Starting phenix.real_space_refine on Mon Sep 30 03:59:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvh_11456/09_2024/6zvh_11456.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvh_11456/09_2024/6zvh_11456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvh_11456/09_2024/6zvh_11456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvh_11456/09_2024/6zvh_11456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvh_11456/09_2024/6zvh_11456.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvh_11456/09_2024/6zvh_11456.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 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 3 6.06 5 P 1814 5.49 5 Mg 30 5.21 5 S 180 5.16 5 C 42751 2.51 5 N 14493 2.21 5 O 19743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 248 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 79014 Number of models: 1 Model: "" Number of chains: 43 Chain: "2" Number of atoms: 36896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1740, 36896 Classifications: {'DNA': 15, 'RNA': 1725} Modifications used: {'5*END': 1, 'rna2p_pur': 147, 'rna2p_pyr': 130, 'rna3p_pur': 759, 'rna3p_pyr': 686} Link IDs: {'rna2p': 276, 'rna3p': 1463} Chain breaks: 4 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {' G:plan2': 3, ' A:plan': 1, ' C:plan': 11, ' U:plan': 3, ' G:plan': 3, ' C:plan2': 11, ' A:plan2': 1} Unresolved non-hydrogen planarities: 203 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1741 Classifications: {'peptide': 221} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 207} Chain: "B" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1738 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "D" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "H" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1497 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 1 Chain: "I" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 827 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "L" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1247 Classifications: {'peptide': 153} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 144} Chain: "P" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1061 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "Q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "R" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 125} Chain: "S" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1198 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 136} Chain: "U" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 135} Chain: "a" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "c" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "d" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain: "g" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "C" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "G" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "J" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "O" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1049 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 131} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "Y" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1065 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "Z" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "e" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "f" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "x" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1589 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 28, 'rna3p_pyr': 33} Link IDs: {'rna2p': 14, 'rna3p': 60} Chain: "y" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 603 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "i" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 865 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Unusual residues: {' MG': 28} Classifications: {'undetermined': 28} Link IDs: {None: 27} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" 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: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" 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: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 59270 SG CYS a 23 86.265 112.727 73.541 1.00 24.30 S ATOM 59291 SG CYS a 26 85.515 114.382 76.924 1.00 24.21 S ATOM 59674 SG CYS a 74 88.767 112.262 76.395 1.00 21.87 S ATOM 59693 SG CYS a 77 85.625 110.664 76.755 1.00 22.18 S ATOM 75729 SG CYS f 126 97.649 49.063 178.568 1.00103.50 S ATOM 75847 SG CYS f 141 95.813 52.919 179.090 1.00 98.40 S ATOM 75866 SG CYS f 144 94.004 51.506 178.413 1.00100.14 S Time building chain proxies: 32.94, per 1000 atoms: 0.42 Number of scatterers: 79014 At special positions: 0 Unit cell: (238.275, 242.511, 213.918, 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 3 29.99 S 180 16.00 P 1814 15.00 Mg 30 11.99 O 19743 8.00 N 14493 7.00 C 42751 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 - 3.00 Amino acid : True - 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: 13.68 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb=" ZN f 200 " pdb="ZN ZN f 200 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 200 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 200 " - pdb=" SG CYS f 141 " Number of angles added : 6 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9412 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 56 sheets defined 36.1% alpha, 16.5% beta 537 base pairs and 945 stacking pairs defined. Time for finding SS restraints: 26.50 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'B' and resid 23 through 26 