Starting phenix.real_space_refine on Tue Mar 19 09:42:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/03_2024/6i0y_0322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/03_2024/6i0y_0322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/03_2024/6i0y_0322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/03_2024/6i0y_0322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/03_2024/6i0y_0322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/03_2024/6i0y_0322.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 143 5.21 5 S 93 5.16 5 C 46506 2.51 5 N 17294 2.21 5 O 26533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "h ARG 6": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "7 ASP 16": "OD1" <-> "OD2" 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: 93619 Number of models: 1 Model: "" Number of chains: 48 Chain: "h" 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: "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: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 139 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} 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': 144, 'rna3p_pur': 1380, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 412, 'rna3p': 2441} 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: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'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: "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_pur': 33, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 65} 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: "z" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 688 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 84} 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: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 151 Unusual residues: {' MG': 136} Classifications: {'peptide': 1, 'undetermined': 136} Modifications used: {'COO': 1} Link IDs: {None: 136} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 415 Classifications: {'water': 415} Link IDs: {None: 414} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2598 SG CYS 4 11 117.476 81.135 174.955 1.00 27.97 S ATOM 2623 SG CYS 4 14 116.674 82.419 173.551 1.00 12.31 S ATOM 2726 SG CYS 4 27 118.523 82.794 174.395 1.00 25.55 S Time building chain proxies: 36.32, per 1000 atoms: 0.39 Number of scatterers: 93619 At special positions: 0 Unit cell: (201.4, 213.06, 260.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 93 16.00 P 3049 15.00 Mg 143 11.99 O 26533 8.00 N 17294 7.00 C 46506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 89722 O4' C V 56 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.43 Conformation dependent library (CDL) restraints added in 4.8 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 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6490 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 53 sheets defined 29.2% alpha, 13.6% beta 984 base pairs and 1493 stacking pairs defined. Time for finding SS restraints: 37.38 Creating SS restraints... Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 37 Processing helix chain '3' and resid 6 through 11 removed outlier: 3.551A pdb=" N ALA 3 10 " --> pdb=" O VAL 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 43 Processing helix chain '3' and resid 53 through 61 Processing helix chain '4' and resid 30 through 34 Processing helix chain '5' and resid 3 through 8 Processing helix chain '5' and resid 8 through 19 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: 3.848A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 47 removed outlier: 4.190A pdb=" N LYS 5 37 " --> pdb=" O VAL 5 33 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 64 Processing helix chain '5' and resid 94 through 104 removed outlier: 3.665A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 138 removed outlier: 3.890A pdb=" N ILE 5 136 " --> pdb=" O GLU 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 139 through 148 removed outlier: 3.737A pdb=" N MET 5 143 " --> pdb=" O LEU 5 139 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU 5 145 " --> pdb=" O ALA 5 141 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 7 Processing helix chain '6' and resid 15 through 20 Processing helix chain '6' and resid 24 through 29 removed outlier: 3.885A pdb=" N GLU 6 28 " --> pdb=" O SER 6 24 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS 6 29 " --> pdb=" O ALA 6 25 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 24 through 29' Processing helix chain '7' and resid 11 through 16 Processing helix chain '7' and resid 16 through 22 removed outlier: 3.898A pdb=" N HIS 7 22 " --> pdb=" O LYS 7 18 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 23 Processing helix chain '8' and resid 44 through 52 Processing helix chain '8' and resid 54 through 59 removed outlier: 3.744A pdb=" N SER 8 58 " --> pdb=" O ALA 8 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.147A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.502A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.592A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.623A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.548A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.584A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 11 through 20 removed outlier: 3.600A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 40 through 44 removed outlier: 3.903A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.907A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.671A 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 91 through 105 Processing helix chain 'F' and resid 133 through 137 removed outlier: 4.246A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 161 through 171 Processing helix chain 'G' and resid 61 through 81 Processing helix chain 'G' and resid 136 through 150 removed outlier: 3.578A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'I' and resid 23 through 28 removed outlier: 3.619A pdb=" N LEU I 27 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 37 removed outlier: 3.920A pdb=" N PHE I 37 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 106 through 111 Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.636A pdb=" N ASP I 115 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET I 116 " --> pdb=" O ALA I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 112 through 116' Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.928A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.777A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 