Starting phenix.real_space_refine on Thu Feb 22 03:39:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/02_2024/5o60_3750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/02_2024/5o60_3750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/02_2024/5o60_3750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/02_2024/5o60_3750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/02_2024/5o60_3750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o60_3750/02_2024/5o60_3750.pdb" } resolution = 3.18 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= 0.002 sd= 0.036 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 4 6.06 5 P 3240 5.49 5 Mg 408 5.21 5 S 59 5.16 5 C 48533 2.51 5 N 18260 2.21 5 O 27649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "M PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "P PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "d ARG 17": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 98153 Number of models: 1 Model: "" Number of chains: 47 Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 298, 'rna2p_pyr': 146, 'rna3p_pur': 1485, 'rna3p_pyr': 1190} Link IDs: {'rna2p': 444, 'rna3p': 2674} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "W" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "Z" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "a" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "b" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "f" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "g" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 388 Unusual residues: {' MG': 388} Classifications: {'undetermined': 388} Link IDs: {None: 387} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" 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: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93846 SG CYS Y 5 119.815 118.754 64.840 1.00 53.37 S ATOM 93868 SG CYS Y 8 120.363 122.576 65.760 1.00 60.93 S ATOM 94210 SG CYS Y 52 116.661 121.162 65.574 1.00 59.56 S ATOM 94229 SG CYS Y 55 118.701 121.744 62.286 1.00 76.47 S ATOM 95797 SG CYS c 15 77.043 161.710 104.387 1.00 64.89 S ATOM 95819 SG CYS c 18 80.239 162.341 102.520 1.00 71.49 S ATOM 96034 SG CYS c 42 80.370 162.671 106.317 1.00 64.98 S ATOM 96055 SG CYS c 45 78.702 165.434 104.228 1.00 73.33 S ATOM 97087 SG CYS f 11 87.005 90.092 195.795 1.00 81.82 S ATOM 97110 SG CYS f 14 90.095 91.356 194.630 1.00 69.01 S ATOM 97219 SG CYS f 27 90.603 88.283 196.538 1.00 86.08 S ATOM 97429 SG CYS g 16 10.851 150.717 138.361 1.00135.20 S ATOM 97439 SG CYS g 18 9.055 152.064 141.587 1.00131.74 S ATOM 97587 SG CYS g 38 12.804 151.042 141.778 1.00124.22 S ATOM 97608 SG CYS g 41 9.930 148.542 141.141 1.00115.66 S Time building chain proxies: 41.26, per 1000 atoms: 0.42 Number of scatterers: 98153 At special positions: 0 Unit cell: (221.01, 207.11, 259.93, 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 4 29.99 S 59 16.00 P 3240 15.00 Mg 408 11.99 O 27649 8.00 N 18260 7.00 C 48533 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.37 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 8 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 55 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 52 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 5 " pdb=" ZN c 101 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 18 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 45 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 15 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 32 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 41 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 18 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 16 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 38 " Number of angles added : 21 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 51 sheets defined 31.5% alpha, 22.5% beta 1058 base pairs and 1733 stacking pairs defined. Time for finding SS restraints: 38.46 Creating SS restraints... Processing helix chain '3' and resid 2 through 12 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.577A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 88 through 94 removed outlier: 3.832A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 103 through 121 Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.819A pdb=" N ALA E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.834A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.595A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'F' and resid 9 through 18 Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.510A pdb=" N ILE F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 68 removed outlier: 4.368A pdb=" N ASN F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.630A pdb=" N GLN F 128 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE F 129 " --> pdb=" O PRO F 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 125 through 129' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.633A pdb=" N PHE F 145 " --> pdb=" O GLN F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 169 through 180 removed outlier: 3.502A pdb=" N GLY F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.105A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 41 through 60 removed outlier: 4.345A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 73 removed outlier: 3.838A pdb=" N ALA H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 61 removed outlier: 3.838A pdb=" N ARG I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 70 removed outlier: 4.063A pdb=" N GLY I 68 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP I 70 " --> pdb=" O GLU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'J' and resid 26 through 32 removed outlier: 3.744A pdb=" N GLN J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 3.842A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.599A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.701A pdb=" N ILE K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.594A pdb=" N HIS K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 107 removed outlier: 4.385A pdb=" N VAL K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.972A pdb=" N LYS K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 136 removed outlier: 4.015A pdb=" N ALA K 133 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA K 134 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 3.838A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 118 removed outlier: 4.035A pdb=" N VAL L 115 " --> pdb=" O PHE L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 39 through 44 removed outlier: 4.101A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.511A pdb=" N LEU M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 94 through 101 removed outlier: 3.575A pdb=" N LEU M 98 " --> pdb=" O GLY M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.558A pdb=" N HIS N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 57 Proline residue: O 46 - end of helix removed outlier: 4.042A pdb=" N LYS O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.830A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'P' and resid 9 through 27 removed outlier: 3.554A pdb=" N ARG P 24 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU P 25 " --> pdb=" O ARG P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 72 Processing helix chain 'P' and resid 76 through 95 removed outlier: 3.646A pdb=" N ALA P 89 " --> pdb=" O GLY P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 123 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.483A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 removed outlier: 3.691A pdb=" N SER Q 55 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 96 through 101 Processing helix chain 'Q' and resid 103 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 4.305A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.952A pdb=" N ARG R 28 " --> pdb=" O ARG R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.607A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 116 Processing helix chain 'S' and resid 51 through 58 Processing helix chain 'T' and resid 20 through 29 removed outlier: 4.015A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 46 Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 72 through 74 No H-bonds generated for 'chain 'T' and resid 72 through 74' Processing helix chain 'T' and resid 96 through 98 No H-bonds generated for 'chain 'T' and resid 96 through 98' Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.469A pdb=" N ILE U 10 " --> pdb=" O ASP U 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 17 through 25 Processing helix chain 'U' and resid 38 through 50 Processing helix chain 'W' and resid 20 through 30 Processing helix chain 'W' and resid 51 through 62 Processing helix chain 'W' and resid 160 through 162 No H-bonds generated for 'chain 'W' and resid 160 through 162' Processing helix chain 'W' and resid 186 through 191 Processing helix chain 'Y' and resid 53 through 59 Processing helix chain 'Z' and resid 6 through 11 Processing helix chain 'Z' and resid 14 through 39 removed outlier: 3.611A pdb=" N ARG Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 67 Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'b' and resid 43 through 49 Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 20 through 27 removed outlier: 4.077A pdb=" N THR d 27 " --> pdb=" O LEU d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 40 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.540A pdb=" N LYS e 12 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 44 Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.508A pdb=" N SER e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 32 Processing helix chain 'g' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 106 removed outlier: 3.619A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 96 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL C 79 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 5.781A pdb=" N LEU C 165 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 176 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 17 removed outlier: 5.679A pdb=" N LYS D 10 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS D 30 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 191 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL D 185 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 193 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 181 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR D 176 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY D 116 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLN D 178 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 114 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.822A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA D 53 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL D 36 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 124 through 127 removed outlier: 6.629A pdb=" N HIS E 125 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.652A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'G' and