removed outlier: 3.653A pdb=" N SER B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.651A pdb=" N GLY B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.593A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.623A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 30 through 33 Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 97 through 112 Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.019A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.715A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 263 Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.586A pdb=" N LYS F 22 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 67 through 77 Processing helix chain 'F' and resid 85 through 105 removed outlier: 3.711A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 144 through 162 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 203 removed outlier: 3.627A pdb=" N ASN F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 29 removed outlier: 4.177A pdb=" N SER H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.560A pdb=" N GLN H 39 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 40 " --> pdb=" O LYS H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 36 through 40' Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 75 through 87 removed outlier: 3.518A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 4.026A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 25 through 29 removed outlier: 3.504A pdb=" N GLU I 28 " --> pdb=" O ARG I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 129 through 138 removed outlier: 4.904A pdb=" N GLU I 135 " --> pdb=" O PRO I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'K' and resid 4 through 18 removed outlier: 3.677A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 55 removed outlier: 3.605A pdb=" N VAL K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'P' and resid 21 through 27 Processing helix chain 'P' and resid 29 through 37 removed outlier: 4.258A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.980A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.614A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 59 Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 76 through 100 Processing helix chain 'Q' and resid 101 through 114 Processing helix chain 'Q' and resid 116 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 21 through 24 removed outlier: 3.543A pdb=" N LEU R 24 " --> pdb=" O TYR R 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 21 through 24' Processing helix chain 'R' and resid 27 through 38 Processing helix chain 'R' and resid 43 through 64 Processing helix chain 'R' and resid 70 through 83 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'S' and resid 25 through 31 Processing helix chain 'S' and resid 37 through 49 Processing helix chain 'S' and resid 60 through 72 Processing helix chain 'S' and resid 74 through 78 Processing helix chain 'S' and resid 80 through 84 removed outlier: 3.604A pdb=" N LEU S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 117 removed outlier: 3.802A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 127 Processing helix chain 'T' and resid 10 through 25 Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.649A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 Processing helix chain 'T' and resid 124 through 144 Processing helix chain 'U' and resid 28 through 45 Processing helix chain 'U' and resid 94 through 104 removed outlier: 4.073A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 63 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'X' and resid 9 through 22 Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.624A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 93 Processing helix chain 'X' and resid 129 through 135 Processing helix chain 'a' and resid 46 through 48 No H-bonds generated for 'chain 'a' and resid 46 through 48' Processing helix chain 'a' and resid 49 through 57 removed outlier: 3.834A pdb=" N ILE a 53 " --> pdb=" O ALA a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'a' and resid 88 through 93 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 5.204A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.201A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 218 Processing helix chain 'C' and resid 232 through 250 removed outlier: 4.738A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.828A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.702A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 4.804A pdb=" N MET G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 63 removed outlier: 4.109A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 93 through 99 Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.789A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.535A pdb=" N ALA J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 removed outlier: 3.603A pdb=" N GLN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 151 through 155' Processing helix chain 'J' and resid 171 through 185 Processing helix chain 'M' and resid 12 through 29 removed outlier: 4.561A pdb=" N ALA M 17 " --> pdb=" O ASP M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 43 Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.900A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 89 removed outlier: 3.556A pdb=" N LEU M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 29 through 43 removed outlier: 3.595A pdb=" N VAL N 33 " --> pdb=" O THR N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 59 removed outlier: 4.166A pdb=" N GLY N 59 