38 removed outlier: 3.892A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 95 Processing helix chain 'J' and resid 98 through 107 Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.572A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.812A pdb=" N GLY K 74 " --> pdb=" O ARG K 71 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER K 75 " --> pdb=" O PRO K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 75' Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 21 through 26 removed outlier: 4.404A pdb=" N SER L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY L 26 " --> pdb=" O GLY L 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 26' Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.379A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 Processing helix chain 'M' and resid 43 through 58 removed outlier: 3.873A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 removed outlier: 3.650A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.528A 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: 3.718A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.564A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 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 82 through 87 Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.274A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 85 removed outlier: 3.552A 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 103 through 113 removed outlier: 5.069A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 4.125A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) 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) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 77 through 81 Processing helix chain 'P' and resid 96 through 102 Processing helix chain 'P' and resid 103 through 107 Processing helix chain 'Q' and resid 6 through 20 removed outlier: 3.726A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 71 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: 4.079A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'Q' and resid 96 through 101 removed outlier: 3.546A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.602A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.643A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.533A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 24 Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.598A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 53 No H-bonds generated for 'chain 'T' and resid 51 through 53' Processing helix chain 'X' and resid 53 through 62 Processing helix chain 'X' and resid 62 through 72 removed outlier: 3.958A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.617A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.864A 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 23 through 34 Processing helix chain 'Y' and resid 40 through 59 removed outlier: 3.956A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain 'Z' and resid 51 through 54 Processing sheet with id=AA1, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'h' and resid 41 through 46 removed outlier: 3.531A pdb=" N GLN h 46 " --> pdb=" O GLY h 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 83 through 88 Processing sheet with id=AA4, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AA5, first strand: chain '0' and resid 47 through 48 removed outlier: 3.611A pdb=" N ARG 0 51 " --> pdb=" O TYR 0 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain '4' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain '8' and resid 62 through 65 removed outlier: 7.010A pdb=" N ILE 8 4 " --> pdb=" O VAL 8 64 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASN 8 5 " --> pdb=" O ASP 8 43 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP 8 43 " --> pdb=" O ASN 8 5 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N LYS 8 25 " --> pdb=" O GLN 8 87 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ILE 8 89 " --> pdb=" O LYS 8 25 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N PHE 8 91 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE 8 29 " --> pdb=" O PHE 8 91 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG 8 93 " --> pdb=" O ILE 8 29 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR 8 31 " --> pdb=" O ARG 8 93 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN 8 78 " --> pdb=" O GLN 8 87 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE 8 89 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP 8 76 " --> pdb=" O ILE 8 89 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE 8 91 " --> pdb=" O ALA 8 74 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA 8 74 " --> pdb=" O PHE 8 91 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG 8 93 " --> pdb=" O VAL 8 72 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL 8 72 " --> pdb=" O ARG 8 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, 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=AB4, first strand: chain 'C' and resid 162 through 165 removed outlier: 5.876A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 12 through 15 Processing sheet with id=AB6, first strand: chain 'D' and resid 12 through 15 Processing sheet with id=AB7, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.560A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 68 Processing sheet with id=AB9, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AC1, first strand: chain 'G' and resid 22 through 24 Processing sheet with id=AC2, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AC3, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AC4, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.564A pdb=" N THR I 67 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 122 through 123 removed outlier: 6.344A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 75 through 77 Processing sheet with id=AC9, first strand: chain 'K' and resid 92 through 94 removed outlier: 4.938A pdb=" N GLN K 93 " --> pdb=" O ASN K 88 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 76 through 79 removed outlier: 6.780A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 74 through 76 removed outlier: 3.599A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AD4, first strand: chain 'M' and resid 63 through 65 removed outlier: 3.692A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 39 through 42 Processing sheet with id=AD6, first strand: chain 'M' and resid 74 through 75 removed outlier: 3.960A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 37 Processing sheet with id=AD8, first