resid 122 through 126 Processing sheet with id=AB4, first strand: chain 'G' and resid 96 through 100 Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.393A pdb=" N VAL H 78 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL H 149 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU H 80 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR H 133 " --> pdb=" O GLN H 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.622A pdb=" N ALA I 22 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR I 23 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY I 108 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL I 104 " --> pdb=" O GLU I 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 11 through 15 Processing sheet with id=AB9, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.721A pdb=" N TRP K 15 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC3, first strand: chain 'L' and resid 92 through 93 removed outlier: 3.735A pdb=" N ASP L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL L 24 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA L 84 " --> pdb=" O ARG L 7 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE L 86 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.441A pdb=" N THR Q 57 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG Q 49 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR Q 24 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS Q 82 " --> pdb=" O HIS Q 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS Q 30 " --> pdb=" O ILE Q 80 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE Q 80 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 76 through 79 removed outlier: 5.721A pdb=" N GLN M 76 " --> pdb=" O LYS M 111 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU M 113 " --> pdb=" O GLN M 76 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL M 78 " --> pdb=" O LEU M 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 91 through 93 removed outlier: 7.501A pdb=" N THR M 145 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL M 124 " --> pdb=" O THR M 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.508A pdb=" N VAL N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA N 36 " --> pdb=" O VAL N 102 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE N 104 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.554A pdb=" N SER N 89 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU N 74 " --> pdb=" O GLU N 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.212A pdb=" N MET O 110 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 58 through 64 removed outlier: 5.760A pdb=" N THR P 59 " --> pdb=" O ASN P 53 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN P 53 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA P 61 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL P 40 " --> pdb=" O ASP P 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 89 through 90 removed outlier: 4.491A pdb=" N LYS Q 110 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 12 through 16 removed outlier: 5.953A pdb=" N LYS S 8 " --> pdb=" O VAL S 39 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL S 39 " --> pdb=" O LYS S 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 21 through 25 removed outlier: 6.777A pdb=" N LEU S 94 " --> pdb=" O HIS S 67 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS S 67 " --> pdb=" O LEU S 94 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL S 96 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR S 61 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.876A pdb=" N TYR S 84 " --> pdb=" O LYS S 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 9 through 17 removed outlier: 3.756A pdb=" N TYR T 16 " --> pdb=" O SER T 108 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS T 109 " --> pdb=" O GLU T 85 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU T 85 " --> pdb=" O HIS T 109 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR T 111 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA T 83 " --> pdb=" O THR T 111 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE T 113 " --> pdb=" O VAL T 81 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL T 81 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU T 115 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA T 79 " --> pdb=" O GLU T 115 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 11 through 14 removed outlier: 4.060A pdb=" N LYS U 80 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 66 through 67 Processing sheet with id=AD9, first strand: chain 'V' and resid 66 through 67 removed outlier: 3.517A pdb=" N VAL V 25 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR V 8 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL V 73 " --> pdb=" O THR V 81 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 40 through 45 Processing sheet with id=AE2, first strand: chain 'V' and resid 83 through 88 Processing sheet with id=AE3, first strand: chain 'W' and resid 9 through 15 removed outlier: 7.644A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN W 93 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL W 99 " --> pdb=" O TYR W 38 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP W 84 " --> pdb=" O GLN W 93 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA W 95 " --> pdb=" O ALA W 82 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA W 82 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU W 97 " --> pdb=" O THR W 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR W 80 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL W 99 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA W 78 " --> pdb=" O VAL W 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 143 through 149 Processing sheet with id=AE5, first strand: chain 'W' and resid 122 through 126 Processing sheet with id=AE6, first strand: chain 'X' and resid 22 through 23 removed outlier: 3.515A pdb=" N ARG X 39 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU X 59 " --> pdb=" O LEU X 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.525A pdb=" N HIS X 46 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ILE X 80 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE9, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AF1, first strand: chain 'a' and resid 34 through 38 Processing sheet with id=AF2, first strand: chain 'b' and resid 27 through 32 Processing sheet with id=AF3, first strand: chain 'c' and resid 21 through 26 removed outlier: 6.485A pdb=" N ARG c 21 " --> pdb=" O CYS c 15 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS c 15 " --> pdb=" O ARG c 21 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR c 12 " --> pdb=" O SER c 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF5, first strand: chain 'f' and resid 2 through 4 removed outlier: 6.173A pdb=" N LYS f 2 " --> pdb=" O ARG f 35 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL f 23 " --> pdb=" O GLN f 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 21 through 26 removed outlier: 7.557A pdb=" N ILE g 33 " --> pdb=" O ASP g 11 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR g 13 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL g 35 " --> pdb=" O THR g 13 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN g 15 " --> pdb=" O VAL g 35 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2705 hydrogen bonds 4384 hydrogen bond angles 0 basepair planarities 1058 basepair parallelities 1733 stacking parallelities Total time for adding SS restraints: 188.05 Time building geometry restraints manager: 47.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10284 1.32 - 1.45: 48305 1.45 - 1.58: 41332 1.58 - 1.71: 6448 1.71 - 1.84: 99 Bond restraints: 106468 Sorted by residual: bond pdb=" C1' U A1630 " pdb=" N1 U A1630 " ideal model delta sigma weight residual 1.480 1.582 -0.102 1.50e-02 4.44e+03 4.61e+01 bond pdb=" N VAL a 59 " pdb=" CA VAL a 59 " ideal model delta sigma weight residual 1.459 1.525 -0.066 1.27e-02 6.20e+03 2.73e+01 bond pdb=" CA PRO J 24 " pdb=" C PRO J 24 " ideal model delta sigma weight residual 1.517 1.564 -0.047 9.30e-03 1.16e+04 2.52e+01 bond pdb=" CB SER V 56 " pdb=" OG SER V 56 " ideal model delta sigma weight residual 1.417 1.510 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CA VAL D 144 " pdb=" CB VAL D 144 " ideal model delta sigma weight residual 1.540 1.480 0.060 1.36e-02 5.41e+03 1.94e+01 ... (remaining 106463 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.89: 18173 105.89 - 112.98: 61519 112.98 - 120.08: 38530 120.08 - 127.17: 34094 127.17 - 134.26: 7672 Bond angle restraints: 159988 Sorted by residual: angle pdb=" C LEU N 125 " pdb=" N PRO N 126 " pdb=" CA PRO N 126 " ideal model delta sigma weight residual 119.82 129.95 -10.13 9.80e-01 1.04e+00 1.07e+02 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 112.83 121.20 -8.37 9.90e-01 1.02e+00 7.14e+01 angle pdb=" C HIS K 130 " pdb=" N PRO K 131 " pdb=" CA PRO K 131 " ideal model delta sigma weight residual 119.87 128.52 -8.65 1.04e+00 9.25e-01 6.91e+01 angle pdb=" C LEU E 20 " pdb=" N PRO E 21 " pdb=" CA PRO E 21 " ideal model delta sigma weight residual 119.90 128.38 -8.48 1.02e+00 9.61e-01 6.91e+01 angle pdb=" C LYS E 94 " pdb=" N PRO E 95 " pdb=" CA PRO E 95 " ideal model delta sigma weight residual 119.90 111.78 8.12 1.05e+00 9.07e-01 5.98e+01 ... (remaining 159983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 59000 35.97 - 71.94: 8519 71.94 - 107.91: 912 107.91 - 143.88: 35 143.88 - 179.85: 35 Dihedral angle restraints: 68501 sinusoidal: 58114 harmonic: 10387 Sorted by residual: dihedral pdb=" O4' U A1757 " pdb=" C1' U A1757 " pdb=" N1 U A1757 " pdb=" C2 U A1757 " ideal model delta sinusoidal sigma weight residual 200.00 20.15 179.85 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1534 " pdb=" C1' C A1534 " pdb=" N1 C A1534 " pdb=" C2 C A1534 " ideal model delta sinusoidal sigma weight residual 200.00 21.08 178.92 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual 200.00 23.07 176.93 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 68498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 18602 0.077 - 0.154: 1795 0.154 - 0.231: 147 0.231 - 0.307: 13 0.307 - 0.384: 6 Chirality restraints: 20563 Sorted by residual: chirality pdb=" C3' C A2085 " pdb=" C4' C A2085 " pdb=" O3' C A2085 " pdb=" C2' C A2085 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL W 146 " pdb=" CA VAL W 146 " pdb=" CG1 VAL W 146 " pdb=" CG2 VAL W 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" C4' A A1369 " pdb=" C5' A A1369 " pdb=" O4' A A1369 " pdb=" C3' A A1369 " both_signs ideal model delta sigma weight residual False -2.50 -2.14 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 20560 not shown) Planarity restraints: 8264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG T 117 " -0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ARG T 117 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG T 117 " -0.035 2.00e-02 2.50e+03 pdb=" N PRO T 118 