final: 167 residues processed: 954 average time/residue: 0.9681 time to fit residues: 1525.4158 Evaluate side-chains 918 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 742 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain 6 residue 26 MET Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 24 ASN Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 77 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 321 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 481 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 579 optimal weight: 9.9990 chunk 626 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 574 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 464 optimal weight: 4.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 18 HIS ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 ASN ** 6 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN 7 22 HIS ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.157 100614 Z= 0.426 Angle : 0.957 20.587 150960 Z= 0.480 Chirality : 0.044 0.343 19359 Planarity : 0.008 0.166 7768 Dihedral : 24.494 179.030 51496 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 69.88 Ramachandran Plot: Outliers : 2.91 % Allowed : 17.55 % Favored : 79.54 % Rotamer: Outliers : 12.87 % Allowed : 24.03 % Favored : 63.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.12), residues: 3402 helix: -2.13 (0.15), residues: 837 sheet: -2.51 (0.21), residues: 518 loop : -3.27 (0.12), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 78 HIS 0.085 0.003 HIS J 80 PHE 0.033 0.004 PHE C 239 TYR 0.026 0.003 TYR C 95 ARG 0.019 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 970 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 3 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: 0 18 HIS cc_start: 0.7922 (m-70) cc_final: 0.7176 (m170) REVERT: 0 36 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6823 (mttm) REVERT: 0 38 LEU cc_start: 0.7661 (mp) cc_final: 0.7395 (mp) REVERT: 1 29 LYS cc_start: 0.7046 (mttt) cc_final: 0.6679 (tppt) REVERT: 3 34 LYS cc_start: 0.7710 (ptmt) cc_final: 0.7248 (ptmt) REVERT: 5 61 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.4201 (mmt180) REVERT: 5 132 TYR cc_start: 0.4313 (OUTLIER) cc_final: 0.2581 (m-10) REVERT: 5 143 MET cc_start: 0.0533 (tmt) cc_final: -0.0765 (mmp) REVERT: 6 26 MET cc_start: 0.4222 (mpp) cc_final: 0.1473 (ppp) REVERT: 8 17 SER cc_start: 0.7930 (m) cc_final: 0.7490 (t) REVERT: C 180 MET cc_start: 0.7164 (mtt) cc_final: 0.6904 (mtt) REVERT: C 261 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6574 (ptm160) REVERT: C 263 ASP cc_start: 0.6460 (OUTLIER) cc_final: 0.6251 (m-30) REVERT: D 70 LYS cc_start: 0.7498 (mmmt) cc_final: 0.6725 (mttp) REVERT: D 150 GLN cc_start: 0.6510 (tt0) cc_final: 0.6186 (tp40) REVERT: F 71 LYS cc_start: 0.5760 (OUTLIER) cc_final: 0.4929 (pttp) REVERT: G 115 GLN cc_start: 0.6395 (pm20) cc_final: 0.5614 (tp40) REVERT: G 138 GLN cc_start: 0.6543 (tt0) cc_final: 0.6261 (tt0) REVERT: I 16 MET cc_start: 0.3059 (OUTLIER) cc_final: 0.2724 (mtt) REVERT: J 1 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7124 (tmm) REVERT: J 116 ARG cc_start: 0.7286 (mtp180) cc_final: 0.6558 (mtp85) REVERT: J 119 PHE cc_start: 0.8410 (t80) cc_final: 0.8047 (t80) REVERT: L 36 LYS cc_start: 0.8421 (mttt) cc_final: 0.7922 (mptt) REVERT: L 117 THR cc_start: 0.5864 (p) cc_final: 0.5539 (t) REVERT: N 94 TYR cc_start: 0.7773 (m-80) cc_final: 0.7234 (m-80) REVERT: N 106 ASP cc_start: 0.7651 (p0) cc_final: 0.7393 (p0) REVERT: Q 29 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6504 (mmt90) REVERT: Q 63 ARG cc_start: 0.7592 (ppt170) cc_final: 0.7078 (ptt90) REVERT: R 1 MET cc_start: 0.8073 (tpt) cc_final: 0.6464 (pmm) REVERT: R 93 PHE cc_start: 0.7736 (p90) cc_final: 0.7486 (p90) REVERT: S 9 HIS cc_start: 0.8175 (m90) cc_final: 0.7876 (m-70) REVERT: S 29 VAL cc_start: 0.8685 (m) cc_final: 0.8402 (t) REVERT: T 70 HIS cc_start: 0.5641 (OUTLIER) cc_final: 0.5231 (m-70) REVERT: U 3 LYS cc_start: 0.7888 (mttt) cc_final: 0.7430 (tttt) REVERT: U 84 PHE cc_start: 0.5483 (m-80) cc_final: 0.5246 (m-80) REVERT: W 14 ASP cc_start: 0.7450 (m-30) cc_final: 0.7229 (m-30) REVERT: W 19 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.5526 (ppt-90) REVERT: W 61 LYS cc_start: 0.7821 (mmmm) cc_final: 0.7529 (mmmm) REVERT: X 1 SER cc_start: 0.8627 (m) cc_final: 0.8314 (p) REVERT: Z 2 LYS cc_start: 0.4453 (OUTLIER) cc_final: 0.3034 (mmtp) REVERT: Z 44 ARG cc_start: 0.6214 (mmt-90) cc_final: 0.5668 (mtt-85) outliers start: 361 outliers final: 234 residues processed: 1148 average time/residue: 0.9554 time to fit residues: 1808.2269 Evaluate side-chains 1113 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 867 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 61 ARG Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 8 residue 31 TYR Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain P residue 110 LYS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain W residue 16 GLU Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 572 optimal