strand: chain 'O' and resid 47 through 50 removed outlier: 6.726A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 37 through 43 removed outlier: 3.780A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id=AE1, 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: 6.916A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 20 through 23 removed outlier: 3.876A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id=AE3, 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=AE4, first strand: chain 'S' and resid 4 through 11 removed outlier: 5.632A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 82 through 83 Processing sheet with id=AE6, first strand: chain 'S' and resid 86 through 88 removed outlier: 3.548A pdb=" N MET S 86 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG S 88 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 11 through 14 Processing sheet with id=AE8, first strand: chain 'T' and resid 61 through 63 removed outlier: 3.836A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AF1, first strand: chain 'W' and resid 49 through 50 removed outlier: 3.830A pdb=" N VAL W 50 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE W 59 " --> pdb=" O VAL W 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'W' and resid 65 through 66 Processing sheet with id=AF3, first strand: chain 'X' and resid 12 through 14 Processing sheet with id=AF4, first strand: chain 'X' and resid 35 through 38 Processing sheet with id=AF5, first strand: chain 'Z' and resid 35 through 37 Processing sheet with id=AF6, first strand: chain 'z' and resid 11 through 13 removed outlier: 3.665A pdb=" N LYS z 85 " --> pdb=" O VAL z 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL z 13 " --> pdb=" O LYS z 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'z' and resid 19 through 24 removed outlier: 3.523A pdb=" N PHE z 21 " --> pdb=" O LEU z 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS z 56 " --> pdb=" O ILE z 23 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'z' and resid 74 through 75 828 hydrogen bonds defined for protein. 2163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2475 hydrogen bonds 3952 hydrogen bond angles 0 basepair planarities 984 basepair parallelities 1493 stacking parallelities Total time for adding SS restraints: 173.78 Time building geometry restraints manager: 48.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 7397 1.28 - 1.43: 45735 1.43 - 1.57: 41927 1.57 - 1.72: 6030 1.72 - 1.87: 168 Bond restraints: 101257 Sorted by residual: 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 1.43e+02 bond pdb=" CA MET S 86 " pdb=" C MET S 86 " ideal model delta sigma weight residual 1.524 1.389 0.135 1.26e-02 6.30e+03 1.15e+02 bond pdb=" O3' A A2602 " pdb=" P G A2603 " ideal model delta sigma weight residual 1.607 1.486 0.121 1.50e-02 4.44e+03 6.49e+01 bond pdb=" C ASP S 94 " pdb=" O ASP S 94 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.22e-02 6.72e+03 5.88e+01 bond pdb=" C ALA S 89 " pdb=" O ALA S 89 " ideal model delta sigma weight residual 1.234 1.139 0.096 1.28e-02 6.10e+03 5.57e+01 ... (remaining 101252 not shown) Histogram of bond angle deviations from ideal: 54.46 - 72.71: 1 72.71 - 90.95: 2 90.95 - 109.19: 37989 109.19 - 127.43: 107213 127.43 - 145.67: 6624 Bond angle restraints: 151829 Sorted by residual: angle pdb=" C4' G A2608 " pdb=" C3' G A2608 " pdb=" O3' G A2608 " ideal model delta sigma weight residual 113.00 141.45 -28.45 1.50e+00 4.44e-01 3.60e+02 angle pdb=" C MET S 86 " pdb=" N PRO S 87 " pdb=" CD PRO S 87 " ideal model delta sigma weight residual 125.00 54.46 70.54 4.10e+00 5.95e-02 2.96e+02 angle pdb=" N ARG S 88 " pdb=" CA ARG S 88 " pdb=" C ARG S 88 " ideal model delta sigma weight residual 109.41 85.93 23.48 1.52e+00 4.33e-01 2.39e+02 angle pdb=" C4' A A 751 " pdb=" C3' A A 751 " pdb=" O3' A A 751 " ideal model delta sigma weight residual 113.00 135.48 -22.48 1.50e+00 4.44e-01 2.25e+02 angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.19 104.05 15.14 1.06e+00 8.90e-01 2.04e+02 ... (remaining 151824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 56655 35.26 - 70.52: 7330 70.52 - 105.78: 847 105.78 - 141.04: 17 141.04 - 176.30: 20 Dihedral angle restraints: 64869 sinusoidal: 54799 harmonic: 10070 Sorted by residual: dihedral pdb=" CA ALA S 89 " pdb=" C ALA S 89 " pdb=" N LYS S 90 " pdb=" CA LYS S 90 " ideal model delta harmonic sigma weight residual -180.00 -133.19 -46.81 0 5.00e+00 4.00e-02 8.77e+01 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 28.30 171.70 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U A2076 " pdb=" C1' U A2076 " pdb=" N1 U A2076 " pdb=" C2 U A2076 " ideal model delta sinusoidal sigma weight residual 200.00 29.46 170.54 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 64866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 19424 0.349 - 0.699: 30 0.699 - 1.048: 2 1.048 - 1.398: 2 1.398 - 1.747: 6 Chirality restraints: 19464 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 -0.88 -1.75 2.00e-01 2.50e+01 7.63e+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 -0.93 -1.66 2.00e-01 2.50e+01 6.90e+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 1.04 1.61 2.00e-01 2.50e+01 6.47e+01 ... (remaining 19461 not shown) Planarity restraints: 7881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G V 39 " -0.183 2.00e-02 2.50e+03 1.75e-01 9.19e+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 " 0.190 2.00e-02 2.50e+03 pdb=" C5 G V 39 " 0.054 2.00e-02 2.50e+03 pdb=" C6 G V 39 " -0.084 2.00e-02 2.50e+03 pdb=" O6 G V 39 " -0.212 2.00e-02 2.50e+03 pdb=" N1 G V 39 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G V 39 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G V 39 " 0.307 2.00e-02 2.50e+03 pdb=" N3 G V 39 " -0.262 2.00e-02 2.50e+03 pdb=" C4 G V 39 " -0.102 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 6.43e+02 pdb=" N1 C V 4 " 0.015 2.00e-02 2.50e+03 pdb=" C2 C V 4 " 0.070 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 " -0.289 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 delta sigma weight rms_deltas residual plane pdb=" C1' G V 3 " -0.091 2.00e-02 2.50e+03 1.43e-01 6.11e+02 pdb=" N9 G V 3 " -0.082 2.00e-02 2.50e+03 pdb=" C8 G V 3 " -0.195 2.00e-02 2.50e+03 pdb=" N7 G V 3 " 0.040 2.00e-02 2.50e+03 pdb=" C5 G V 3 " 0.221 2.00e-02 2.50e+03 pdb=" C6 G V 3 " -0.026 2.00e-02 2.50e+03 pdb=" O6 G V 3 " -0.038 2.00e-02 2.50e+03 pdb=" N1 G V 3 " -0.130 2.00e-02 2.50e+03 pdb=" C2 G V 3 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G V 3 " -0.163 2.00e-02 2.50e+03 pdb=" N3 G V 3 " 0.221 2.00e-02 2.50e+03 pdb=" C4 G V 3 " 0.214 2.00e-02 2.50e+03 ... (remaining 7878 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.53: 9 1.53 - 2.37: 938 2.37 - 3.21: 90509 3.21 - 4.06: 314076 4.06 - 4.90: 474379 Warning: very small nonbonded interaction distances. Nonbonded interactions: 879911 Sorted by model distance: nonbonded pdb=" O PRO 7 24 " pdb=" O2' A V 76 " model vdw 0.682 2.440 nonbonded pdb=" NH1 ARG F 79 " pdb=" C1' C V 56 " model vdw 0.878 3.550 nonbonded pdb=" O2 U A 746 " pdb=" O TRP A3001 " model vdw 1.149 3.040 nonbonded pdb=" NE2 GLN h 46 " pdb=" CG2 VAL h 59 " model vdw 1.233 3.540 nonbonded pdb=" NH1 ARG F 79 " pdb=" O4' C V 56 " model vdw 1.238 2.520 ... (remaining 879906 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.900 Check model and map are aligned: 1.050 Set scattering table: 0.640 Process input model: 376.880 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 400.