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1098 " 0.065 2.00e-02 2.50e+03 2.92e-02 2.34e+01 pdb=" N9 A A1098 " -0.067 2.00e-02 2.50e+03 pdb=" C8 A A1098 " -0.009 2.00e-02 2.50e+03 pdb=" N7 A A1098 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A A1098 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A1098 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A A1098 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A1098 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A1098 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A1098 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A A1098 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 899 " 0.068 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 G A 899 " -0.051 2.00e-02 2.50e+03 pdb=" C8 G A 899 " -0.018 2.00e-02 2.50e+03 pdb=" N7 G A 899 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 899 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 899 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 899 " 0.019 2.00e-02 2.50e+03 pdb=" N1 G A 899 " 0.016 2.00e-02 2.50e+03 pdb=" C2 G A 899 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A 899 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 899 " -0.017 2.00e-02 2.50e+03 pdb=" C4 G A 899 " -0.018 2.00e-02 2.50e+03 ... (remaining 8261 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 137 2.15 - 2.84: 28275 2.84 - 3.53: 130468 3.53 - 4.21: 317810 4.21 - 4.90: 416517 Nonbonded interactions: 893207 Sorted by model distance: nonbonded pdb=" O3' A 2 76 " pdb=" C PHE 21002 " model vdw 1.463 3.270 nonbonded pdb=" O2' A A2422 " pdb=" NH1 ARG Y 63 " model vdw 1.740 2.520 nonbonded pdb=" OP1 A A1832 " pdb="MG MG A4006 " model vdw 1.774 2.170 nonbonded pdb=" OP2 A B 46 " pdb="MG MG B 202 " model vdw 1.842 2.170 nonbonded pdb=" OP1 A A1144 " pdb="MG MG A4111 " model vdw 1.857 2.170 ... (remaining 893202 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 7.020 Check model and map are aligned: 1.130 Set scattering table: 0.710 Process input model: 398.820 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 413.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 : 0.008 0.105 106468 Z= 0.491 Angle : 1.118 12.463 159988 Z= 0.629 Chirality : 0.047 0.384 20563 Planarity : 0.006 0.087 8264 Dihedral : 24.722 179.845 61829 Min Nonbonded Distance : 1.463 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 10.34 % Allowed : 10.41 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.11), residues: 3615 helix: -3.06 (0.12), residues: 1026 sheet: -0.94 (0.16), residues: 807 loop : -1.77 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 250 HIS 0.008 0.002 HIS D 130 PHE 0.024 0.003 PHE N 69 TYR 0.023 0.003 TYR L 76 ARG 0.007 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1091 time to evaluate : 4.387 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: C 23 GLU cc_start: 0.9070 (mp0) cc_final: 0.8683 (mp0) REVERT: C 97 TYR cc_start: 0.8503 (m-80) cc_final: 0.8092 (m-80) REVERT: C 117 ILE cc_start: 0.8992 (mt) cc_final: 0.8730 (mt) REVERT: C 148 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8655 (mtm180) REVERT: C 240 THR cc_start: 0.8881 (t) cc_final: 0.8602 (p) REVERT: C 241 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8249 (p) REVERT: C 254 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6915 (mt-10) REVERT: C 272 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8427 (ptt-90) REVERT: D 54 TYR cc_start: 0.9003 (t80) cc_final: 0.8789 (t80) REVERT: D 58 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8254 (t) REVERT: D 60 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7599 (ptt90) REVERT: D 79 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8417 (ttm110) REVERT: D 133 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8485 (ptp-170) REVERT: D 142 GLN cc_start: 0.8798 (tp40) cc_final: 0.8482 (tp40) REVERT: D 151 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8766 (tt) REVERT: D 166 MET cc_start: 0.9180 (mtp) cc_final: 0.8745 (mtm) REVERT: E 28 GLU cc_start: 0.7722 (tp30) cc_final: 0.7300 (pm20) REVERT: E 98 TYR cc_start: 0.8267 (m-80) cc_final: 0.7762 (m-80) REVERT: E 117 ASP cc_start: 0.8491 (t70) cc_final: 0.8271 (t0) REVERT: E 149 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7508 (m) REVERT: E 151 ASN cc_start: 0.7900 (m110) cc_final: 0.7623 (m110) REVERT: E 162 ASP cc_start: 0.7426 (t0) cc_final: 0.6763 (m-30) REVERT: E 186 TYR cc_start: 0.8975 (t80) cc_final: 0.8737 (t80) REVERT: F 27 PHE cc_start: 0.8533 (m-80) cc_final: 0.8080 (m-80) REVERT: F 58 ASN cc_start: 0.7918 (m-40) cc_final: 0.7574 (m-40) REVERT: F 63 ASP cc_start: 0.8607 (m-30) cc_final: 0.8066 (m-30) REVERT: F 108 ASP cc_start: 0.8653 (t70) cc_final: 0.8375 (t0) REVERT: F 110 LEU cc_start: 0.8620 (tp) cc_final: 0.8278 (tt) REVERT: F 128 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7716 (mm-40) REVERT: F 154 ASP cc_start: 0.6101 (p0) cc_final: 0.5682 (p0) REVERT: G 42 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.6807 (p) REVERT: G 48 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.5644 (p0) REVERT: G 99 LEU cc_start: 0.7833 (tp) cc_final: 0.7597 (tt) REVERT: G 110 TYR cc_start: 0.8160 (m-80) cc_final: 0.7911 (m-10) REVERT: G 153 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7872 (tpp-160) REVERT: G 161 LYS cc_start: 0.8492 (mttt) cc_final: 0.8281 (mttt) REVERT: G 171 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7968 (ptm-80) REVERT: H 29 TYR cc_start: 0.8893 (t80) cc_final: 0.8571 (t80) REVERT: H 31 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8105 (tp) REVERT: H 33 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7176 (mtp-110) REVERT: H 143 LYS cc_start: 0.7745 (mttt) cc_final: 0.7445 (mtpp) REVERT: I 3 LYS cc_start: 0.4017 (mttt) cc_final: 0.2296 (mmtm) REVERT: I 31 LEU cc_start: 0.4755 (mt) cc_final: 0.4387 (tp) REVERT: I 33 VAL cc_start: 0.3501 (t) cc_final: 0.3094 (m) REVERT: I 94 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6182 (mtpt) REVERT: I 103 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5163 (tp) REVERT: J 30 LEU cc_start: 0.2565 (OUTLIER) cc_final: 0.2344 (pp) REVERT: J 56 ILE cc_start: 0.4494 (OUTLIER) cc_final: 0.4280 (mt) REVERT: J 101 LYS cc_start: 0.6575 (tttt) cc_final: 0.6088 (tptp) REVERT: J 113 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.5229 (t) REVERT: K 75 TYR cc_start: 0.8909 (m-80) cc_final: 0.8439 (m-80) REVERT: K 89 ILE cc_start: 0.9324 (mm) cc_final: 0.9089 (mm) REVERT: K 105 ILE cc_start: 0.9296 (mt) cc_final: 0.9082 (mt) REVERT: K 108 MET cc_start: 0.9258 (mtt) cc_final: 0.8979 (mtm) REVERT: L 1 MET cc_start: 0.8120 (tpt) cc_final: 0.7543 (tpp) REVERT: L 6 SER cc_start: 0.9303 (t) cc_final: 0.9101 (t) REVERT: L 54 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7261 (ptt180) REVERT: L 90 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.6010 (t70) REVERT: L 106 LEU cc_start: 0.8880 (mt) cc_final: 0.8664 (mp) REVERT: L 116 SER cc_start: 0.8131 (m) cc_final: 0.7865 (p) REVERT: M 24 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8579 (mmt-90) REVERT: M 31 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8626 (pptt) REVERT: M 93 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8208 (t) REVERT: M 105 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8020 (mtt180) REVERT: M 119 THR cc_start: 0.7890 (m) cc_final: 0.7540 (m) REVERT: M 127 ASN cc_start: 0.8953 (m-40) cc_final: 0.8663 (m110) REVERT: M 146 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: N 72 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8491 (mtp180) REVERT: N 103 LEU cc_start: 0.9214 (mt) cc_final: 0.8930 (mt) REVERT: N 108 TYR cc_start: 0.7755 (t80) cc_final: 0.7357 (t80) REVERT: N 130 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8150 (ptt180) REVERT: O 37 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9204 (p) REVERT: O 64 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8367 (mmt-90) REVERT: P 32 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8560 (p) REVERT: P 41 ASN cc_start: 0.8496 (m-40) cc_final: 0.8238 (m-40) REVERT: Q 2 ASN cc_start: 0.7386 (t0) cc_final: 0.7084 (m110) REVERT: Q 12 LEU cc_start: 0.9159 (mt) cc_final: 0.8941 (mt) REVERT: Q 15 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.5839 (t0) REVERT: Q 67 VAL cc_start: 0.8645 (t) cc_final: 0.8131 (t) REVERT: Q 96 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8965 (mp) REVERT: R 6 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8573 (mtp180) REVERT: R 32 TYR cc_start: 0.9099 (t80) cc_final: 0.8789 (t80) REVERT: S 72 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9053 (tptt) REVERT: S 74 ARG cc_start: 0.8731 (mmt180) cc_final: 0.8310 (mmt-90) REVERT: T 15 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8520 (mtp-110) REVERT: T 40 LEU cc_start: 0.9196 (mt) cc_final: 0.8721 (mt) REVERT: T 117 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6967 (mtt-85) REVERT: U 29 TYR cc_start: 0.8995 (m-80) cc_final: 0.8760 (m-80) REVERT: U 54 VAL cc_start: 0.8968 (t) cc_final: 0.8749 (t) REVERT: U 56 SER cc_start: 0.9197 (p) cc_final: 0.8882 (m) REVERT: U 62 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8297 (ttm170) REVERT: U 66 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8250 (mtp-110) REVERT: V 1 MET cc_start: 0.7521 (ptp) cc_final: 0.7313 (ptt) REVERT: V 12 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8736 (mt) REVERT: V 24 LEU cc_start: 0.8688 (mt) cc_final: 0.8289 (mm) REVERT: V 60 VAL cc_start: 0.7070 (m) cc_final: 0.6856 (p) REVERT: V 63 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8562 (mp0) REVERT: V 72 MET cc_start: 0.8535 (tpp) cc_final: 0.8105 (ttt) REVERT: V 100 THR cc_start: 0.8399 (p) cc_final: 0.7992 (t) REVERT: V 101 ASN cc_start: 0.7144 (m-40) cc_final: 0.6905 (m110) REVERT: W 6 ASN cc_start: 0.6627 (m-40) cc_final: 0.6242 (t0) REVERT: W 7 ILE cc_start: 0.8241 (pt) cc_final: 0.7980 (tp) REVERT: W 8 PRO cc_start: 0.8559 (Cg_exo) cc_final: 0.8315 (Cg_endo) REVERT: W 33 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8472 (m) REVERT: W 48 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7562 (mp0) REVERT: W 70 ASP cc_start: 0.8520 (t0) cc_final: 0.8125 (p0) REVERT: W 87 PRO cc_start: 0.8729 (Cg_exo) cc_final: 0.8397 (Cg_endo) REVERT: W 91 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8213 (m-40) REVERT: W 119 THR cc_start: 0.4744 (OUTLIER) cc_final: 0.3073 (t) REVERT: W 131 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8086 (pt) REVERT: W 134 GLU cc_start: 0.8173 (tt0) cc_final: 0.7869 (tm-30) REVERT: W 180 ASN cc_start: 0.8998 (t0) cc_final: 0.8660 (t0) REVERT: X 41 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8402 (mmp80) REVERT: Y 24 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8520 (mtp85) REVERT: Y 26 SER cc_start: 0.8984 (t) cc_final: 0.8571 (m) REVERT: Y 30 ASN cc_start: 0.8787 (m-40) cc_final: 0.8481 (m110) REVERT: Z 10 LEU cc_start: 0.9045 (mt) cc_final: 0.8748 (mm) REVERT: Z 25 SER cc_start: 0.8882 (m) cc_final: 0.8446 (m) REVERT: c 6 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6556 (t0) REVERT: c 9 PRO cc_start: 0.9005 (Cg_endo) cc_final: 0.8777 (Cg_exo) REVERT: c 23 TYR cc_start: 0.8936 (m-80) cc_final: 0.8497 (m-80) REVERT: c 26 LYS cc_start: 0.8710 (mttt) cc_final: 0.8440 (mttp) REVERT: c 53 GLU cc_start: 0.8633 (tt0) cc_final: 0.8262 (tt0) REVERT: d 12 ASN cc_start: 0.8870 (m-40) cc_final: 0.8478 (m-40) REVERT: e 11 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8272 (m) REVERT: e 45 ASP cc_start: 0.8435 (p0) cc_final: 0.8207 (p0) REVERT: e 59 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8901 (t0) REVERT: f 2 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8779 (mtmm) REVERT: g 12 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.6927 (m) REVERT: g 22 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7151 (m-80) outliers start: 304 outliers final: 87 residues processed: 1292 average time/residue: 1.0837 time to fit residues: 2251.1109 Evaluate side-chains 912 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 776 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 94 LYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 146 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 22 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 569 optimal weight: 7.9990 chunk 510 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 344 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 528 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 612 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 17 ASN 3 18 HIS C 38 HIS C 87 ASN C 113 GLN C 122 ASN C 205 ASN C 261 ASN D 20 ASN D 34 ASN D 179 ASN D 189 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN F 31 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 HIS H 147 ASN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 HIS K 96 HIS K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 GLN K 132 HIS L 3 GLN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 HIS M 84 ASN M 127 ASN N 17 GLN N 35 GLN N 123 HIS O 17 GLN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN R 41 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 ASN S 67 HIS S 76 HIS S 85 HIS S 93 GLN U 58 ASN U 61 ASN V 31 ASN V 67 HIS W 6 ASN W 45 GLN W 46 HIS W 76 GLN W 94 HIS W 126 GLN W 156 GLN X 29 GLN X 44 HIS X 50 ASN X 79 ASN Y 22 HIS ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 12 ASN c 22 ASN c 48 HIS e 25 GLN e 63 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 106468 Z= 0.264 Angle : 0.658 12.633 159988 Z= 0.339 Chirality : 0.038 0.388 20563 Planarity : 0.006 0.086 8264 Dihedral : 24.715 179.764 55188 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.49 % Favored : 97.43 % Rotamer: Outliers : 6.98 % Allowed : 17.86 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 3615 helix: -0.67 (0.15), residues: 1055 sheet: -0.43 (0.16), residues: 816 loop : -1.15 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 65 HIS 0.011 0.001 HIS U 34 PHE 0.020 0.002 PHE I 81 TYR 0.020 0.002 TYR O 47 ARG 0.017 0.001 ARG g 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 842 time to evaluate : 4.225 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: C 10 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 23 GLU cc_start: 0.8984 (mp0) cc_final: 0.8641 (mp0) REVERT: C 63 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8905 (mpt-90) REVERT: C 69 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7241 (mtp180) REVERT: C 117 ILE cc_start: 0.8911 (mt) cc_final: 0.8599 (mt) REVERT: C 188 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8513 (mtp180) REVERT: C 200 GLU cc_start: 0.8165 (mp0) cc_final: 0.7815 (mt-10) REVERT: C 254 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6810 (mt-10) REVERT: D 60 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7527 (ptt90) REVERT: D 63 ILE cc_start: 0.9081 (mm) cc_final: 0.8706 (tt) REVERT: D 133 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8458 (ptp-170) REVERT: E 28 GLU cc_start: 0.7633 (tp30) cc_final: 0.7396 (pm20) REVERT: E 76 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8224 (mm-40) REVERT: E 98 TYR cc_start: 0.8197 (m-80) cc_final: 0.7755 (m-80) REVERT: E 149 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7506 (m) REVERT: E 162 ASP cc_start: 0.7438 (t0) cc_final: 0.6710 (m-30) REVERT: F 33 MET cc_start: 0.8477 (mmm) cc_final: 0.8201 (mpp) REVERT: F 63 ASP cc_start: 0.8421 (m-30) cc_final: 0.8147 (m-30) REVERT: F 108 ASP cc_start: 0.8448 (t70) cc_final: 0.8136 (t0) REVERT: F 141 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7251 (mm-30) REVERT: F 159 MET cc_start: 0.8283 (ptp) cc_final: 0.7882 (pmm) REVERT: G 48 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5318 (p0) REVERT: G 99 LEU cc_start: 0.8275 (tp) cc_final: 0.7997 (tt) REVERT: G 110 TYR cc_start: 0.8389 (m-80) cc_final: 0.8151 (m-10) REVERT: G 117 GLU cc_start: 0.6708 (mp0) cc_final: 0.6348 (mp0) REVERT: G 153 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (tpm170) REVERT: I 3 LYS cc_start: 0.4139 (mttt) cc_final: 0.2563 (mmtp) REVERT: I 31 LEU cc_start: 0.4799 (mt) cc_final: 0.4278 (tp) REVERT: I 110 MET cc_start: 0.5564 (tmm) cc_final: 0.5336 (tmm) REVERT: J 30 LEU cc_start: 0.2547 (OUTLIER) cc_final: 0.2220 (pp) REVERT: J 89 LYS cc_start: 0.4816 (mttt) cc_final: 0.4143 (mmtt) REVERT: J 101 LYS cc_start: 0.6971 (tttt) cc_final: 0.6266 (tptp) REVERT: J 108 ARG cc_start: 0.7491 (ttm110) cc_final: 0.5874 (mtp180) REVERT: J 113 THR cc_start: 0.6272 (OUTLIER) cc_final: 0.5015 (t) REVERT: J 114 LYS cc_start: 0.6219 (mmmt) cc_final: 0.5973 (mmmt) REVERT: J 115 LYS cc_start: 0.7098 (tmtt) cc_final: 0.6840 (tptt) REVERT: K 37 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8139 (ttt90) REVERT: K 89 ILE cc_start: 0.9195 (mm) cc_final: 0.8982 (mm) REVERT: K 93 LEU cc_start: 0.9075 (mt) cc_final: 0.8661 (mt) REVERT: L 44 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8563 (mmtt) REVERT: L 54 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7533 (ptt180) REVERT: L 68 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7370 (mp0) REVERT: L 76 TYR cc_start: 0.9190 (m-80) cc_final: 0.8844 (m-80) REVERT: L 90 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.6160 (t70) REVERT: L 116 SER cc_start: 0.8263 (m) cc_final: 0.7932 (p) REVERT: M 24 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6656 (tpp80) REVERT: M 85 LYS cc_start: 0.8794 (mttt) cc_final: 0.8152 (mmtm) REVERT: M 105 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7699 (mtt180) REVERT: M 119 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7714 (m) REVERT: M 146 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: N 60 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7801 (ttp-110) REVERT: O 37 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9019 (p) REVERT: P 24 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8452 (ptt-90) REVERT: P 32 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8555 (p) REVERT: P 41 ASN cc_start: 0.8282 (m110) cc_final: 0.8080 (m-40) REVERT: P 118 ASP cc_start: 0.8214 (m-30) cc_final: 0.7844 (m-30) REVERT: Q 15 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5934 (m-30) REVERT: Q 96 LEU cc_start: 0.9209 (mt) cc_final: 0.8974 (mp) REVERT: R 6 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7810 (mtm-85) REVERT: R 73 ASP cc_start: 0.8367 (t0) cc_final: 0.7994 (t0) REVERT: S 28 ASP cc_start: 0.7393 (t0) cc_final: 0.7118 (t70) REVERT: S 94 LEU cc_start: 0.9029 (mt) cc_final: 0.8718 (mt) REVERT: T 117 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6819 (mmt90) REVERT: U 34 HIS cc_start: 0.8714 (t70) cc_final: 0.8284 (t70) REVERT: U 36 ASP cc_start: 0.8209 (p0) cc_final: 0.7915 (p0) REVERT: U 56 SER cc_start: 0.8755 (p) cc_final: 0.8372 (m) REVERT: V 12 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8780 (mt) REVERT: V 24 LEU cc_start: 0.8731 (mt) cc_final: 0.8512 (mm) REVERT: V 72 MET cc_start: 0.8157 (tpp) cc_final: 0.7903 (ttm) REVERT: W 19 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7227 (m) REVERT: W 33 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8572 (t) REVERT: W 48 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7435 (mp0) REVERT: W 70 ASP cc_start: 0.8569 (t0) cc_final: 0.8289 (p0) REVERT: W 89 ARG cc_start: 0.8506 (mtm180) cc_final: 0.8194 (mtm-85) REVERT: W 134 GLU cc_start: 0.8063 (tt0) cc_final: 0.7760 (tm-30) REVERT: W 180 ASN cc_start: 0.9032 (t0) cc_final: 0.8638 (t0) REVERT: W 185 PRO cc_start: 0.7069 (Cg_endo) cc_final: 0.6705 (Cg_exo) REVERT: X 73 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7707 (mmm-85) REVERT: Y 24 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8485 (mtp85) REVERT: Y 26 SER cc_start: 0.8850 (t) cc_final: 0.8541 (m) REVERT: Y 30 ASN cc_start: 0.8597 (m-40) cc_final: 0.8357 (m110) REVERT: Z 29 LEU cc_start: 0.9265 (tp) cc_final: 0.9043 (tp) REVERT: b 31 SER cc_start: 0.9209 (p) cc_final: 0.8867 (m) REVERT: c 6 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.6822 (t0) REVERT: c 9 PRO cc_start: 0.8907 (Cg_endo) cc_final: 0.8682 (Cg_exo) REVERT: c 21 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7726 (mtt180) REVERT: c 23 TYR cc_start: 0.8705 (m-80) cc_final: 0.8458 (m-80) REVERT: c 26 LYS cc_start: 0.8613 (mttt) cc_final: 0.8267 (mttp) REVERT: d 12 ASN cc_start: 0.8540 (m-40) cc_final: 0.8174 (m-40) REVERT: d 17 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8633 (mtp180) REVERT: e 11 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8264 (m) REVERT: g 22 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: g 24 THR cc_start: 0.8186 (m) cc_final: 0.7981 (p) REVERT: g 28 LYS cc_start: 0.7552 (mtpt) cc_final: 0.7134 (mtpt) outliers start: 205 outliers final: 104 residues processed: 973 average time/residue: 1.0010 time to fit residues: 1616.3613 Evaluate side-chains 894 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 762 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 146 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 22 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 509 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 613 optimal weight: 10.0000 chunk 662 optimal weight: 6.9990 chunk 546 optimal weight: 20.0000 chunk 608 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 491 optimal weight: 30.