weight: 5.9990 chunk 435 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 389 optimal weight: 0.7980 chunk 581 optimal weight: 6.9990 chunk 615 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 551 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 3 GLN 1 44 GLN ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN F 51 ASN G 114 HIS H 20 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS U 45 GLN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** X 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Z 33 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 100614 Z= 0.235 Angle : 0.629 16.061 150960 Z= 0.331 Chirality : 0.034 0.299 19359 Planarity : 0.005 0.140 7768 Dihedral : 24.038 179.922 51465 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 53.02 Ramachandran Plot: Outliers : 2.53 % Allowed : 14.02 % Favored : 83.45 % Rotamer: Outliers : 10.41 % Allowed : 28.84 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.13), residues: 3402 helix: -1.50 (0.17), residues: 842 sheet: -2.34 (0.22), residues: 505 loop : -3.06 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 212 HIS 0.031 0.002 HIS C 57 PHE 0.018 0.002 PHE F 176 TYR 0.023 0.002 TYR H 25 ARG 0.014 0.001 ARG O 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 907 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7882 (m-70) cc_final: 0.6997 (m170) REVERT: 0 36 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6761 (mttm) REVERT: 3 34 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7499 (ptmt) REVERT: 3 42 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8128 (m-70) REVERT: 5 40 GLU cc_start: 0.6227 (tp30) cc_final: 0.5946 (tp30) REVERT: 5 61 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.4452 (mmt180) REVERT: 5 123 ILE cc_start: 0.1792 (OUTLIER) cc_final: 0.1023 (pt) REVERT: 5 132 TYR cc_start: 0.4397 (OUTLIER) cc_final: 0.3385 (m-80) REVERT: 5 143 MET cc_start: 0.0341 (tmt) cc_final: -0.0545 (mmt) REVERT: 7 23 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6621 (ptt90) REVERT: 8 17 SER cc_start: 0.7851 (m) cc_final: 0.7415 (t) REVERT: D 70 LYS cc_start: 0.7455 (mmmt) cc_final: 0.6849 (mttm) REVERT: D 150 GLN cc_start: 0.6374 (tt0) cc_final: 0.6085 (tp40) REVERT: D 167 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8868 (t0) REVERT: F 25 MET cc_start: 0.3227 (OUTLIER) cc_final: 0.2436 (tpt) REVERT: F 176 PHE cc_start: -0.1793 (OUTLIER) cc_final: -0.2368 (t80) REVERT: G 38 ASP cc_start: 0.5718 (p0) cc_final: 0.5044 (p0) REVERT: G 115 GLN cc_start: 0.6446 (pm20) cc_final: 0.6071 (tt0) REVERT: I 16 MET cc_start: 0.2445 (OUTLIER) cc_final: 0.1799 (mtp) REVERT: J 116 ARG cc_start: 0.6931 (mtp180) cc_final: 0.6346 (mtp85) REVERT: J 119 PHE cc_start: 0.8207 (t80) cc_final: 0.7905 (t80) REVERT: L 117 THR cc_start: 0.5768 (p) cc_final: 0.5517 (t) REVERT: N 2 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7135 (ttm-80) REVERT: N 94 TYR cc_start: 0.7917 (m-80) cc_final: 0.7186 (m-80) REVERT: P 37 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7794 (tmtt) REVERT: Q 63 ARG cc_start: 0.7413 (ppt170) cc_final: 0.6299 (ttp-170) REVERT: Q 82 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7878 (tp) REVERT: Q 88 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.4998 (tp30) REVERT: R 93 PHE cc_start: 0.7711 (p90) cc_final: 0.7362 (p90) REVERT: S 2 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7092 (mm-30) REVERT: S 9 HIS cc_start: 0.8128 (m90) cc_final: 0.7754 (m-70) REVERT: S 29 VAL cc_start: 0.8609 (m) cc_final: 0.8287 (t) REVERT: U 3 LYS cc_start: 0.7849 (mttt) cc_final: 0.7320 (tttt) REVERT: U 38 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5668 (mm) REVERT: U 84 PHE cc_start: 0.5416 (m-80) cc_final: 0.5208 (m-80) REVERT: W 55 ASP cc_start: 0.7279 (p0) cc_final: 0.6947 (p0) REVERT: W 61 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7708 (mmmm) REVERT: W 65 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7854 (ptpp) REVERT: X 1 SER cc_start: 0.8544 (m) cc_final: 0.8249 (p) REVERT: Y 1 MET cc_start: 0.5469 (tpt) cc_final: 0.4481 (ttm) REVERT: Y 2 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7519 (mtmt) REVERT: Z 2 LYS cc_start: 0.4365 (OUTLIER) cc_final: 0.3126 (mmtp) outliers start: 292 outliers final: 204 residues processed: 1044 average time/residue: 0.9298 time to fit residues: 1605.8886 Evaluate side-chains 1062 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 843 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 5 residue 35 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 61 ARG Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 8 residue 40 ILE Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain 8 residue 77 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 167 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 65 LYS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 512 optimal weight: 0.0670 chunk 349 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 458 optimal weight: 0.0970 chunk 254 optimal weight: 10.0000 chunk 525 optimal weight: 0.7980 chunk 425 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 552 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 overall best weight: 2.1318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 18 HIS ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN O 38 GLN O 98 GLN P 2 ASN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Z 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 100614 Z= 0.148 Angle : 0.516 13.274 150960 Z= 0.276 Chirality : 0.029 0.282 19359 Planarity : 0.005 0.137 7768 Dihedral : 23.734 176.442 51455 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 48.23 Ramachandran Plot: Outliers : 2.41 % Allowed : 13.82 % Favored : 83.77 % Rotamer: Outliers : 8.56 % Allowed : 31.37 % Favored : 60.