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 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 0.149 101257 Z= 0.616 Angle : 1.487 70.535 151829 Z= 0.790 Chirality : 0.072 1.747 19464 Planarity : 0.010 0.291 7881 Dihedral : 23.521 176.301 58379 Min Nonbonded Distance : 0.682 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 6.52 % Allowed : 16.02 % Favored : 77.47 % Rotamer: Outliers : 11.41 % Allowed : 13.05 % Favored : 75.54 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -5.00 (0.11), residues: 3484 helix: -3.74 (0.11), residues: 854 sheet: -2.80 (0.20), residues: 597 loop : -3.42 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP R 92 HIS 0.017 0.003 HIS S 7 PHE 0.038 0.004 PHE D 118 TYR 0.030 0.004 TYR J 75 ARG 0.027 0.002 ARG h 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1331 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 7 19 ILE cc_start: 0.6242 (pp) cc_final: 0.5937 (pt) REVERT: D 86 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: F 46 LYS cc_start: 0.0738 (OUTLIER) cc_final: 0.0269 (mmtt) REVERT: F 95 MET cc_start: 0.4103 (ttp) cc_final: 0.3806 (ttp) REVERT: I 112 LYS cc_start: 0.0034 (mtpp) cc_final: -0.0617 (tttt) outliers start: 328 outliers final: 97 residues processed: 1502 average time/residue: 1.0199 time to fit residues: 2476.8099 Evaluate side-chains 1003 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 904 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 70 GLU Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 107 GLU Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 6 residue 17 MET Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 90 LEU 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 94 ARG Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 3 VAL 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 73 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 41 ILE 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 127 VAL Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 13 VAL Chi-restraints excluded: chain z residue 20 HIS Chi-restraints excluded: chain z residue 35 LYS Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain z residue 48 GLU Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 8.9990 chunk 488 optimal weight: 5.9990 chunk 270 optimal weight: 40.0000 chunk 166 optimal weight: 50.0000 chunk 329 optimal weight: 8.9990 chunk 260 optimal weight: 0.8980 chunk 504 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 375 optimal weight: 5.9990 chunk 584 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 45 HIS ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN 0 18 HIS 7 22 HIS 8 44 HIS 8 78 GLN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN D 130 GLN D 150 GLN E 46 GLN E 90 GLN E 97 ASN E 156 ASN E 195 GLN F 26 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS P 11 GLN Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS T 15 HIS T 59 ASN X 15 ASN Y 15 ASN Y 41 HIS z 31 HIS z 74 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 101257 Z= 0.324 Angle : 0.877 18.670 151829 Z= 0.440 Chirality : 0.045 0.319 19464 Planarity : 0.007 0.117 7881 Dihedral : 23.537 179.702 51652 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 2.90 % Allowed : 12.66 % Favored : 84.44 % Rotamer: Outliers : 10.61 % Allowed : 22.58 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.85 (0.12), residues: 3484 helix: -1.95 (0.15), residues: 881 sheet: -2.50 (0.19), residues: 626 loop : -2.96 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP Q 60 HIS 0.015 0.003 HIS E 92 PHE 0.031 0.003 PHE J 119 TYR 0.037 0.003 TYR E 35 ARG 0.022 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1038 time to evaluate : 3.897 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: h 87 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7270 (m-10) REVERT: 0 39 ARG cc_start: 0.5421 (ttt90) cc_final: 0.5138 (ttm-80) REVERT: 1 8 ILE cc_start: 0.6257 (mp) cc_final: 0.5988 (mt) REVERT: 5 60 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6693 (mp) REVERT: C 57 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6614 (t70) REVERT: E 111 GLU cc_start: 0.5507 (tt0) cc_final: 0.5017 (tt0) REVERT: F 37 MET cc_start: 0.0673 (OUTLIER) cc_final: 0.0177 (ptm) REVERT: F 46 LYS cc_start: 0.0754 (OUTLIER) cc_final: 0.0107 (mmtm) REVERT: R 64 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7683 (t) outliers start: 305 outliers final: 166 residues processed: 1193 average time/residue: 0.9137 time to fit residues: 1841.3907 Evaluate side-chains 1070 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 898 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 17 LYS Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 60 LEU Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 118 ILE Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 87 GLN Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 267 VAL 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 61 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 16 MET 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 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 36 GLN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 28 GLU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 chunk 398 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 585 optimal weight: 0.0040 chunk 632 optimal weight: 0.2980 chunk 521 optimal weight: 7.9990 chunk 580 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 470 optimal weight: 50.0000 overall best weight: 4.