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'O' and resid 57 through 61 Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 111 through 122 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.651A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 78 through 85 Processing helix chain 'Y' and resid 87 through 94 removed outlier: 4.105A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 117 Processing helix chain 'Y' and resid 120 through 127 Processing helix chain 'Z' and resid 51 through 62 Processing helix chain 'Z' and resid 69 through 77 Processing helix chain 'Z' and resid 81 through 95 removed outlier: 3.503A pdb=" N ARG Z 85 " --> pdb=" O GLY Z 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.507A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 removed outlier: 4.606A pdb=" N ARG e 8 " --> pdb=" O SER e 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA e 9 " --> pdb=" O LEU e 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 5 through 9' Processing helix chain 'e' and resid 11 through 16 Processing helix chain 'e' and resid 30 through 40 Processing helix chain 'y' and resid 310 through 321 Processing helix chain 'y' and resid 322 through 324 No H-bonds generated for 'chain 'y' and resid 322 through 324' Processing helix chain 'y' and resid 329 through 344 Processing helix chain 'y' and resid 350 through 364 Processing helix chain 'i' and resid 25 through 33 Processing helix chain 'i' and resid 57 through 64 Processing helix chain 'i' and resid 74 through 87 Processing helix chain 'i' and resid 91 through 99 Processing helix chain 'i' and resid 102 through 111 removed outlier: 3.782A pdb=" N ILE i 106 " --> pdb=" O LYS i 102 " (cutoff:3.500A) Processing helix chain 'i' and resid 117 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.842A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.760A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER A 75 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.791A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 70 removed outlier: 8.728A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.504A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.793A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.670A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB1, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.486A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.601A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.920A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 123 through 126 removed outlier: 4.114A pdb=" N GLN F 137 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 47 through 49 removed outlier: 3.655A pdb=" N ALA H 47 " --> pdb=" O PHE H 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 139 through 142 removed outlier: 6.215A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 139 through 142 removed outlier: 6.215A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU W 49 " --> pdb=" O ASN W 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.394A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS I 37 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR I 36 " --> pdb=" O LEU I 96 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 62 through 66 removed outlier: 5.219A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 20 through 21 Processing sheet with id=AC2, first strand: chain 'L' and resid 72 through 79 removed outlier: 17.854A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.220A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AC4, first strand: chain 'Q' and resid 9 through 16 removed outlier: 6.207A pdb=" N LEU Q 31 " --> pdb=" O ILE Q 68 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL Q 70 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 97 through 98 Processing sheet with id=AC6, first strand: chain 'S' and resid 12 through 14 Processing sheet with id=AC7, first strand: chain 'T' and resid 81 through 85 removed outlier: 4.957A pdb=" N ASN T 85 " --> pdb=" O PRO T 89 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AC9, first strand: chain 'U' and resid 51 through 61 removed outlier: 8.938A pdb=" N ASP U 90 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG U 55 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU U 88 " --> pdb=" O ARG U 55 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS U 86 " --> pdb=" O PRO U 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 64 through 65 Processing sheet with id=AD2, first strand: chain 'V' and resid 32 through 39 removed outlier: 5.256A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 46 through 58 removed outlier: 6.620A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AD5, first strand: chain 'a' and resid 36 through 40 Processing sheet with id=AD6, first strand: chain 'c' and resid 41 through 42 Processing sheet with id=AD7, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AD8, first strand: chain 'g' and resid 4 through 11 removed outlier: 3.520A pdb=" N ARG g 8 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR g 297 " --> pdb=" O TRP g 291 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP g 291 " --> pdb=" O THR g 297 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE g 299 " --> pdb=" O LEU g 289 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU g 289 " --> pdb=" O PHE g 299 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY g 301 " --> pdb=" O THR g 287 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 18 through 23 removed outlier: 6.625A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG g 57 " --> pdb=" O MET g 42 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'g' and resid 66 through 71 removed outlier: 4.157A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 108 through 113 removed outlier: 6.738A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU g 131 " --> pdb=" O TYR g 140 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 154 through 156 removed outlier: 7.037A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'g' and resid 195 through 200 removed outlier: 3.633A pdb=" N THR g 197 " --> pdb=" O GLY g 210 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'g' and resid 236 through 240 removed outlier: 6.407A pdb=" N ALA g 251 " --> pdb=" O ASN g 237 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU g 239 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS g 249 " --> pdb=" O LEU g 239 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 103 through 116 removed outlier: 5.657A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AE8, first strand: chain 'G' and resid 11 through 17 removed outlier: 4.677A pdb=" N CYS G 12 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE G 7 " --> pdb=" O CYS G 12 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL G 108 " --> pdb=" O ASN G 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL G 114 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL G 50 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AF1, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AF2, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AF3, first strand: chain 'M' and resid 32 through 33 removed outlier: 6.379A pdb=" N CYS M 50 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL M 79 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN M 52 " --> pdb=" O VAL M 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 52 through 54 removed outlier: 7.467A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 80 through 81 removed outlier: 6.770A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.636A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY Y 67 " --> pdb=" O HIS Y 29 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 97 through 99 Processing sheet with id=AF8, first strand: chain 'b' and resid 44 through 47 Processing sheet with id=AF9, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AG1, first strand: chain 'f' and resid 138 through 140 Processing sheet with id=AG2, first strand: chain 'y' and resid 326 through 328 1596 hydrogen bonds defined for protein. 4539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1329 hydrogen bonds 2068 hydrogen bond angles 0 basepair planarities 537 basepair parallelities 945 stacking parallelities Total time for adding SS restraints: 67.46 Time building geometry restraints manager: 16.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9498 1.31 - 1.44: 32198 1.44 - 1.56: 38593 1.56 - 1.69: 3626 1.69 - 1.81: 275 Bond restraints: 84190 Sorted by residual: bond pdb=" CB VAL F 111 " pdb=" CG1 VAL F 111 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.49e+00 bond pdb=" C PRO F 143 " pdb=" N LEU F 144 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.30e+00 bond pdb=" CB VAL C 112 " pdb=" CG2 VAL C 112 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.20e+00 bond pdb=" C6 G 21422 " pdb=" N1 G 21422 " ideal model delta sigma weight residual 1.391 1.342 0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" C6 G 21422 " pdb=" O6 G 21422 " ideal model delta sigma weight residual 1.237 1.190 0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 84185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 121464 4.14 - 8.28: 718 8.28 - 12.43: 72 12.43 - 16.57: 6 16.57 - 20.71: 3 Bond angle restraints: 122263 Sorted by residual: angle pdb=" N3 C 21417 " pdb=" C4 C 21417 " pdb=" N4 C 21417 " ideal model delta sigma weight residual 118.00 97.29 20.71 3.00e+00 1.11e-01 4.77e+01 angle pdb=" C THR g 93 " pdb=" N THR g 94 " pdb=" CA THR g 94 " ideal model delta sigma weight residual 124.31 134.83 -10.52 1.67e+00 3.59e-01 3.97e+01 angle pdb=" N VAL R 85 " pdb=" CA VAL R 85 " pdb=" C VAL R 85 " ideal model delta sigma weight residual 107.76 101.44 6.32 1.01e+00 9.80e-01 3.92e+01 angle pdb=" C VAL R 85 " pdb=" CA VAL R 85 " pdb=" CB VAL R 85 " ideal model delta sigma weight residual 110.71 117.37 -6.66 1.07e+00 8.73e-01 3.88e+01 angle pdb=" C ILE E 92 " pdb=" N ASP E 93 " pdb=" CA ASP E 93 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 ... (remaining 122258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 48775 35.88 - 71.76: 4397 71.76 - 107.64: 537 107.64 - 143.53: 12 143.53 - 179.41: 17 Dihedral angle restraints: 53738 sinusoidal: 39152 harmonic: 14586 Sorted by residual: dihedral pdb=" CA ASN Z 46 " pdb=" C ASN Z 46 " pdb=" N LEU Z 47 " pdb=" CA LEU Z 47 " ideal model delta harmonic sigma weight residual 180.00 115.06 64.94 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CA ILE V 78 " pdb=" C ILE V 78 " pdb=" N VAL V 79 " pdb=" CA VAL V 79 " ideal model delta harmonic sigma weight residual -180.00 -118.65 -61.35 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA ALA X 126 " pdb=" C ALA X 126 " pdb=" N ASN X 127 " pdb=" CA ASN X 127 " ideal model delta harmonic sigma weight residual -180.00 -119.69 -60.31 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 53735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 13473 0.083 - 0.166: 1491 0.166 - 0.249: 141 0.249 - 0.332: 20 0.332 - 0.415: 4 Chirality restraints: 15129 Sorted by residual: chirality pdb=" CB ILE S 26 " pdb=" CA ILE S 26 " pdb=" CG1 ILE S 26 " pdb=" CG2 ILE S 26 