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.14), residues: 3402 helix: -0.68 (0.18), residues: 846 sheet: -2.09 (0.22), residues: 503 loop : -2.77 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 212 HIS 0.017 0.001 HIS T 70 PHE 0.016 0.001 PHE E 158 TYR 0.015 0.001 TYR J 44 ARG 0.013 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 888 time to evaluate : 4.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7761 (m-70) cc_final: 0.7065 (m170) REVERT: 3 29 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7446 (ttm-80) REVERT: 3 34 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7376 (ptmt) REVERT: 3 42 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.8092 (m-70) REVERT: 4 24 ARG cc_start: 0.8649 (tpp80) cc_final: 0.7985 (mmt90) REVERT: 5 40 GLU cc_start: 0.6282 (tp30) cc_final: 0.6064 (tp30) REVERT: 5 61 ARG cc_start: 0.5195 (OUTLIER) cc_final: 0.4219 (mmt180) REVERT: 5 106 PHE cc_start: 0.4459 (OUTLIER) cc_final: 0.4131 (t80) REVERT: 5 132 TYR cc_start: 0.4225 (OUTLIER) cc_final: 0.3392 (m-80) REVERT: 5 143 MET cc_start: 0.0150 (tmt) cc_final: -0.0562 (mmp) REVERT: 6 26 MET cc_start: 0.4087 (mpp) cc_final: 0.1411 (ppp) REVERT: C 101 ARG cc_start: 0.6936 (mtt180) cc_final: 0.6719 (mtt180) REVERT: D 11 MET cc_start: 0.5912 (mmm) cc_final: 0.5634 (mmm) REVERT: D 70 LYS cc_start: 0.7201 (mmmt) cc_final: 0.6866 (mttp) REVERT: F 95 MET cc_start: 0.2940 (ttt) cc_final: 0.2662 (ttt) REVERT: G 115 GLN cc_start: 0.6297 (pm20) cc_final: 0.5987 (tt0) REVERT: H 25 TYR cc_start: 0.7517 (t80) cc_final: 0.7313 (t80) REVERT: I 16 MET cc_start: 0.2904 (mtp) cc_final: 0.2238 (mtp) REVERT: I 35 MET cc_start: 0.3909 (mtp) cc_final: 0.3609 (mmt) REVERT: J 19 ASP cc_start: 0.7415 (t0) cc_final: 0.7153 (t0) REVERT: L 117 THR cc_start: 0.5782 (p) cc_final: 0.5500 (t) REVERT: N 2 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6786 (ttm-80) REVERT: N 5 LYS cc_start: 0.7683 (mttm) cc_final: 0.7378 (mttm) REVERT: N 94 TYR cc_start: 0.7759 (m-80) cc_final: 0.7032 (m-80) REVERT: O 8 ILE cc_start: 0.7847 (tt) cc_final: 0.7508 (tt) REVERT: Q 63 ARG cc_start: 0.7267 (ppt170) cc_final: 0.6408 (tmm160) REVERT: Q 88 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.4869 (tp30) REVERT: Q 96 ASP cc_start: 0.6483 (t0) cc_final: 0.6147 (t0) REVERT: R 11 GLN cc_start: 0.5734 (mt0) cc_final: 0.5466 (pm20) REVERT: R 93 PHE cc_start: 0.7464 (p90) cc_final: 0.7216 (p90) REVERT: S 70 LYS cc_start: 0.8310 (ptpt) cc_final: 0.8085 (pttm) REVERT: T 37 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5771 (p0) REVERT: U 3 LYS cc_start: 0.7890 (mttt) cc_final: 0.7322 (tttt) REVERT: U 84 PHE cc_start: 0.5620 (m-80) cc_final: 0.5060 (m-10) REVERT: W 19 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6039 (ppt-90) REVERT: W 55 ASP cc_start: 0.7083 (p0) cc_final: 0.6647 (p0) REVERT: W 61 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7649 (mmmm) REVERT: W 65 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7678 (ptpp) REVERT: X 1 SER cc_start: 0.8551 (m) cc_final: 0.8275 (p) REVERT: X 36 ARG cc_start: 0.7724 (mtp-110) cc_final: 0.7511 (mtm110) REVERT: Y 1 MET cc_start: 0.5601 (tpt) cc_final: 0.4726 (ttm) REVERT: Y 2 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7415 (mtmt) REVERT: Z 2 LYS cc_start: 0.4440 (OUTLIER) cc_final: 0.3693 (mmtp) outliers start: 240 outliers final: 171 residues processed: 1004 average time/residue: 0.9448 time to fit residues: 1576.2304 Evaluate side-chains 1026 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 845 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 61 ARG Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 8 residue 24 ASN Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 65 LYS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 43 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 10.0000 chunk 554 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 361 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 616 optimal weight: 3.9990 chunk 511 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 overall best weight: 5.