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 HIS 2 13 ASN 5 88 HIS ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN G 138 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 135 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN N 23 ASN O 98 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN X 19 HIS ** z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 101257 Z= 0.330 Angle : 0.803 15.450 151829 Z= 0.409 Chirality : 0.042 0.329 19464 Planarity : 0.007 0.113 7881 Dihedral : 23.426 179.166 51555 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 2.35 % Allowed : 13.23 % Favored : 84.41 % Rotamer: Outliers : 10.26 % Allowed : 26.27 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.43 (0.13), residues: 3484 helix: -1.33 (0.16), residues: 876 sheet: -2.26 (0.20), residues: 596 loop : -2.82 (0.12), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP G 61 HIS 0.031 0.002 HIS R 66 PHE 0.038 0.003 PHE I 37 TYR 0.049 0.003 TYR 5 51 ARG 0.021 0.001 ARG 2 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1008 time to evaluate : 5.410 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: h 87 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: 1 8 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6000 (mt) REVERT: 5 38 MET cc_start: 0.1870 (mpp) cc_final: 0.1542 (tpt) REVERT: 6 26 MET cc_start: 0.3889 (pmm) cc_final: 0.3648 (pmm) REVERT: 8 80 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6610 (t70) REVERT: C 57 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6322 (t-90) REVERT: C 163 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6580 (mt) REVERT: F 37 MET cc_start: 0.1296 (OUTLIER) cc_final: 0.1044 (ptm) REVERT: F 46 LYS cc_start: 0.1223 (OUTLIER) cc_final: 0.0046 (mmtm) REVERT: H 11 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7352 (m-40) REVERT: I 80 LYS cc_start: 0.1123 (mmtt) cc_final: 0.0661 (mmtt) REVERT: J 36 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5298 (mm) REVERT: M 14 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6293 (mtpt) REVERT: T 1 MET cc_start: 0.5671 (mmp) cc_final: 0.5377 (mmp) REVERT: X 61 LYS cc_start: 0.7864 (tppp) cc_final: 0.7566 (ttmt) outliers start: 295 outliers final: 163 residues processed: 1161 average time/residue: 0.8828 time to fit residues: 1752.5926 Evaluate side-chains 1074 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 901 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 17 LYS Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 65 ILE Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 13 ASN Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 17 MET Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 80 HIS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 7.9990 chunk 440 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 393 optimal weight: 8.9990 chunk 587 optimal weight: 1.9990 chunk 622 optimal weight: 0.0040 chunk 307 optimal weight: 10.0000 chunk 557 optimal weight: 4.9990 chunk 167 optimal weight: 50.0000 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** H 28 ASN ** 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 66 HIS R 86 GLN S 7 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 101257 Z= 0.315 Angle : 0.777 15.995 151829 Z= 0.394 Chirality : 0.042 0.524 19464 Planarity : 0.006 0.114 7881 Dihedral : 23.379 179.406 51531 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 2.38 % Allowed : 12.11 % Favored : 85.51 % Rotamer: Outliers : 9.81 % Allowed : 28.50 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.16 (0.13), residues: 3484 helix: -1.06 (0.17), residues: 878 sheet: -2.01 (0.20), residues: 642 loop : -2.71 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 212 HIS 0.075 0.003 HIS J 80 PHE 0.029 0.003 PHE P 58 TYR 0.039 0.003 TYR Q 31 ARG 0.016 0.001 ARG F 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 975 time to evaluate : 3.855 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: 1 8 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6315 (mt) REVERT: 5 38 MET cc_start: 0.1451 (OUTLIER) cc_final: 0.1143 (mpp) REVERT: 5 52 MET cc_start: -0.0582 (OUTLIER) cc_final: -0.1047 (tmm) REVERT: C 33 LEU cc_start: 0.7770 (mt) cc_final: 0.7555 (mt) REVERT: C 57 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6299 (t-90) REVERT: F 37 MET cc_start: 0.1983 (OUTLIER) cc_final: 0.1749 (ptm) REVERT: F 46 LYS cc_start: 0.0583 (OUTLIER) cc_final: -0.0262 (pptt) REVERT: F 176 PHE cc_start: -0.0711 (OUTLIER) cc_final: -0.2306 (t80) REVERT: I 80 LYS cc_start: 0.1153 (mmtt) cc_final: 0.0446 (mmtt) REVERT: J 36 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5709 (mm) REVERT: K 47 ILE cc_start: 0.7470 (tp) cc_final: 0.7265 (tt) REVERT: M 14 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6383 (mtpt) REVERT: M 111 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6307 (tm-30) REVERT: N 118 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6820 (ttp80) REVERT: O 58 ILE cc_start: 0.7435 (mm) cc_final: 0.7199 (mm) REVERT: T 1 MET cc_start: 0.6056 (mmp) cc_final: 0.5630 (mmp) outliers start: 282 outliers final: 209 residues processed: 1121 average time/residue: 0.9620 time to fit residues: 1860.1963 Evaluate side-chains 1133 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 915 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 17 LYS Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 38 MET Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 8 residue 12 GLN Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 157 THR 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 76 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain z residue 46 ASP Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 463 optimal weight: 0.0870 chunk 256 optimal weight: 9.9990 chunk 531 optimal weight: 5.9990 chunk 430 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 558 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 overall best weight: 5.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 69 ASN 2 13 ASN 5 4 ASN 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN K 13 ASN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.7910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 101257 Z= 0.342 Angle : 0.798 15.115 151829 Z= 0.402 Chirality : 0.042 0.342 19464 Planarity : 0.006 0.114 7881 Dihedral : 23.410 179.751 51522 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 2.35 % Allowed : 13.23 % Favored : 84.41 % Rotamer: Outliers : 10.47 % Allowed : 29.61 % Favored : 59.