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN C 164 GLN D 20 ASN D 21 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 58 ASN F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN M 76 GLN M 84 ASN O 54 HIS ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN V 31 ASN W 126 GLN W 156 GLN a 8 GLN ** g 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 106468 Z= 0.398 Angle : 0.726 12.209 159988 Z= 0.366 Chirality : 0.042 0.389 20563 Planarity : 0.006 0.084 8264 Dihedral : 24.730 179.510 55052 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 7.83 % Allowed : 20.31 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3615 helix: -0.10 (0.16), residues: 1048 sheet: -0.39 (0.16), residues: 856 loop : -1.10 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 65 HIS 0.008 0.002 HIS c 51 PHE 0.022 0.002 PHE g 44 TYR 0.020 0.002 TYR O 47 ARG 0.008 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 770 time to evaluate : 4.205 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: 3 21 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8538 (ttt90) REVERT: C 23 GLU cc_start: 0.9072 (mp0) cc_final: 0.8719 (mp0) REVERT: C 63 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8925 (mpt-90) REVERT: C 69 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.7173 (mtp180) REVERT: C 126 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8392 (mmtt) REVERT: C 186 ASP cc_start: 0.8174 (t0) cc_final: 0.7598 (t0) REVERT: C 188 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8541 (mtp180) REVERT: C 200 GLU cc_start: 0.8074 (mp0) cc_final: 0.7689 (mt-10) REVERT: C 272 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8216 (ptt-90) REVERT: D 54 TYR cc_start: 0.8712 (t80) cc_final: 0.8380 (t80) REVERT: D 133 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8312 (ptp-170) REVERT: E 28 GLU cc_start: 0.7531 (tp30) cc_final: 0.7225 (pm20) REVERT: E 30 ASN cc_start: 0.8405 (t0) cc_final: 0.8142 (t0) REVERT: E 36 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: E 162 ASP cc_start: 0.7650 (t0) cc_final: 0.6878 (m-30) REVERT: F 13 GLN cc_start: 0.8935 (tp40) cc_final: 0.8689 (tp40) REVERT: F 29 TYR cc_start: 0.7923 (m-80) cc_final: 0.7549 (m-80) REVERT: F 63 ASP cc_start: 0.8471 (m-30) cc_final: 0.8223 (m-30) REVERT: F 141 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7422 (mm-30) REVERT: F 147 GLU cc_start: 0.6723 (tp30) cc_final: 0.6035 (mm-30) REVERT: F 174 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7283 (ttm-80) REVERT: G 48 ASP cc_start: 0.6037 (OUTLIER) cc_final: 0.5070 (p0) REVERT: G 117 GLU cc_start: 0.6789 (mp0) cc_final: 0.6439 (mp0) REVERT: H 33 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7076 (mtp-110) REVERT: H 101 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7331 (m) REVERT: H 118 GLN cc_start: 0.8078 (mt0) cc_final: 0.7510 (mt0) REVERT: I 3 LYS cc_start: 0.5035 (mttt) cc_final: 0.2857 (tppp) REVERT: I 103 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.5418 (tt) REVERT: I 110 MET cc_start: 0.5401 (tmm) cc_final: 0.5110 (tmm) REVERT: J 36 ASN cc_start: 0.3500 (OUTLIER) cc_final: 0.3230 (p0) REVERT: J 83 LYS cc_start: 0.7016 (ttpp) cc_final: 0.6534 (pptt) REVERT: J 89 LYS cc_start: 0.5503 (mttt) cc_final: 0.4727 (mmtt) REVERT: J 101 LYS cc_start: 0.7382 (tttt) cc_final: 0.6367 (tptp) REVERT: J 108 ARG cc_start: 0.7314 (ttm110) cc_final: 0.5591 (mtp180) REVERT: J 113 THR cc_start: 0.5753 (OUTLIER) cc_final: 0.4570 (t) REVERT: J 114 LYS cc_start: 0.5758 (mmmt) cc_final: 0.5266 (mmmt) REVERT: K 93 LEU cc_start: 0.9128 (mt) cc_final: 0.8754 (mt) REVERT: L 44 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8763 (mmtt) REVERT: L 54 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7567 (ptt180) REVERT: L 112 MET cc_start: 0.9013 (mmm) cc_final: 0.8665 (mmm) REVERT: M 24 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6722 (tpp80) REVERT: M 105 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8024 (mtt180) REVERT: M 108 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7933 (p) REVERT: M 109 LEU cc_start: 0.8546 (tp) cc_final: 0.8330 (tp) REVERT: M 146 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: N 60 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7839 (ttp-110) REVERT: O 37 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9011 (p) REVERT: O 64 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8361 (mtt-85) REVERT: P 32 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8609 (p) REVERT: Q 30 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8829 (mtpt) REVERT: R 6 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7793 (mtm180) REVERT: R 73 ASP cc_start: 0.8603 (t0) cc_final: 0.8242 (t0) REVERT: R 95 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9073 (tt) REVERT: T 117 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7174 (mtt-85) REVERT: U 56 SER cc_start: 0.8665 (p) cc_final: 0.8317 (m) REVERT: U 66 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8014 (mtp85) REVERT: V 12 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8571 (mt) REVERT: V 41 ILE cc_start: 0.8895 (pt) cc_final: 0.8615 (pt) REVERT: W 19 THR cc_start: 0.7577 (OUTLIER) cc_final: 0.7354 (m) REVERT: W 70 ASP cc_start: 0.8289 (t0) cc_final: 0.7887 (p0) REVERT: W 134 GLU cc_start: 0.8290 (tt0) cc_final: 0.8013 (tm-30) REVERT: W 156 GLN cc_start: 0.7002 (mt0) cc_final: 0.6786 (mt0) REVERT: Y 24 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8711 (mtp85) REVERT: Y 26 SER cc_start: 0.9037 (t) cc_final: 0.8686 (m) REVERT: Z 27 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: Z 29 LEU cc_start: 0.9305 (tp) cc_final: 0.9078 (tp) REVERT: c 8 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8762 (tpt170) REVERT: c 19 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8853 (mmtm) REVERT: c 22 ASN cc_start: 0.8798 (m-40) cc_final: 0.8531 (m-40) REVERT: c 23 TYR cc_start: 0.8747 (m-80) cc_final: 0.8497 (m-80) REVERT: c 35 ARG cc_start: 0.6650 (mtp85) cc_final: 0.6409 (mtp85) REVERT: c 52 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9035 (tttm) REVERT: c 53 GLU cc_start: 0.8866 (tt0) cc_final: 0.8495 (tt0) REVERT: d 17 ARG cc_start: 0.8971 (mtm180) cc_final: 0.8541 (mtp85) REVERT: e 11 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8359 (m) REVERT: g 2 LYS cc_start: 0.8203 (mttt) cc_final: 0.7941 (mtmt) REVERT: g 20 HIS cc_start: 0.6550 (t70) cc_final: 0.6221 (t70) REVERT: g 22 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: g 28 LYS cc_start: 0.7530 (mtpt) cc_final: 0.7304 (mtpt) outliers start: 230 outliers final: 147 residues processed: 922 average time/residue: 1.0061 time to fit residues: 1536.0350 Evaluate side-chains 891 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 715 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 146 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 162 ILE Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 54 SER Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 8 ARG Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain c residue 52 LYS Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 22 PHE Chi-restraints excluded: chain g residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 9.9990 chunk 461 optimal weight: 40.0000 chunk 318 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 615 optimal weight: 5.9990 chunk 651 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 583 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS J 36 ASN J 95 HIS K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN e 31 HIS g 20 HIS g 42 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 106468 Z= 0.279 Angle : 0.620 10.991 159988 Z= 0.316 Chirality : 0.037 0.327 20563 Planarity : 0.005 0.081 8264 Dihedral : 24.587 179.315 55024 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 7.35 % Allowed : 21.81 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3615 helix: 0.39 (0.16), residues: 1047 sheet: -0.32 (0.17), residues: 838 loop : -0.95 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 65 HIS 0.008 0.001 HIS U 34 PHE 0.023 0.002 PHE g 44 TYR 0.019 0.002 TYR G 95 ARG 0.011 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 748 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8495 (ttt90) REVERT: C 23 GLU cc_start: 0.9053 (mp0) cc_final: 0.8741 (mp0) REVERT: C 63 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8928 (mpt-90) REVERT: C 126 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8393 (mmtt) REVERT: C 186 ASP cc_start: 0.7989 (t0) cc_final: 0.7772 (t0) REVERT: C 188 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8601 (mtp180) REVERT: D 133 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8445 (ptp-170) REVERT: E 28 GLU cc_start: 0.7444 (tp30) cc_final: 0.7212 (pm20) REVERT: E 30 ASN cc_start: 0.8390 (t0) cc_final: 0.8190 (t0) REVERT: E 162 ASP cc_start: 0.7660 (t0) cc_final: 0.6693 (m-30) REVERT: F 18 GLU cc_start: 0.8159 (mp0) cc_final: 0.7875 (mp0) REVERT: F 63 ASP cc_start: 0.8499 (m-30) cc_final: 0.8265 (m-30) REVERT: F 141 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7373 (mm-30) REVERT: G 48 ASP cc_start: 0.5828 (OUTLIER) cc_final: 0.5264 (p0) REVERT: G 113 PRO cc_start: 0.6765 (Cg_endo) cc_final: 0.6559 (Cg_exo) REVERT: G 117 GLU cc_start: 0.6864 (mp0) cc_final: 0.6614 (mp0) REVERT: G 171 ARG cc_start: 0.8314 (ptp-110) cc_final: 0.7851 (mtp-110) REVERT: H 10 GLU cc_start: 0.7383 (tp30) cc_final: 0.7099 (tt0) REVERT: H 118 GLN cc_start: 0.7883 (mt0) cc_final: 0.7283 (mt0) REVERT: I 3 LYS cc_start: 0.4962 (mttt) cc_final: 0.2724 (tppp) REVERT: I 103 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.5959 (tp) REVERT: J 36 ASN cc_start: 0.3353 (OUTLIER) cc_final: 0.2930 (p0) REVERT: J 56 ILE cc_start: 0.2506 (OUTLIER) cc_final: 0.2148 (mt) REVERT: J 101 LYS cc_start: 0.7376 (tttt) cc_final: 0.6314 (tptp) REVERT: J 108 ARG cc_start: 0.7191 (ttm110) cc_final: 0.5848 (mtp180) REVERT: J 115 LYS cc_start: 0.6791 (tmtt) cc_final: 0.6383 (tppt) REVERT: K 93 LEU cc_start: 0.9142 (mt) cc_final: 0.8796 (mt) REVERT: L 44 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8697 (mmtt) REVERT: L 54 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7605 (ptt180) REVERT: L 90 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.5955 (t70) REVERT: M 105 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7843 (mtt180) REVERT: O 64 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8327 (mtt-85) REVERT: P 32 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8477 (p) REVERT: P 98 GLU cc_start: 0.8147 (tp30) cc_final: 0.7936 (tp30) REVERT: Q 30 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8937 (mtpt) REVERT: R 6 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7548 (mtm180) REVERT: R 31 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8567 (mt) REVERT: R 73 ASP cc_start: 0.8443 (t0) cc_final: 0.8109 (t0) REVERT: U 56 SER cc_start: 0.8633 (p) cc_final: 0.8268 (m) REVERT: V 12 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8760 (mt) REVERT: W 19 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7268 (m) REVERT: W 70 ASP cc_start: 0.8294 (t0) cc_final: 0.7898 (p0) REVERT: W 134 GLU cc_start: 0.8297 (tt0) cc_final: 0.7933 (tm-30) REVERT: W 156 GLN cc_start: 0.6914 (mt0) cc_final: 0.6680 (mt0) REVERT: X 73 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7621 (mmm-85) REVERT: Y 24 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8673 (mtp85) REVERT: Y 26 SER cc_start: 0.9037 (t) cc_final: 0.8649 (m) REVERT: Y 28 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8705 (ptm160) REVERT: Z 27 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: c 19 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8783 (mmtm) REVERT: c 53 GLU cc_start: 0.8815 (tt0) cc_final: 0.8406 (tt0) REVERT: d 17 ARG cc_start: 0.8869 (mtm180) cc_final: 0.8470 (mtp85) outliers start: 216 outliers final: 149 residues processed: 884 