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN P 9 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Z 33 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.8423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 100614 Z= 0.317 Angle : 0.711 12.834 150960 Z= 0.366 Chirality : 0.036 0.268 19359 Planarity : 0.006 0.135 7768 Dihedral : 24.180 179.757 51442 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 64.44 Ramachandran Plot: Outliers : 2.44 % Allowed : 16.61 % Favored : 80.95 % Rotamer: Outliers : 11.44 % Allowed : 30.30 % Favored : 58.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.13), residues: 3402 helix: -1.18 (0.17), residues: 834 sheet: -2.00 (0.23), residues: 487 loop : -3.01 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 64 HIS 0.013 0.002 HIS J 77 PHE 0.035 0.003 PHE H 47 TYR 0.026 0.002 TYR H 25 ARG 0.032 0.001 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 898 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7915 (m-70) cc_final: 0.7179 (m170) REVERT: 0 36 LYS cc_start: 0.7353 (mmtt) cc_final: 0.7042 (mttm) REVERT: 3 34 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7418 (ptmt) REVERT: 4 15 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6615 (tptp) REVERT: 5 61 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.4161 (mmt180) REVERT: 5 106 PHE cc_start: 0.4388 (OUTLIER) cc_final: 0.3681 (t80) REVERT: 5 132 TYR cc_start: 0.4142 (OUTLIER) cc_final: 0.3185 (m-80) REVERT: 5 143 MET cc_start: 0.0354 (tmt) cc_final: -0.0317 (mmp) REVERT: 6 26 MET cc_start: 0.4348 (mpp) cc_final: 0.1471 (ppp) REVERT: C 235 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6761 (mt-10) REVERT: D 70 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7032 (mttm) REVERT: F 127 TYR cc_start: 0.3590 (OUTLIER) cc_final: 0.2830 (t80) REVERT: F 153 ILE cc_start: 0.0794 (OUTLIER) cc_final: -0.0094 (pp) REVERT: G 115 GLN cc_start: 0.6827 (pm20) cc_final: 0.6200 (tt0) REVERT: G 166 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: H 12 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.4209 (mt) REVERT: I 16 MET cc_start: 0.3137 (OUTLIER) cc_final: 0.2318 (mtp) REVERT: I 48 ILE cc_start: -0.0312 (OUTLIER) cc_final: -0.1298 (tt) REVERT: J 1 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6904 (tmm) REVERT: J 108 MET cc_start: 0.7400 (mtt) cc_final: 0.7041 (mtt) REVERT: J 119 PHE cc_start: 0.8416 (t80) cc_final: 0.8153 (t80) REVERT: K 105 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.4672 (ptt-90) REVERT: M 115 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: N 2 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7231 (ttm-80) REVERT: N 94 TYR cc_start: 0.8184 (m-80) cc_final: 0.7488 (m-80) REVERT: N 106 ASP cc_start: 0.7597 (p0) cc_final: 0.7343 (p0) REVERT: Q 29 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6361 (mmt90) REVERT: Q 55 GLN cc_start: 0.7400 (mp10) cc_final: 0.7178 (mp10) REVERT: Q 63 ARG cc_start: 0.7585 (ppt170) cc_final: 0.6409 (ttp-170) REVERT: Q 88 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6168 (tp30) REVERT: R 93 PHE cc_start: 0.7638 (p90) cc_final: 0.7343 (p90) REVERT: S 29 VAL cc_start: 0.8595 (m) cc_final: 0.8298 (t) REVERT: U 3 LYS cc_start: 0.8062 (mttt) cc_final: 0.7553 (tttt) REVERT: U 8 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5143 (p0) REVERT: U 30 SER cc_start: 0.6603 (OUTLIER) cc_final: 0.6400 (t) REVERT: U 84 PHE cc_start: 0.5588 (m-80) cc_final: 0.5351 (m-80) REVERT: W 14 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: W 55 ASP cc_start: 0.7545 (p0) cc_final: 0.7238 (p0) REVERT: W 61 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7744 (mmmm) REVERT: W 65 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7645 (ptpp) REVERT: X 1 SER cc_start: 0.8673 (m) cc_final: 0.8444 (p) REVERT: Y 1 MET cc_start: 0.5458 (tpt) cc_final: 0.4665 (ttm) REVERT: Y 2 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7511 (mtmt) REVERT: Z 2 LYS cc_start: 0.4910 (OUTLIER) cc_final: 0.3966 (mmtp) outliers start: 321 outliers final: 244 residues processed: 1050 average time/residue: 0.9363 time to fit residues: 1644.5745 Evaluate side-chains 1132 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 867 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 26 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 35 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 61 ARG Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 21 ARG Chi-restraints excluded: chain 8 residue 24 ASN Chi-restraints excluded: chain 8 residue 40 ILE Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 77 PHE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 45 GLN Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 68 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 45 HIS Chi-restraints excluded: chain W residue 65 LYS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 chunk 450 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 chunk 518 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 613 optimal weight: 7.9990 chunk 384 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 2 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.8968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 100614 Z= 0.324 Angle : 0.689 16.590 150960 Z= 0.355 Chirality : 0.036 0.361 19359 Planarity : 0.006 0.129 