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.13 (0.13), residues: 3484 helix: -1.05 (0.17), residues: 895 sheet: -1.91 (0.20), residues: 620 loop : -2.73 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP C 212 HIS 0.054 0.003 HIS S 7 PHE 0.039 0.003 PHE C 29 TYR 0.030 0.003 TYR 5 51 ARG 0.016 0.001 ARG X 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 975 time to evaluate : 3.956 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: h 6 ARG cc_start: 0.7702 (ptp-170) cc_final: 0.7354 (ptp-170) REVERT: h 19 LYS cc_start: 0.8588 (tttt) cc_final: 0.8198 (ttmm) REVERT: h 87 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: 3 42 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7143 (t-90) REVERT: 5 86 MET cc_start: 0.4667 (ppp) cc_final: 0.4367 (ppp) REVERT: C 57 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6277 (t-90) REVERT: E 46 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6333 (mp10) REVERT: F 95 MET cc_start: 0.4519 (ttt) cc_final: 0.3961 (ttt) REVERT: I 80 LYS cc_start: 0.1176 (mmtt) cc_final: 0.0416 (mmtt) REVERT: K 29 HIS cc_start: 0.6060 (OUTLIER) cc_final: 0.5784 (m-70) REVERT: M 14 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6278 (mtpt) REVERT: O 29 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.6558 (t70) REVERT: O 116 GLN cc_start: 0.7780 (mp10) cc_final: 0.7510 (mp10) REVERT: R 46 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: X 47 THR cc_start: 0.7363 (p) cc_final: 0.7106 (p) REVERT: Y 27 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.5897 (t0) outliers start: 301 outliers final: 218 residues processed: 1136 average time/residue: 0.8775 time to fit residues: 1711.8265 Evaluate side-chains 1130 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 903 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 30 ASP Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 118 ILE Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 12 GLN Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 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 29 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 36 GLN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 61 LYS Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 10.0000 chunk 560 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 623 optimal weight: 5.9990 chunk 517 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 69 ASN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN G 127 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.8650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 101257 Z= 0.384 Angle : 0.842 14.377 151829 Z= 0.422 Chirality : 0.044 0.396 19464 Planarity : 0.006 0.114 7881 Dihedral : 23.491 178.799 51513 Min Nonbonded Distance : 0.858 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 2.24 % Allowed : 12.94 % Favored : 84.82 % Rotamer: Outliers : 10.40 % Allowed : 31.52 % Favored : 58.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.21 (0.13), residues: 3484 helix: -1.19 (0.17), residues: 893 sheet: -1.84 (0.21), residues: 589 loop : -2.78 (0.12), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.004 TRP C 212 HIS 0.052 0.003 HIS S 7 PHE 0.038 0.003 PHE C 29 TYR 0.025 0.003 TYR K 32 ARG 0.016 0.001 ARG W 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 932 time to evaluate : 3.916 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: h 6 ARG cc_start: 0.7876 (ptp-170) cc_final: 0.7503 (ptp-170) REVERT: h 74 ASN cc_start: 0.8180 (t0) cc_final: 0.7903 (t0) REVERT: h 87 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7809 (m-10) REVERT: h 94 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6952 (ptp-170) REVERT: 3 2 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7351 (mmtm) REVERT: 3 42 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7311 (t-90) REVERT: 5 52 MET cc_start: -0.0473 (mmt) cc_final: -0.1051 (ppp) REVERT: 8 35 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: C 57 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6322 (t-90) REVERT: E 4 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7687 (m) REVERT: E 46 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: F 95 MET cc_start: 0.4764 (ttt) cc_final: 0.4395 (ttt) REVERT: I 80 LYS cc_start: 0.1000 (mmtt) cc_final: 0.0669 (mmtt) REVERT: J 52 ASP cc_start: 0.6401 (m-30) cc_final: 0.6071 (m-30) REVERT: M 14 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6314 (mtpt) REVERT: P 13 LYS cc_start: 0.7183 (mtpp) cc_final: 0.6959 (mtpp) REVERT: T 70 HIS cc_start: 0.2839 (OUTLIER) cc_final: 0.2401 (m-70) outliers start: 299 outliers final: 224 residues processed: 1096 average time/residue: 0.8740 time to fit residues: 1648.4726 Evaluate side-chains 1124 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 890 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 13 ASN Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 34 THR Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 35 GLU Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 60 GLN Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 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 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 455 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 524 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 620 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 378 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** 8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.9053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 101257 Z= 0.354 Angle : 0.808 14.331 151829 Z= 0.406 Chirality : 0.043 0.371 19464 Planarity : 0.006 0.113 7881 Dihedral : 23.475 179.960 51506 Min Nonbonded Distance : 0.969 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 2.18 % Allowed : 13.46 % Favored : 84.36 % Rotamer: Outliers : 9.60 % Allowed : 33.65 % Favored : 56.