average time/residue: 1.0029 time to fit residues: 1476.7014 Evaluate side-chains 874 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 707 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 79 ASN Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 9.9990 chunk 369 optimal weight: 0.0980 chunk 9 optimal weight: 20.0000 chunk 485 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 555 optimal weight: 9.9990 chunk 450 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 584 optimal weight: 8.9990 chunk 164 optimal weight: 50.0000 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN G 98 GLN J 36 ASN K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 4 GLN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 106468 Z= 0.256 Angle : 0.602 9.886 159988 Z= 0.306 Chirality : 0.036 0.309 20563 Planarity : 0.005 0.080 8264 Dihedral : 24.500 179.926 55000 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 7.15 % Allowed : 22.73 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 3615 helix: 0.57 (0.16), residues: 1058 sheet: -0.23 (0.17), residues: 835 loop : -0.91 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 65 HIS 0.009 0.001 HIS O 54 PHE 0.024 0.002 PHE g 44 TYR 0.016 0.002 TYR c 23 ARG 0.011 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 751 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8521 (ttt90) REVERT: C 23 GLU cc_start: 0.9052 (mp0) cc_final: 0.8735 (mp0) REVERT: C 63 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8900 (mpt-90) REVERT: C 69 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.6551 (mtp180) REVERT: C 97 TYR cc_start: 0.8372 (m-80) cc_final: 0.8171 (m-80) REVERT: C 188 ARG cc_start: 0.8960 (mtp85) cc_final: 0.8661 (mtp180) REVERT: C 272 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8382 (ptt-90) REVERT: D 38 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8101 (ttt-90) REVERT: D 54 TYR cc_start: 0.8645 (t80) cc_final: 0.8227 (t80) REVERT: E 28 GLU cc_start: 0.7833 (tp30) cc_final: 0.7382 (pm20) REVERT: E 30 ASN cc_start: 0.8347 (t0) cc_final: 0.8059 (t0) REVERT: E 34 MET cc_start: 0.8988 (mtm) cc_final: 0.8752 (mtt) REVERT: E 36 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: E 162 ASP cc_start: 0.7691 (t0) cc_final: 0.6814 (m-30) REVERT: F 63 ASP cc_start: 0.8467 (m-30) cc_final: 0.8182 (m-30) REVERT: F 141 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7396 (mm-30) REVERT: G 117 GLU cc_start: 0.6847 (mp0) cc_final: 0.6603 (mp0) REVERT: H 10 GLU cc_start: 0.7453 (tp30) cc_final: 0.7137 (tt0) REVERT: H 20 GLU cc_start: 0.7506 (tp30) cc_final: 0.7107 (tp30) REVERT: I 24 VAL cc_start: 0.6056 (OUTLIER) cc_final: 0.5498 (p) REVERT: I 103 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5306 (tt) REVERT: J 36 ASN cc_start: 0.3648 (OUTLIER) cc_final: 0.3003 (p0) REVERT: J 38 MET cc_start: 0.4883 (mmm) cc_final: 0.4353 (ppp) REVERT: J 83 LYS cc_start: 0.6795 (ttpp) cc_final: 0.6269 (pptt) REVERT: J 89 LYS cc_start: 0.6016 (mttt) cc_final: 0.5358 (mmtt) REVERT: J 101 LYS cc_start: 0.7220 (tttt) cc_final: 0.6248 (tmtt) REVERT: J 115 LYS cc_start: 0.6578 (tmtt) cc_final: 0.6164 (tppt) REVERT: K 93 LEU cc_start: 0.9150 (mt) cc_final: 0.8820 (mt) REVERT: L 54 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7604 (ptt180) REVERT: L 90 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6163 (t70) REVERT: M 105 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: M 129 PHE cc_start: 0.8768 (m-80) cc_final: 0.8435 (m-80) REVERT: N 41 TYR cc_start: 0.9104 (m-10) cc_final: 0.8700 (m-10) REVERT: O 64 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: P 32 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8417 (p) REVERT: Q 30 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8929 (mtpt) REVERT: R 6 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7584 (mtm180) REVERT: R 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7992 (t0) REVERT: U 36 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8054 (t0) REVERT: U 56 SER cc_start: 0.8534 (p) cc_final: 0.8157 (m) REVERT: U 66 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8316 (mtp-110) REVERT: W 10 LYS cc_start: 0.7734 (tppp) cc_final: 0.7371 (tppp) REVERT: W 19 THR cc_start: 0.7432 (m) cc_final: 0.7012 (p) REVERT: W 32 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8152 (mmmt) REVERT: W 70 ASP cc_start: 0.8341 (t0) cc_final: 0.7941 (p0) REVERT: W 101 GLN cc_start: 0.7737 (pm20) cc_final: 0.7417 (pm20) REVERT: W 109 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6973 (tp30) REVERT: W 134 GLU cc_start: 0.8334 (tt0) cc_final: 0.7962 (tm-30) REVERT: W 156 GLN cc_start: 0.6897 (mt0) cc_final: 0.6616 (mt0) REVERT: X 73 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7561 (mmm-85) REVERT: Y 24 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8744 (mtp85) REVERT: Y 26 SER cc_start: 0.9031 (t) cc_final: 0.8626 (m) REVERT: Y 28 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8729 (ptt180) REVERT: Z 27 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: c 8 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8383 (tpt170) REVERT: c 19 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8803 (mmtm) REVERT: c 21 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8058 (tpp80) REVERT: c 53 GLU cc_start: 0.8604 (tt0) cc_final: 0.8204 (tt0) REVERT: d 17 ARG cc_start: 0.8886 (mtm180) cc_final: 0.8572 (mtp180) REVERT: g 1 MET cc_start: 0.8772 (tpp) cc_final: 0.8138 (tpp) REVERT: g 22 PHE cc_start: 0.7595 (m-80) cc_final: 0.7354 (m-80) outliers start: 210 outliers final: 153 residues processed: 883 average time/residue: 1.0229 time to fit residues: 1491.3563 Evaluate side-chains 894 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 722 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 79 ASN Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 8 ARG Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 20.0000 chunk 586 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 382 optimal weight: 6.9990 chunk 160 optimal weight: 50.0000 chunk 652 optimal weight: 6.9990 chunk 541 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 342 optimal weight: 9.9990 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 34 GLN F 146 HIS G 86 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN W 76 GLN Z 44 ASN c 20 HIS ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 106468 Z= 0.390 Angle : 0.703 9.116 159988 Z= 0.354 Chirality : 0.041 0.332 20563 Planarity : 0.006 0.082 8264 Dihedral : 24.617 179.916 54986 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 7.72 % Allowed : 23.34 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 3615 helix: 0.36 (0.16), residues: 1056 sheet: -0.30 (0.17), residues: 835 loop : -1.10 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 93 HIS 0.006 0.001 HIS f 32 PHE 0.033 0.002 PHE K 53 TYR 0.017 0.002 TYR c 23 ARG 0.011 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 734 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8537 (ttt90) REVERT: C 23 GLU cc_start: 0.9130 (mp0) cc_final: 0.8784 (mp0) REVERT: C 63 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8941 (mpt-90) REVERT: C 69 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.6880 (mtp180) REVERT: C 118 GLU cc_start: 0.8149 (pt0) cc_final: 0.7852 (pt0) REVERT: C 188 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8602 (mtp180) REVERT: C 272 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8265 (ptt-90) REVERT: D 38 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8054 (ttt-90) REVERT: D 54 TYR cc_start: 0.8647 (t80) cc_final: 0.8394 (t80) REVERT: E 30 ASN cc_start: 0.8386 (t0) cc_final: 0.8163 (t0) REVERT: E 36 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: E 162 ASP cc_start: 0.7465 (t0) cc_final: 0.6536 (m-30) REVERT: F 63 ASP cc_start: 0.8494 (m-30) cc_final: 0.8252 (m-30) REVERT: G 48 ASP cc_start: 0.5708 (OUTLIER) cc_final: 0.5156 (p0) REVERT: G 171 ARG cc_start: 0.8251 (ptp-110) cc_final: 0.7931 (ptm-80) REVERT: G 176 LYS cc_start: 0.7489 (mttm) cc_final: 0.7130 (pttp) REVERT: H 10 GLU cc_start: 0.7501 (tp30) cc_final: 0.7149 (tt0) REVERT: H 20 GLU cc_start: 0.7470 (tp30) cc_final: 0.7146 (tp30) REVERT: I 24 VAL cc_start: 0.6229 (OUTLIER) cc_final: 0.5747 (p) REVERT: I 103 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5450 (tt) REVERT: I 117 VAL cc_start: 0.5204 (OUTLIER) cc_final: 0.4992 (p) REVERT: J 36 ASN cc_start: 0.3633 (OUTLIER) cc_final: 0.3009 (p0) REVERT: J 38 MET cc_start: 0.4738 (mmm) cc_final: 0.3871 (ppp) REVERT: J 101 LYS cc_start: 0.7435 (tttt) cc_final: 0.6412 (tmtt) REVERT: K 93 LEU cc_start: 0.9273 (mt) cc_final: 0.8932 (mt) REVERT: L 54 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7456 (ptt180) REVERT: M 105 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7871 (mtt180) REVERT: M 129 PHE cc_start: 0.8830 (m-80) cc_final: 0.8538 (m-80) REVERT: N 41 TYR cc_start: 0.9183 (m-10) cc_final: 0.8843 (m-10) REVERT: O 64 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8292 (mtt-85) REVERT: Q 2 ASN cc_start: 0.7196 (t0) cc_final: 0.6422 (m-40) REVERT: R 6 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7809 (mtm180) REVERT: R 31 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8622 (mt) REVERT: R 73 ASP cc_start: 0.8640 (t0) cc_final: 0.8286 (t0) REVERT: R 120 ASP cc_start: 0.8180 (p0) cc_final: 0.7089 (p0) REVERT: U 56 SER cc_start: 0.8605 (p) cc_final: 0.8242 (m) REVERT: V 40 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7762 (mmt180) REVERT: V 63 GLU cc_start: 0.8514 (mp0) cc_final: 0.8242 (mp0) REVERT: W 10 LYS cc_start: 0.7820 (tppp) cc_final: 0.7436 (tppp) REVERT: W 32 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8292 (mmmt) REVERT: W 70 ASP cc_start: 0.8278 (t0) cc_final: 0.7916 (p0) REVERT: W 101 GLN cc_start: 0.7914 (pm20) cc_final: 0.7657 (pm20) REVERT: W 109 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6964 (tp30) REVERT: W 134 GLU cc_start: 0.8324 (tt0) cc_final: 0.7938 (tm-30) REVERT: W 156 GLN cc_start: 0.6911 (mt0) cc_final: 0.6686 (mt0) REVERT: W 161 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: X 73 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7568 (mmm-85) REVERT: Y 24 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8795 (mtp85) REVERT: Y 26 SER cc_start: 0.9064 (t) cc_final: 0.8700 (m) REVERT: Z 27 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: c 8 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8433 (tpt170) REVERT: d 17 ARG cc_start: 0.8957 (mtm180) cc_final: 0.8540 (mtp-110) outliers start: 227 outliers final: 171 residues processed: 881 average time/residue: 1.0401 time to fit residues: 1535.6449 Evaluate side-chains 905 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 715 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 79 ASN Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 8 ARG Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 23 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 476 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 548 optimal weight: 7.9990 chunk 364 optimal weight: 