7768 Dihedral : 24.228 176.807 51438 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 63.10 Ramachandran Plot: Outliers : 2.38 % Allowed : 16.84 % Favored : 80.78 % Rotamer: Outliers : 10.94 % Allowed : 31.48 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.13), residues: 3402 helix: -1.28 (0.17), residues: 820 sheet: -2.12 (0.22), residues: 486 loop : -3.04 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 212 HIS 0.012 0.002 HIS J 77 PHE 0.027 0.002 PHE 1 38 TYR 0.020 0.002 TYR X 77 ARG 0.009 0.001 ARG 5 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 897 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7873 (m-70) cc_final: 0.7261 (m170) REVERT: 3 34 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7399 (ptmt) REVERT: 5 61 ARG cc_start: 0.5150 (OUTLIER) cc_final: 0.4236 (mmt180) REVERT: 5 106 PHE cc_start: 0.4462 (OUTLIER) cc_final: 0.3992 (t80) REVERT: 5 132 TYR cc_start: 0.4091 (OUTLIER) cc_final: 0.3243 (m-80) REVERT: 5 140 MET cc_start: 0.2394 (mtt) cc_final: 0.2134 (mtt) REVERT: 5 143 MET cc_start: 0.0602 (tmt) cc_final: -0.0160 (mmp) REVERT: 6 26 MET cc_start: 0.3532 (mpp) cc_final: 0.2259 (ppp) REVERT: C 166 ARG cc_start: 0.6795 (ptp90) cc_final: 0.5998 (ptm160) REVERT: D 70 LYS cc_start: 0.7739 (mmmt) cc_final: 0.7157 (mttm) REVERT: E 46 GLN cc_start: 0.7488 (mt0) cc_final: 0.7204 (mt0) REVERT: E 181 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8910 (tt) REVERT: F 37 MET cc_start: 0.0049 (OUTLIER) cc_final: -0.0775 (mtt) REVERT: F 103 ILE cc_start: 0.0240 (OUTLIER) cc_final: -0.1130 (pt) REVERT: F 153 ILE cc_start: 0.1161 (OUTLIER) cc_final: 0.0436 (pp) REVERT: G 115 GLN cc_start: 0.6950 (pm20) cc_final: 0.6400 (tt0) REVERT: I 16 MET cc_start: 0.3036 (OUTLIER) cc_final: 0.2159 (mtp) REVERT: I 48 ILE cc_start: -0.0268 (OUTLIER) cc_final: -0.1210 (tt) REVERT: J 108 MET cc_start: 0.7492 (mtt) cc_final: 0.7231 (mtt) REVERT: K 105 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.4312 (ptt-90) REVERT: L 76 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: M 3 GLN cc_start: 0.6638 (pp30) cc_final: 0.6127 (pt0) REVERT: N 2 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7249 (ttm-80) REVERT: N 94 TYR cc_start: 0.8167 (m-80) cc_final: 0.7553 (m-80) REVERT: N 106 ASP cc_start: 0.7513 (p0) cc_final: 0.7302 (p0) REVERT: P 20 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7379 (mtp-110) REVERT: P 86 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8107 (ptmm) REVERT: P 99 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7544 (tp) REVERT: Q 29 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6362 (mmt90) REVERT: Q 55 GLN cc_start: 0.7273 (mp10) cc_final: 0.7026 (mp10) REVERT: Q 63 ARG cc_start: 0.7515 (ppt170) cc_final: 0.6523 (ttp-170) REVERT: Q 88 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.5816 (tp30) REVERT: R 11 GLN cc_start: 0.6629 (mt0) cc_final: 0.6152 (pm20) REVERT: R 93 PHE cc_start: 0.7691 (p90) cc_final: 0.7463 (p90) REVERT: S 82 MET cc_start: 0.8078 (mtt) cc_final: 0.7858 (mtt) REVERT: T 25 GLU cc_start: 0.7032 (tp30) cc_final: 0.6773 (tm-30) REVERT: U 3 LYS cc_start: 0.8075 (mttt) cc_final: 0.7592 (tttt) REVERT: U 84 PHE cc_start: 0.5919 (m-80) cc_final: 0.5642 (m-80) REVERT: W 55 ASP cc_start: 0.7645 (p0) cc_final: 0.7404 (p0) REVERT: W 61 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7728 (mmmm) REVERT: W 65 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8083 (ptpp) REVERT: X 1 SER cc_start: 0.8694 (m) cc_final: 0.8471 (p) REVERT: Y 1 MET cc_start: 0.5453 (tpt) cc_final: 0.4846 (ttm) REVERT: Y 2 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7565 (mtmt) REVERT: Y 30 MET cc_start: 0.7272 (mmm) cc_final: 0.6497 (mmm) REVERT: Z 2 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.4851 (mmtp) outliers start: 307 outliers final: 247 residues processed: 1044 average time/residue: 0.9414 time to fit residues: 1643.7608 Evaluate side-chains 1128 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 863 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 26 VAL Chi-restraints excluded: chain 5 residue 35 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 61 ARG Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 8 residue 17 SER Chi-restraints excluded: chain 8 residue 21 ARG Chi-restraints excluded: chain 8 residue 24 ASN Chi-restraints excluded: chain 8 residue 40 ILE Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 120 GLU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 5 LYS Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 65 LYS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 482 optimal weight: 9.9990 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 GLN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN O 98 GLN O 116 GLN P 2 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.9632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 100614 Z= 0.453 Angle : 0.875 13.469 150960 Z= 0.439 Chirality : 0.042 0.473 19359 Planarity : 0.007 0.125 7768 Dihedral : 24.773 177.083 51432 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 78.54 Ramachandran Plot: Outliers : 2.35 % Allowed : 20.08 % Favored : 77.57 % Rotamer: Outliers : 12.16 % Allowed : 31.55 % Favored : 56.