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.15 (0.13), residues: 3484 helix: -1.01 (0.17), residues: 881 sheet: -1.78 (0.21), residues: 599 loop : -2.82 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.004 TRP C 212 HIS 0.015 0.003 HIS X 33 PHE 0.045 0.003 PHE F 172 TYR 0.020 0.002 TYR 5 51 ARG 0.016 0.001 ARG Y 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 946 time to evaluate : 4.126 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: h 6 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7593 (ptp-170) REVERT: h 19 LYS cc_start: 0.8575 (tttt) cc_final: 0.8286 (ttmm) REVERT: h 74 ASN cc_start: 0.8252 (t0) cc_final: 0.7989 (t0) REVERT: h 87 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: h 94 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6920 (ptp-170) REVERT: 3 2 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7322 (mmtm) REVERT: 3 42 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7155 (t-90) REVERT: 5 5 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6733 (tp) REVERT: 5 52 MET cc_start: -0.0233 (mmt) cc_final: -0.0733 (ppp) REVERT: 5 86 MET cc_start: 0.4384 (ppp) cc_final: 0.4129 (ppp) REVERT: 8 35 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: C 57 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6404 (t-90) REVERT: D 94 GLN cc_start: 0.7267 (tp40) cc_final: 0.6786 (tp40) REVERT: E 46 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6357 (mp10) REVERT: I 44 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.5068 (pttm) REVERT: L 78 ARG cc_start: 0.5940 (OUTLIER) cc_final: 0.5696 (mtt-85) REVERT: M 14 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6269 (mtpt) REVERT: Q 93 ILE cc_start: 0.4734 (OUTLIER) cc_final: 0.4529 (pt) outliers start: 276 outliers final: 230 residues processed: 1088 average time/residue: 0.8849 time to fit residues: 1651.5520 Evaluate side-chains 1131 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 889 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 140 MET Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 35 GLU Chi-restraints excluded: chain 8 residue 63 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 16 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 61 LYS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 384 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 370 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 394 optimal weight: 0.9990 chunk 422 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 487 optimal weight: 1.9990 overall best weight: 4.7790 ------------------------------------------------------------------------------- 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** 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 138 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN N 9 GLN N 31 HIS N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 71 ASN ** 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 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.9288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 101257 Z= 0.301 Angle : 0.764 14.400 151829 Z= 0.385 Chirality : 0.041 0.426 19464 Planarity : 0.006 0.114 7881 Dihedral : 23.436 179.477 51502 Min Nonbonded Distance : 0.986 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 2.04 % Allowed : 13.26 % Favored : 84.70 % Rotamer: Outliers : 9.29 % Allowed : 34.93 % Favored : 55.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 3484 helix: -0.93 (0.17), residues: 894 sheet: -1.72 (0.21), residues: 604 loop : -2.77 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP C 212 HIS 0.017 0.002 HIS J 77 PHE 0.038 0.003 PHE C 29 TYR 0.018 0.002 TYR 5 51 ARG 0.013 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 921 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: h 6 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7637 (ptp-170) REVERT: h 74 ASN cc_start: 0.8310 (t0) cc_final: 0.7975 (t0) REVERT: h 87 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: h 94 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6932 (ptp-170) REVERT: 3 2 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7373 (mmtm) REVERT: 3 42 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7178 (t-90) REVERT: 5 5 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6722 (tp) REVERT: 5 52 MET cc_start: -0.0581 (mmt) cc_final: -0.0907 (ppp) REVERT: 8 35 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: C 57 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6438 (t-90) REVERT: D 1 MET cc_start: 0.6751 (tmm) cc_final: 0.6268 (ttt) REVERT: D 94 GLN cc_start: 0.7193 (tp40) cc_final: 0.6706 (tp40) REVERT: E 46 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6195 (mp10) REVERT: F 95 MET cc_start: 0.4690 (ttt) cc_final: 0.4421 (ttt) REVERT: I 44 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.5078 (pttm) REVERT: M 14 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6354 (mtpt) REVERT: M 73 ILE cc_start: 0.7174 (mm) cc_final: 0.6929 (mm) REVERT: Z 52 PHE cc_start: 0.5652 (p90) cc_final: 0.5295 (p90) outliers start: 267 outliers final: 227 residues processed: 1059 average time/residue: 0.8768 time to fit residues: 1604.8920 Evaluate side-chains 1115 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 878 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 69 ASN Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 6 residue 30 PHE Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 35 GLU Chi-restraints excluded: chain 8 residue 49 ASN Chi-restraints excluded: chain 8 residue 63 ILE Chi-restraints excluded: chain 8 residue 87 GLN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 48 ILE 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 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 75 SER 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 145 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 24 MET 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 T residue 70 HIS Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain z residue 50 ILE Chi-restraints excluded: chain z residue 62 ASN Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 564 optimal weight: 5.9990 chunk 594 optimal weight: 9.9990 chunk 542 optimal weight: 3.9990 chunk 578 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 454 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 522 optimal weight: 0.7980 chunk 547 optimal weight: 10.0000 chunk 576 optimal weight: 0.4980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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** 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 138 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.9384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 101257 Z= 0.179 Angle : 0.656 14.155 151829 Z= 0.334 Chirality : 0.035 0.391 19464 Planarity : 0.005 0.114 7881 Dihedral : 23.312 179.701 51502 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 2.01 % Allowed : 11.91 % Favored : 86.08 % Rotamer: Outliers : 6.54 % Allowed : 37.72 % Favored : 55.