10.0000 chunk 649 optimal weight: 0.9990 chunk 406 optimal weight: 30.0000 chunk 396 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN K 103 ASN ** K 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 106468 Z= 0.233 Angle : 0.588 10.071 159988 Z= 0.300 Chirality : 0.035 0.332 20563 Planarity : 0.005 0.080 8264 Dihedral : 24.497 179.601 54984 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 7.04 % Allowed : 24.57 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3615 helix: 0.60 (0.16), residues: 1058 sheet: -0.18 (0.17), residues: 808 loop : -0.98 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 65 HIS 0.008 0.001 HIS U 34 PHE 0.024 0.002 PHE F 27 TYR 0.016 0.002 TYR O 47 ARG 0.009 0.001 ARG S 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 734 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8543 (ttt90) REVERT: C 23 GLU cc_start: 0.9071 (mp0) cc_final: 0.8718 (mp0) REVERT: C 63 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8908 (mpt-90) REVERT: C 69 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7057 (mtp180) REVERT: C 118 GLU cc_start: 0.8206 (pt0) cc_final: 0.7890 (pt0) REVERT: C 188 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8629 (mtp180) REVERT: C 272 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8323 (ptt-90) REVERT: D 38 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8454 (ttt-90) REVERT: D 54 TYR cc_start: 0.8574 (t80) cc_final: 0.8207 (t80) REVERT: E 30 ASN cc_start: 0.8230 (t0) cc_final: 0.7982 (t0) REVERT: E 34 MET cc_start: 0.8979 (mtm) cc_final: 0.8747 (mtt) REVERT: E 36 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: E 162 ASP cc_start: 0.7443 (t0) cc_final: 0.6492 (m-30) REVERT: F 63 ASP cc_start: 0.8468 (m-30) cc_final: 0.8223 (m-30) REVERT: G 87 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7993 (ttmm) REVERT: G 156 ASP cc_start: 0.8136 (t70) cc_final: 0.7812 (t0) REVERT: G 171 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8099 (ptm-80) REVERT: G 176 LYS cc_start: 0.7514 (mttm) cc_final: 0.6908 (ptmm) REVERT: H 10 GLU cc_start: 0.7424 (tp30) cc_final: 0.7114 (tt0) REVERT: H 20 GLU cc_start: 0.7488 (tp30) cc_final: 0.7172 (tp30) REVERT: I 24 VAL cc_start: 0.6052 (OUTLIER) cc_final: 0.5550 (p) REVERT: I 99 ASP cc_start: 0.4551 (OUTLIER) cc_final: 0.4141 (p0) REVERT: I 103 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5757 (tp) REVERT: J 38 MET cc_start: 0.5353 (mmm) cc_final: 0.4482 (ppp) REVERT: J 101 LYS cc_start: 0.7348 (tttt) cc_final: 0.6312 (tmtt) REVERT: K 93 LEU cc_start: 0.9207 (mt) cc_final: 0.8896 (mt) REVERT: L 54 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7313 (ptt180) REVERT: M 24 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.6534 (tpp80) REVERT: M 129 PHE cc_start: 0.8762 (m-80) cc_final: 0.8477 (m-80) REVERT: N 41 TYR cc_start: 0.9123 (m-10) cc_final: 0.8780 (m-10) REVERT: O 64 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8046 (mtt-85) REVERT: P 12 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: P 32 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8535 (p) REVERT: Q 30 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8861 (mtpt) REVERT: R 6 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7451 (mtm180) REVERT: R 73 ASP cc_start: 0.8395 (t0) cc_final: 0.8074 (t0) REVERT: U 56 SER cc_start: 0.8529 (p) cc_final: 0.8150 (m) REVERT: U 66 ARG cc_start: 0.8750 (mtp85) cc_final: 0.7686 (mtp85) REVERT: U 76 ARG cc_start: 0.8399 (mtt180) cc_final: 0.8105 (mtt180) REVERT: V 62 GLN cc_start: 0.8202 (mm110) cc_final: 0.7986 (mm110) REVERT: W 10 LYS cc_start: 0.7838 (tppp) cc_final: 0.7424 (tppp) REVERT: W 19 THR cc_start: 0.7498 (m) cc_final: 0.7271 (m) REVERT: W 32 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8266 (mmmt) REVERT: W 48 GLU cc_start: 0.8317 (mp0) cc_final: 0.8095 (mp0) REVERT: W 70 ASP cc_start: 0.8511 (t0) cc_final: 0.7979 (p0) REVERT: W 101 GLN cc_start: 0.7912 (pm20) cc_final: 0.7631 (pm20) REVERT: W 109 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7026 (tp30) REVERT: W 134 GLU cc_start: 0.8204 (tt0) cc_final: 0.7911 (tm-30) REVERT: Y 24 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8817 (mtp85) REVERT: Y 26 SER cc_start: 0.9010 (t) cc_final: 0.8610 (m) REVERT: Z 27 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: c 19 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8727 (mmtm) REVERT: d 5 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8501 (ttmt) REVERT: d 17 ARG cc_start: 0.8901 (mtm180) cc_final: 0.8580 (mtp180) REVERT: g 25 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7961 (mtp85) outliers start: 207 outliers final: 165 residues processed: 862 average time/residue: 0.9883 time to fit residues: 1418.7919 Evaluate side-chains 899 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 717 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 GLN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 79 ASN Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 442 optimal weight: 40.0000 chunk 321 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 510 optimal weight: 7.9990 overall best weight: 15.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 146 HIS G 86 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN H 147 ASN K 103 ASN L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 HIS ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN V 31 ASN V 44 HIS W 156 GLN Z 31 ASN Z 44 ASN ** g 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 106468 Z= 0.546 Angle : 0.829 10.945 159988 Z= 0.409 Chirality : 0.047 0.337 20563 Planarity : 0.007 0.083 8264 Dihedral : 24.743 179.393 54976 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 7.79 % Allowed : 24.26 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3615 helix: 0.13 (0.16), residues: 1059 sheet: -0.44 (0.17), residues: 815 loop : -1.22 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP N 93 HIS 0.008 0.002 HIS M 58 PHE 0.032 0.003 PHE K 53 TYR 0.021 0.003 TYR c 23 ARG 0.012 0.001 ARG S 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 713 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8530 (ttt90) REVERT: C 23 GLU cc_start: 0.9189 (mp0) cc_final: 0.8952 (mp0) REVERT: C 63 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8947 (mpt-90) REVERT: C 69 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.7203 (mtp180) REVERT: C 118 GLU cc_start: 0.8211 (pt0) cc_final: 0.7916 (pt0) REVERT: C 188 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8639 (mtp180) REVERT: C 271 ARG cc_start: 0.8320 (ptm160) cc_final: 0.7294 (ptm160) REVERT: C 272 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.6430 (ptm-80) REVERT: D 38 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8126 (ttt-90) REVERT: E 36 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: F 63 ASP cc_start: 0.8450 (m-30) cc_final: 0.8216 (m-30) REVERT: G 48 ASP cc_start: 0.5512 (OUTLIER) cc_final: 0.4958 (p0) REVERT: G 87 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8048 (ttmm) REVERT: G 156 ASP cc_start: 0.8244 (t70) cc_final: 0.7878 (t0) REVERT: G 171 ARG cc_start: 0.8387 (ptp-110) cc_final: 0.8003 (ptm-80) REVERT: G 176 LYS cc_start: 0.7590 (mttm) cc_final: 0.7153 (pttp) REVERT: H 10 GLU cc_start: 0.7593 (tp30) cc_final: 0.7286 (tt0) REVERT: H 20 GLU cc_start: 0.7308 (tp30) cc_final: 0.7022 (tp30) REVERT: H 146 LEU cc_start: 0.8496 (mp) cc_final: 0.7892 (tp) REVERT: I 24 VAL cc_start: 0.6134 (OUTLIER) cc_final: 0.5544 (p) REVERT: I 99 ASP cc_start: 0.4216 (OUTLIER) cc_final: 0.3957 (p0) REVERT: I 103 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.5494 (tt) REVERT: I 120 VAL cc_start: 0.6265 (t) cc_final: 0.5756 (p) REVERT: J 38 MET cc_start: 0.4900 (mmm) cc_final: 0.3943 (ppp) REVERT: L 54 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7540 (ptt180) REVERT: M 24 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7052 (tpp80) REVERT: M 129 PHE cc_start: 0.8856 (m-80) cc_final: 0.8563 (m-80) REVERT: N 41 TYR cc_start: 0.9196 (m-10) cc_final: 0.8868 (m-10) REVERT: N 60 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7842 (ttm110) REVERT: O 64 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8390 (mtt-85) REVERT: Q 2 ASN cc_start: 0.6959 (t0) cc_final: 0.6635 (m-40) REVERT: Q 30 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8896 (mtpt) REVERT: R 4 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.8973 (t) REVERT: R 6 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8123 (mtm180) REVERT: R 31 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8681 (mt) REVERT: R 73 ASP cc_start: 0.8699 (t0) cc_final: 0.8362 (t0) REVERT: R 111 ASP cc_start: 0.8821 (p0) cc_final: 0.8575 (p0) REVERT: S 4 TYR cc_start: 0.8546 (p90) cc_final: 0.8233 (p90) REVERT: T 34 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8478 (mmmt) REVERT: U 56 SER cc_start: 0.8665 (p) cc_final: 0.8327 (m) REVERT: U 76 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8210 (mtt180) REVERT: W 10 LYS cc_start: 0.7841 (tppp) cc_final: 0.7469 (tppp) REVERT: W 32 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8488 (mmmt) REVERT: W 48 GLU cc_start: 0.8430 (mp0) cc_final: 0.8173 (mp0) REVERT: W 70 ASP cc_start: 0.8315 (t0) cc_final: 0.7889 (p0) REVERT: W 109 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7176 (tp30) REVERT: W 134 GLU cc_start: 0.8303 (tt0) cc_final: 0.7897 (tm-30) REVERT: X 73 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7612 (mmm-85) REVERT: Y 24 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8862 (mtp85) REVERT: Y 26 SER cc_start: 0.9170 (t) cc_final: 0.8713 (m) REVERT: Z 27 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: Z 31 ASN cc_start: 0.8811 (m110) cc_final: 0.8205 (m110) REVERT: c 21 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8299 (tpp80) outliers start: 229 outliers final: 184 residues processed: 867 average time/residue: 0.9966 time to fit residues: 1443.7412 Evaluate side-chains 903 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 701 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 82 ASN Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 72 MET Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 79 ASN Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 4.9990 chunk 622 optimal weight: 9.9990 chunk 567 optimal weight: 9.9990 chunk 605 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 475 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 547 optimal weight: 6.9990 chunk 572 optimal weight: 0.6980 chunk 603 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN G 98 GLN H 147 ASN K 103 ASN L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 106468 Z= 0.211 Angle : 0.585 10.437 159988 Z= 0.299 Chirality : 0.035 0.319 20563 Planarity : 0.005 0.081 8264 Dihedral : 24.511 179.796 54975 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.82 % Allowed : 26.68 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3615 helix: 0.55 (0.16), residues: 1062 sheet: -0.28 (0.17), residues: 823 loop : -0.97 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 250 HIS 0.009 0.001 HIS U 34 