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.13), residues: 3402 helix: -1.83 (0.16), residues: 796 sheet: -2.39 (0.22), residues: 493 loop : -3.36 (0.12), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 64 HIS 0.015 0.002 HIS J 77 PHE 0.035 0.003 PHE J 119 TYR 0.028 0.003 TYR Q 31 ARG 0.021 0.001 ARG O 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 900 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7970 (m-70) cc_final: 0.7280 (m170) REVERT: 5 106 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.4091 (t80) REVERT: 5 132 TYR cc_start: 0.4048 (OUTLIER) cc_final: 0.3347 (m-80) REVERT: 5 140 MET cc_start: 0.2523 (mtt) cc_final: 0.2277 (mtt) REVERT: 5 143 MET cc_start: 0.1094 (tmt) cc_final: 0.0279 (mmp) REVERT: 6 26 MET cc_start: 0.3395 (mpp) cc_final: 0.2520 (ppp) REVERT: C 166 ARG cc_start: 0.6888 (ptp90) cc_final: 0.6160 (ptm160) REVERT: C 179 GLU cc_start: 0.6895 (tt0) cc_final: 0.6261 (tt0) REVERT: D 70 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7369 (mttp) REVERT: E 2 GLU cc_start: 0.6005 (pm20) cc_final: 0.5788 (pm20) REVERT: E 7 ASP cc_start: 0.4627 (p0) cc_final: 0.3996 (p0) REVERT: F 16 MET cc_start: 0.4620 (mmp) cc_final: 0.4304 (mmt) REVERT: F 71 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5889 (tppt) REVERT: F 95 MET cc_start: 0.3598 (ttt) cc_final: 0.3206 (ttt) REVERT: F 103 ILE cc_start: 0.1168 (OUTLIER) cc_final: -0.0123 (pt) REVERT: F 127 TYR cc_start: 0.5107 (OUTLIER) cc_final: 0.4492 (t80) REVERT: F 153 ILE cc_start: 0.2456 (OUTLIER) cc_final: 0.1801 (pp) REVERT: G 108 PHE cc_start: 0.7051 (m-10) cc_final: 0.6825 (m-80) REVERT: G 115 GLN cc_start: 0.7043 (pm20) cc_final: 0.6771 (tt0) REVERT: I 16 MET cc_start: 0.3419 (OUTLIER) cc_final: 0.2587 (mtp) REVERT: J 108 MET cc_start: 0.7728 (mtt) cc_final: 0.7492 (mtt) REVERT: J 116 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6827 (mtp85) REVERT: J 118 MET cc_start: 0.7799 (ttm) cc_final: 0.7380 (ttm) REVERT: J 119 PHE cc_start: 0.8369 (t80) cc_final: 0.8112 (t80) REVERT: K 30 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.6823 (ttp80) REVERT: K 105 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.4956 (ptt-90) REVERT: M 45 GLN cc_start: 0.8353 (mt0) cc_final: 0.7786 (mp10) REVERT: M 90 GLU cc_start: 0.7139 (tp30) cc_final: 0.6928 (mp0) REVERT: N 94 TYR cc_start: 0.8185 (m-80) cc_final: 0.7574 (m-80) REVERT: N 96 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6976 (ptt-90) REVERT: P 20 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7591 (mtp-110) REVERT: P 86 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8167 (ptmm) REVERT: P 99 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7657 (tp) REVERT: Q 29 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6398 (mmt90) REVERT: Q 55 GLN cc_start: 0.7385 (mp10) cc_final: 0.7154 (mp10) REVERT: Q 63 ARG cc_start: 0.7672 (ppt170) cc_final: 0.6559 (ttp-170) REVERT: Q 88 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.5729 (tp30) REVERT: S 82 MET cc_start: 0.8197 (mtt) cc_final: 0.7986 (mtt) REVERT: T 89 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8192 (tm-30) REVERT: W 14 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: W 61 LYS cc_start: 0.8381 (mmmm) cc_final: 0.7966 (mmmm) REVERT: X 1 SER cc_start: 0.8785 (m) cc_final: 0.8578 (p) REVERT: Y 1 MET cc_start: 0.5604 (tpt) cc_final: 0.5174 (ttm) REVERT: Y 2 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7640 (mtmt) REVERT: Z 2 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5138 (mmtp) outliers start: 341 outliers final: 267 residues processed: 1072 average time/residue: 0.9472 time to fit residues: 1695.0667 Evaluate side-chains 1153 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 869 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 12 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 35 VAL Chi-restraints excluded: chain 5 residue 42 ARG Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 8 residue 17 SER Chi-restraints excluded: chain 8 residue 21 ARG Chi-restraints excluded: chain 8 residue 40 ILE Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 88 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 65 GLN Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 0.9990 chunk 588 optimal weight: 20.0000 chunk 536 optimal weight: 0.8980 chunk 572 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 449 optimal weight: 0.2980 chunk 175 optimal weight: 10.0000 chunk 517 optimal weight: 8.9990 chunk 541 optimal weight: 9.9990 chunk 570 optimal weight: 0.0970 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN K 90 ASN M 17 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** P 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN T 15 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.9533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 100614 Z= 0.121 Angle : 0.544 13.324 150960 Z= 0.287 Chirality : 0.030 0.372 19359 Planarity : 0.005 0.122 7768 Dihedral : 24.100 179.513 51430 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 52.25 Ramachandran Plot: Outliers : 2.32 % Allowed : 12.55 % Favored : 85.13 % Rotamer: Outliers : 6.52 % Allowed : 37.47 % Favored : 56.