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.75 (0.14), residues: 3484 helix: -0.60 (0.17), residues: 897 sheet: -1.67 (0.21), residues: 602 loop : -2.57 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP C 212 HIS 0.017 0.001 HIS J 77 PHE 0.033 0.002 PHE K 79 TYR 0.018 0.002 TYR J 44 ARG 0.009 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 950 time to evaluate : 3.937 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: h 74 ASN cc_start: 0.8148 (t0) cc_final: 0.7829 (t0) REVERT: h 87 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: 3 42 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7191 (t-90) REVERT: 5 52 MET cc_start: -0.0526 (mmt) cc_final: -0.0902 (ppp) REVERT: 8 11 GLU cc_start: 0.6872 (mp0) cc_final: 0.6642 (mp0) REVERT: 8 35 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: C 57 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6252 (t-90) REVERT: C 173 LEU cc_start: 0.6341 (mp) cc_final: 0.6040 (mp) REVERT: D 1 MET cc_start: 0.6687 (tmm) cc_final: 0.6222 (ttt) REVERT: D 94 GLN cc_start: 0.7203 (tp40) cc_final: 0.6915 (tp40) REVERT: F 95 MET cc_start: 0.4548 (ttt) cc_final: 0.4116 (ttt) REVERT: F 153 ILE cc_start: 0.4573 (mp) cc_final: 0.4178 (mt) REVERT: G 79 THR cc_start: 0.7896 (t) cc_final: 0.7572 (t) REVERT: N 102 PHE cc_start: 0.6615 (m-10) cc_final: 0.6407 (m-10) REVERT: N 107 ASN cc_start: 0.6913 (t0) cc_final: 0.6583 (t0) REVERT: X 16 ASN cc_start: 0.5948 (t0) cc_final: 0.5605 (t0) REVERT: Z 52 PHE cc_start: 0.5423 (p90) cc_final: 0.5207 (p90) outliers start: 188 outliers final: 147 residues processed: 1045 average time/residue: 0.8608 time to fit residues: 1561.5842 Evaluate side-chains 1050 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 899 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 6 residue 30 PHE Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 35 GLU Chi-restraints excluded: chain 8 residue 49 ASN Chi-restraints excluded: chain 8 residue 63 ILE Chi-restraints excluded: chain 8 residue 87 GLN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain z residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 379 optimal weight: 9.9990 chunk 611 optimal weight: 0.3980 chunk 373 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 425 optimal weight: 20.0000 chunk 641 optimal weight: 20.0000 chunk 590 optimal weight: 1.9990 chunk 510 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 394 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 overall best weight: 2.2864 ------------------------------------------------------------------------------- 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** C 116 GLN C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.9466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 101257 Z= 0.191 Angle : 0.670 14.406 151829 Z= 0.339 Chirality : 0.035 0.476 19464 Planarity : 0.005 0.115 7881 Dihedral : 23.274 179.859 51498 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 1.92 % Allowed : 12.37 % Favored : 85.71 % Rotamer: Outliers : 6.09 % Allowed : 38.20 % Favored : 55.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.72 (0.14), residues: 3484 helix: -0.57 (0.18), residues: 888 sheet: -1.66 (0.21), residues: 602 loop : -2.53 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP C 212 HIS 0.021 0.001 HIS J 77 PHE 0.030 0.002 PHE F 172 TYR 0.019 0.002 TYR Q 31 ARG 0.017 0.001 ARG W 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 904 time to evaluate : 3.998 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: h 74 ASN cc_start: 0.8143 (t0) cc_final: 0.7821 (t0) REVERT: h 87 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: 3 2 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7421 (mmtm) REVERT: 3 42 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: 5 52 MET cc_start: -0.0826 (mmt) cc_final: -0.1076 (ppp) REVERT: 8 11 GLU cc_start: 0.6863 (mp0) cc_final: 0.6622 (mp0) REVERT: C 57 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6346 (t-90) REVERT: C 173 LEU cc_start: 0.6315 (mp) cc_final: 0.6063 (mp) REVERT: D 1 MET cc_start: 0.6733 (tmm) cc_final: 0.6228 (ttt) REVERT: D 94 GLN cc_start: 0.7417 (tp40) cc_final: 0.6917 (tp40) REVERT: F 95 MET cc_start: 0.4595 (ttt) cc_final: 0.4172 (ttt) REVERT: X 16 ASN cc_start: 0.6062 (t0) cc_final: 0.5730 (t0) outliers start: 175 outliers final: 161 residues processed: 993 average time/residue: 0.8652 time to fit residues: 1493.0109 Evaluate side-chains 1056 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 891 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 82 ARG Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 13 ASN Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 42 HIS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain 5 residue 5 LEU Chi-restraints excluded: chain 5 residue 37 LYS Chi-restraints excluded: chain 5 residue 106 PHE Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain 6 residue 30 PHE Chi-restraints excluded: chain 7 residue 15 ILE Chi-restraints excluded: chain 7 residue 17 ASN Chi-restraints excluded: chain 7 residue 19 ILE Chi-restraints excluded: chain 8 residue 29 ILE Chi-restraints excluded: chain 8 residue 63 ILE Chi-restraints excluded: chain 8 residue 87 GLN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 65 ASN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 47 ILE Chi-restraints excluded: chain z residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 405 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 471 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 511 optimal weight: 0.0870 chunk 214 optimal weight: 10.0000 chunk 525 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 6.2172 ------------------------------------------------------------------------------- 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** 8 49 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 199 HIS D 42 ASN D 49 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 138 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.139306 restraints weight = 201684.051| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.72 r_work: 0.3641 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 101257 Z= 0.378 Angle : 0.828 14.692 151829 Z= 0.411 Chirality : 0.043 0.450 19464 Planarity : 0.006 0.116 7881 Dihedral : 23.347 179.689 51498 Min Nonbonded Distance : 0.939 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 1.95 % Allowed : 14.24 % Favored : 83.81 % Rotamer: Outliers : 6.75 % Allowed : 37.89 % Favored : 55.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.91 (0.13), residues: 3484 helix: -0.75 (0.17), residues: 884 sheet: -1.72 (0.21), residues: 598 loop : -2.66 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP C 212 HIS 0.020 0.002 HIS J 77 PHE 0.044 0.003 PHE K 79 TYR 0.021 0.002 TYR Q 31 ARG 0.015 0.001 ARG Y 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26314.40 seconds wall clock time: 462 minutes 2.58 seconds (27722.58 seconds total)