PHE 0.024 0.002 PHE K 53 TYR 0.016 0.002 TYR O 47 ARG 0.010 0.001 ARG Z 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 727 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 21 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8547 (ttt90) REVERT: C 23 GLU cc_start: 0.9077 (mp0) cc_final: 0.8737 (mp0) REVERT: C 63 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8775 (mpt-90) REVERT: C 118 GLU cc_start: 0.8175 (pt0) cc_final: 0.7862 (pt0) REVERT: C 237 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7512 (mm-30) REVERT: C 272 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8270 (ptt-90) REVERT: D 104 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 36 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: E 162 ASP cc_start: 0.7583 (t0) cc_final: 0.6539 (m-30) REVERT: F 63 ASP cc_start: 0.8467 (m-30) cc_final: 0.8230 (m-30) REVERT: G 48 ASP cc_start: 0.5339 (OUTLIER) cc_final: 0.4903 (p0) REVERT: G 156 ASP cc_start: 0.8061 (t70) cc_final: 0.7835 (t0) REVERT: G 171 ARG cc_start: 0.8371 (ptp-110) cc_final: 0.7948 (ptm-80) REVERT: G 176 LYS cc_start: 0.7590 (mttm) cc_final: 0.6978 (pttp) REVERT: H 10 GLU cc_start: 0.7505 (tp30) cc_final: 0.7244 (tt0) REVERT: H 20 GLU cc_start: 0.7360 (tp30) cc_final: 0.7054 (tp30) REVERT: H 146 LEU cc_start: 0.8377 (mp) cc_final: 0.7686 (tp) REVERT: I 120 VAL cc_start: 0.6083 (t) cc_final: 0.5624 (p) REVERT: J 38 MET cc_start: 0.5243 (mmm) cc_final: 0.4348 (ppp) REVERT: J 101 LYS cc_start: 0.7190 (tttt) cc_final: 0.6152 (tmtt) REVERT: L 54 ARG cc_start: 0.7898 (ttp-170) cc_final: 0.7374 (ptt180) REVERT: L 90 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7112 (p0) REVERT: M 24 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6448 (tpp80) REVERT: M 129 PHE cc_start: 0.8691 (m-80) cc_final: 0.8468 (m-80) REVERT: N 41 TYR cc_start: 0.9103 (m-10) cc_final: 0.8760 (m-10) REVERT: N 60 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7799 (ttm110) REVERT: O 64 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8128 (mtt-85) REVERT: Q 1 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6860 (mmm) REVERT: Q 30 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8888 (mtpt) REVERT: R 6 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7129 (mtm180) REVERT: R 73 ASP cc_start: 0.8370 (t0) cc_final: 0.8047 (t0) REVERT: R 111 ASP cc_start: 0.8804 (p0) cc_final: 0.8547 (p0) REVERT: T 34 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8477 (mmmt) REVERT: U 56 SER cc_start: 0.8532 (p) cc_final: 0.8136 (m) REVERT: U 66 ARG cc_start: 0.8750 (mtp85) cc_final: 0.7714 (mtp85) REVERT: W 10 LYS cc_start: 0.7797 (tppp) cc_final: 0.7392 (tppp) REVERT: W 32 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8313 (mmmt) REVERT: W 70 ASP cc_start: 0.8217 (t0) cc_final: 0.7886 (p0) REVERT: W 109 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7125 (tp30) REVERT: W 134 GLU cc_start: 0.8258 (tt0) cc_final: 0.7842 (tm-30) REVERT: Y 24 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8778 (mtp85) REVERT: Y 26 SER cc_start: 0.9012 (t) cc_final: 0.8598 (m) REVERT: Y 30 ASN cc_start: 0.8476 (m-40) cc_final: 0.8264 (m110) REVERT: Z 27 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: Z 51 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8085 (mtp85) REVERT: c 19 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8791 (mmtm) REVERT: d 12 ASN cc_start: 0.8675 (m-40) cc_final: 0.8271 (m-40) REVERT: d 17 ARG cc_start: 0.8874 (mtm180) cc_final: 0.8581 (mtp180) REVERT: g 13 THR cc_start: 0.8510 (t) cc_final: 0.8215 (p) REVERT: g 25 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7974 (mtp85) outliers start: 171 outliers final: 151 residues processed: 834 average time/residue: 1.0026 time to fit residues: 1394.3195 Evaluate side-chains 869 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 706 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 21 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 27 GLU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 14 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 6.9990 chunk 640 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 303 optimal weight: 30.0000 chunk 445 optimal weight: 50.0000 chunk 671 optimal weight: 40.0000 chunk 618 optimal weight: 2.9990 chunk 534 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 413 optimal weight: 0.7980 chunk 327 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 146 HIS ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN H 147 ASN K 103 ASN L 4 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN W 156 GLN ** W 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 44 ASN ** g 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 106468 Z= 0.191 Angle : 0.558 11.121 159988 Z= 0.283 Chirality : 0.033 0.283 20563 Planarity : 0.005 0.081 8264 Dihedral : 24.392 179.926 54962 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.48 % Allowed : 27.08 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3615 helix: 0.79 (0.16), residues: 1062 sheet: -0.26 (0.18), residues: 807 loop : -0.81 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 45 HIS 0.008 0.001 HIS U 34 PHE 0.021 0.001 PHE g 44 TYR 0.015 0.001 TYR Q 98 ARG 0.008 0.000 ARG S 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7230 Ramachandran restraints generated. 3615 Oldfield, 0 Emsley, 3615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 729 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.9045 (mp0) cc_final: 0.8690 (mp0) REVERT: C 63 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8804 (mpt-90) REVERT: C 118 GLU cc_start: 0.8171 (pt0) cc_final: 0.7844 (pt0) REVERT: C 237 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7688 (mm-30) REVERT: C 272 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8319 (ptt-90) REVERT: D 104 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7981 (tm-30) REVERT: E 36 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: E 162 ASP cc_start: 0.7589 (t0) cc_final: 0.6599 (m-30) REVERT: F 63 ASP cc_start: 0.8323 (m-30) cc_final: 0.8118 (m-30) REVERT: G 48 ASP cc_start: 0.5340 (OUTLIER) cc_final: 0.4907 (p0) REVERT: G 87 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7962 (ttmm) REVERT: G 156 ASP cc_start: 0.8019 (t70) cc_final: 0.7775 (t0) REVERT: G 171 ARG cc_start: 0.8369 (ptp-110) cc_final: 0.7961 (ptm-80) REVERT: G 176 LYS cc_start: 0.7582 (mttm) cc_final: 0.6994 (pttp) REVERT: H 10 GLU cc_start: 0.7518 (tp30) cc_final: 0.7158 (tt0) REVERT: H 20 GLU cc_start: 0.7322 (tp30) cc_final: 0.7021 (tp30) REVERT: H 146 LEU cc_start: 0.8380 (mp) cc_final: 0.7692 (tp) REVERT: I 99 ASP cc_start: 0.4900 (OUTLIER) cc_final: 0.4409 (p0) REVERT: I 120 VAL cc_start: 0.6057 (t) cc_final: 0.5600 (p) REVERT: J 38 MET cc_start: 0.5195 (mmm) cc_final: 0.4346 (ppp) REVERT: J 101 LYS cc_start: 0.7320 (tttt) cc_final: 0.6283 (tmtt) REVERT: K 93 LEU cc_start: 0.9149 (mt) cc_final: 0.8839 (mt) REVERT: L 54 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7376 (ptt180) REVERT: L 68 GLU cc_start: 0.7432 (mp0) cc_final: 0.7160 (mp0) REVERT: M 24 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.6365 (tpp80) REVERT: M 115 ASP cc_start: 0.6968 (t70) cc_final: 0.6546 (t0) REVERT: M 129 PHE cc_start: 0.8630 (m-80) cc_final: 0.8381 (m-80) REVERT: N 41 TYR cc_start: 0.9080 (m-10) cc_final: 0.8732 (m-10) REVERT: O 64 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8171 (mtt-85) REVERT: P 32 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8491 (p) REVERT: Q 30 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8887 (mtpt) REVERT: Q 105 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8253 (pttm) REVERT: R 6 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7179 (mtm180) REVERT: R 73 ASP cc_start: 0.8220 (t0) cc_final: 0.7936 (t0) REVERT: T 34 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8516 (mmmt) REVERT: U 66 ARG cc_start: 0.8701 (mtp85) cc_final: 0.7687 (mtp85) REVERT: U 91 LYS cc_start: 0.8245 (tptp) cc_final: 0.8000 (mmmt) REVERT: W 10 LYS cc_start: 0.7844 (tppp) cc_final: 0.7431 (tppp) REVERT: W 32 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8337 (mmmt) REVERT: W 48 GLU cc_start: 0.8315 (mp0) cc_final: 0.8067 (mp0) REVERT: W 70 ASP cc_start: 0.8488 (t0) cc_final: 0.7956 (p0) REVERT: W 109 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7093 (tp30) REVERT: W 134 GLU cc_start: 0.8280 (tt0) cc_final: 0.7985 (tm-30) REVERT: Y 24 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8862 (mtp85) REVERT: Y 26 SER cc_start: 0.8987 (t) cc_final: 0.8566 (m) REVERT: Y 30 ASN cc_start: 0.8437 (m-40) cc_final: 0.8213 (m110) REVERT: Y 48 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.8014 (tpp-160) REVERT: c 19 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8767 (mmtm) REVERT: d 6 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8261 (mmt-90) REVERT: d 12 ASN cc_start: 0.8674 (m-40) cc_final: 0.8280 (m-40) REVERT: d 17 ARG cc_start: 0.8888 (mtm180) cc_final: 0.8595 (mtp180) REVERT: g 1 MET cc_start: 0.8660 (tpp) cc_final: 0.8229 (tpp) outliers start: 161 outliers final: 134 residues processed: 831 average time/residue: 1.0039 time to fit residues: 1390.3145 Evaluate side-chains 852 residues out of total 2965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 706 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 64 ARG Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 126 LYS Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 7 ASP Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 44 ARG Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 6 ARG Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 45 ASP Chi-restraints excluded: chain e residue 50 VAL Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 11 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 10.0000 chunk 569 optimal weight: 9.9990 chunk 163 optimal weight: 50.0000 chunk 493 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 535 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 549 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS E 208 ASN F 146 HIS G 86 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN K 103 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN V 31 ASN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087055 restraints weight = 200124.531| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.82 r_work: 0.2998 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 106468 Z= 0.354 Angle : 0.665 9.614 159988 Z= 0.334 Chirality : 0.039 0.279 20563 Planarity : 0.006 0.080 8264 Dihedral : 24.496 179.921 54962 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.06 % Allowed : 26.54 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3615 helix: 0.57 (0.16), residues: 1065 sheet: -0.43 (0.18), residues: 814 loop : -0.89 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 93 HIS 0.007 0.001 HIS U 34 PHE 0.029 0.002 PHE K 53 TYR 0.018 0.002 TYR E 98 ARG 0.011 0.001 ARG S 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23648.99 seconds wall clock time: 417 minutes 16.96 seconds (25036.96 seconds total)