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.13), residues: 3402 helix: -0.82 (0.18), residues: 826 sheet: -2.19 (0.23), residues: 467 loop : -3.00 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 212 HIS 0.024 0.002 HIS G 44 PHE 0.025 0.002 PHE 1 38 TYR 0.016 0.001 TYR J 44 ARG 0.011 0.001 ARG W 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 892 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7676 (m-70) cc_final: 0.7214 (m170) REVERT: 0 39 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7697 (tpt170) REVERT: 3 34 LYS cc_start: 0.7731 (ptmt) cc_final: 0.7378 (ptmt) REVERT: 5 87 GLU cc_start: 0.6086 (mm-30) cc_final: 0.4891 (tt0) REVERT: 5 106 PHE cc_start: 0.4554 (OUTLIER) cc_final: 0.4165 (t80) REVERT: 5 132 TYR cc_start: 0.3891 (OUTLIER) cc_final: 0.3448 (m-80) REVERT: 5 140 MET cc_start: 0.2246 (mtt) cc_final: 0.1967 (mtt) REVERT: 5 143 MET cc_start: 0.1044 (tmt) cc_final: 0.0103 (mmp) REVERT: 6 26 MET cc_start: 0.3660 (mpp) cc_final: 0.2526 (ppp) REVERT: 7 19 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5488 (tp) REVERT: 8 1 MET cc_start: 0.2113 (OUTLIER) cc_final: 0.1544 (mtt) REVERT: C 43 ASN cc_start: 0.7659 (t0) cc_final: 0.7324 (t0) REVERT: C 166 ARG cc_start: 0.6494 (ptp90) cc_final: 0.6077 (ptm160) REVERT: D 11 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.5258 (mmm) REVERT: D 70 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7153 (mttp) REVERT: D 104 VAL cc_start: 0.7039 (t) cc_final: 0.6740 (p) REVERT: D 167 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8816 (t160) REVERT: F 25 MET cc_start: 0.6422 (tpp) cc_final: 0.6199 (tpt) REVERT: F 95 MET cc_start: 0.3372 (ttt) cc_final: 0.2880 (ttt) REVERT: F 103 ILE cc_start: 0.0783 (OUTLIER) cc_final: -0.0562 (pt) REVERT: F 127 TYR cc_start: 0.4326 (OUTLIER) cc_final: 0.3390 (t80) REVERT: F 153 ILE cc_start: 0.1587 (OUTLIER) cc_final: 0.0816 (pp) REVERT: G 114 HIS cc_start: 0.6007 (t70) cc_final: 0.5555 (t70) REVERT: G 115 GLN cc_start: 0.7107 (pm20) cc_final: 0.6703 (tt0) REVERT: I 16 MET cc_start: 0.2846 (mtp) cc_final: 0.2055 (mtp) REVERT: J 1 MET cc_start: 0.7227 (tmm) cc_final: 0.6884 (tmm) REVERT: K 30 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6619 (ttp80) REVERT: M 3 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5859 (pt0) REVERT: N 2 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6699 (ttm-80) REVERT: N 56 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7616 (mtpp) REVERT: N 94 TYR cc_start: 0.8061 (m-80) cc_final: 0.7273 (m-80) REVERT: N 96 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6426 (ptt-90) REVERT: P 99 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7402 (tp) REVERT: Q 55 GLN cc_start: 0.7417 (mp10) cc_final: 0.7176 (mp10) REVERT: Q 63 ARG cc_start: 0.7049 (ppt170) cc_final: 0.6309 (ttp-170) REVERT: Q 88 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: S 82 MET cc_start: 0.8041 (mtt) cc_final: 0.7809 (mtt) REVERT: W 61 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7670 (mmmm) REVERT: X 1 SER cc_start: 0.8566 (m) cc_final: 0.8331 (p) REVERT: Y 1 MET cc_start: 0.5585 (tpt) cc_final: 0.5095 (ttm) REVERT: Y 2 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7555 (mtmt) REVERT: Z 2 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.5110 (mmtp) outliers start: 183 outliers final: 135 residues processed: 975 average time/residue: 0.9485 time to fit residues: 1546.3574 Evaluate side-chains 1005 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 854 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 8 residue 21 ARG Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 167 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 120 GLU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 52 CYS Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 7.9990 chunk 605 optimal weight: 20.0000 chunk 369 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 420 optimal weight: 2.9990 chunk 634 optimal weight: 9.9990 chunk 584 optimal weight: 20.0000 chunk 505 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN E 136 GLN G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 2 ASN P 9 GLN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.9705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 100614 Z= 0.326 Angle : 0.684 12.643 150960 Z= 0.350 Chirality : 0.035 0.422 19359 Planarity : 0.006 0.119 7768 Dihedral : 24.232 177.294 51429 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 65.36 Ramachandran Plot: Outliers : 2.29 % Allowed : 17.96 % Favored : 79.75 % Rotamer: Outliers : 6.88 % Allowed : 36.93 % Favored : 56.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.13), residues: 3402 helix: -1.09 (0.18), residues: 811 sheet: -2.23 (0.22), residues: 505 loop : -3.10 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 64 HIS 0.026 0.002 HIS G 44 PHE 0.022 0.002 PHE 1 38 TYR 0.021 0.002 TYR C 82 ARG 0.015 0.001 ARG P 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 865 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 18 HIS cc_start: 0.7836 (m-70) cc_final: 0.7281 (m170) REVERT: 3 34 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7556 (ptmt) REVERT: 5 106 PHE cc_start: 0.4726 (OUTLIER) cc_final: 0.4293 (t80) REVERT: 5 132 TYR cc_start: 0.4083 (OUTLIER) cc_final: 0.3425 (m-80) REVERT: 5 140 MET cc_start: 0.2451 (mtt) cc_final: 0.2202 (mtt) REVERT: 5 143 MET cc_start: 0.1204 (tmt) cc_final: 0.0363 (mmp) REVERT: 6 26 MET cc_start: 0.3795 (mpp) cc_final: 0.2556 (ppp) REVERT: 7 19 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5797 (tp) REVERT: C 166 ARG cc_start: 0.6763 (ptp90) cc_final: 0.6135 (ptm160) REVERT: D 38 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7193 (mttt) REVERT: D 70 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7251 (mttp) REVERT: D 104 VAL cc_start: 0.7335 (t) cc_final: 0.6970 (p) REVERT: E 7 ASP cc_start: 0.3993 (p0) cc_final: 0.3467 (p0) REVERT: E 69 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6783 (mpt-90) REVERT: F 62 GLN cc_start: 0.5591 (mt0) cc_final: 0.5372 (mt0) REVERT: F 95 MET cc_start: 0.3607 (ttt) cc_final: 0.3056 (ttt) REVERT: F 103 ILE cc_start: 0.1197 (OUTLIER) cc_final: -0.0242 (pt) REVERT: F 127 TYR cc_start: 0.4874 (OUTLIER) cc_final: 0.3902 (t80) REVERT: F 153 ILE cc_start: 0.1582 (OUTLIER) cc_final: 0.0778 (pp) REVERT: G 44 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6601 (t-90) REVERT: G 115 GLN cc_start: 0.7379 (pm20) cc_final: 0.6789 (tt0) REVERT: J 35 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7333 (tpp-160) REVERT: K 30 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6834 (ttp80) REVERT: M 3 GLN cc_start: 0.6576 (pp30) cc_final: 0.6106 (pt0) REVERT: N 94 TYR cc_start: 0.8192 (m-80) cc_final: 0.7534 (m-80) REVERT: N 96 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6639 (ptt-90) REVERT: P 99 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7711 (tp) REVERT: Q 29 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6410 (mmt90) REVERT: Q 55 GLN cc_start: 0.7413 (mp10) cc_final: 0.7152 (mp10) REVERT: Q 63 ARG cc_start: 0.7506 (ppt170) cc_final: 0.6548 (ttp-170) REVERT: Q 88 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.5995 (tp30) REVERT: S 82 MET cc_start: 0.8076 (mtt) cc_final: 0.7869 (mtt) REVERT: W 61 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7846 (mmmm) REVERT: X 1 SER cc_start: 0.8648 (m) cc_final: 0.8441 (p) REVERT: Y 1 MET cc_start: 0.5640 (tpt) cc_final: 0.4992 (ttm) REVERT: Y 2 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7649 (mtmt) REVERT: Z 2 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5207 (mmtp) outliers start: 193 outliers final: 157 residues processed: 960 average time/residue: 0.9587 time to fit residues: 1534.2696 Evaluate side-chains 1033 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 861 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 50 SER Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 132 TYR Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 8 residue 7 GLU Chi-restraints excluded: chain 8 residue 21 ARG Chi-restraints excluded: chain 8 residue 42 LEU Chi-restraints excluded: chain 8 residue 48 MET Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 120 GLU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 52 CYS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 0.0170 chunk 538 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 465 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 506 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 519 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 51 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.165561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141816 restraints weight = 184733.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145041 restraints weight = 67369.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146965 restraints weight = 34606.589| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.9716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 100614 Z= 0.125 Angle : 0.511 13.128 150960 Z= 0.271 Chirality : 0.029 0.376 19359 Planarity : 0.005 0.119 7768 Dihedral : 24.050 179.699 51427 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 53.30 Ramachandran Plot: Outliers : 2.15 % Allowed : 12.40 % Favored : 85.45 % Rotamer: Outliers : 5.24 % Allowed : 38.54 % Favored : 56.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.14), residues: 3402 helix: -0.55 (0.18), residues: 826 sheet: -2.05 (0.23), residues: 485 loop : -2.87 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 212 HIS 0.031 0.001 HIS G 44 PHE 0.021 0.001 PHE 1 38 TYR 0.018 0.001 TYR L 58 ARG 0.020 0.000 ARG C 86 =============================================================================== Job complete usr+sys time: 23454.12 seconds wall clock time: 416 minutes 14.60 seconds (24974.60 seconds total)