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C3' U 2 112 " pdb=" C4' U 2 112 " pdb=" O3' U 2 112 " pdb=" C2' U 2 112 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB THR A 82 " pdb=" CA THR A 82 " pdb=" OG1 THR A 82 " pdb=" CG2 THR A 82 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 15126 not shown) Planarity restraints: 8827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 236 " 0.038 2.00e-02 2.50e+03 3.45e-02 2.08e+01 pdb=" CG PHE C 236 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE C 236 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE C 236 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 236 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 236 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE C 236 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 43 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO Q 44 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO Q 44 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO Q 44 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET G 217 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C MET G 217 " 0.063 2.00e-02 2.50e+03 pdb=" O MET G 217 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS G 218 " -0.022 2.00e-02 2.50e+03 ... (remaining 8824 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 769 2.57 - 3.16: 57539 3.16 - 3.74: 143071 3.74 - 4.32: 204186 4.32 - 4.90: 288659 Nonbonded interactions: 694224 Sorted by model distance: nonbonded pdb=" OP2 G 21603 " pdb="MG MG 21920 " model vdw 1.992 2.170 nonbonded pdb=" O6 G 21605 " pdb="MG MG 21920 " model vdw 1.999 2.170 nonbonded pdb=" OP1 U 21072 " pdb="MG MG 21925 " model vdw 2.020 2.170 nonbonded pdb=" OP2 A 2 99 " pdb="MG MG 21909 " model vdw 2.024 2.170 nonbonded pdb=" OP2 C 2 409 " pdb="MG MG 21909 " model vdw 2.029 2.170 ... (remaining 694219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.720 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: 0.080 Extract box with map and model: 2.330 Check model and map are aligned: 0.460 Set scattering table: 0.570 Process input model: 198.220 Find NCS groups from input model: 1.120 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: 0.020 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 0.090 84190 Z= 0.521 Angle : 0.950 20.711 122263 Z= 0.496 Chirality : 0.054 0.415 15129 Planarity : 0.006 0.105 8827 Dihedral : 21.804 179.407 44326 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.88 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.50 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5000 helix: -0.82 (0.12), residues: 1662 sheet: -0.69 (0.18), residues: 840 loop : -2.00 (0.11), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 83 HIS 0.009 0.002 HIS g 62 PHE 0.078 0.003 PHE C 236 TYR 0.055 0.003 TYR A 202 ARG 0.015 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 205 ARG cc_start: 0.3759 (tpt170) cc_final: 0.3462 (mmt180) REVERT: K 17 LYS cc_start: 0.6392 (mmpt) cc_final: 0.6178 (mmpt) REVERT: K 77 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7710 (tp-100) REVERT: R 99 ASP cc_start: 0.6572 (t0) cc_final: 0.6016 (t0) REVERT: R 118 GLN cc_start: 0.8304 (tm-30) cc_final: 0.8038 (tm-30) REVERT: S 63 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8020 (mm-30) REVERT: T 114 GLU cc_start: 0.8273 (pm20) cc_final: 0.8067 (pm20) REVERT: a 52 ASP cc_start: 0.7834 (m-30) cc_final: 0.7420 (m-30) REVERT: G 57 ASP cc_start: 0.8068 (t0) cc_final: 0.7771 (t0) REVERT: G 121 ILE cc_start: 0.8746 (tt) cc_final: 0.8520 (tt) REVERT: f 94 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8145 (ptpp) outliers start: 0 outliers final: 1 residues processed: 641 average time/residue: 1.7404 time to fit residues: 1462.9312 Evaluate side-chains 529 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 528 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 30 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 569 optimal weight: 8.9990 chunk 511 optimal weight: 0.8980 chunk 283 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 345 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 529 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 chunk 393 optimal weight: 6.9990 chunk 612 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN P 103 ASN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 GLN R 74 GLN S 105 ASN T 142 ASN g 14 HIS g 62 HIS J 27 GLN M 48 HIS M 52 GLN O 20 GLN Y 112 ASN i 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 84190 Z= 0.203 Angle : 0.658 21.002 122263 Z= 0.341 Chirality : 0.039 0.275 15129 Planarity : 0.005 0.086 8827 Dihedral : 22.984 178.581 33846 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer: Outliers : 1.44 % Allowed : 9.65 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -1.43 (0.11), residues: 5000 helix: 0.15 (0.12), residues: 1680 sheet: -0.72 (0.18), residues: 858 loop : -1.83 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 90 HIS 0.007 0.001 HIS g 14 PHE 0.031 0.001 PHE C 236 TYR 0.027 0.001 TYR R 84 ARG 0.009 0.000 ARG g 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 582 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9021 (mptp) REVERT: I 205 ARG cc_start: 0.3952 (tpt170) cc_final: 0.3694 (tpt90) REVERT: K 77 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7809 (tp-100) REVERT: L 91 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: R 101 ASP cc_start: 0.8071 (m-30) cc_final: 0.7815 (m-30) REVERT: T 114 GLU cc_start: 0.8207 (pm20) cc_final: 0.7799 (pm20) REVERT: V 74 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8692 (mmtp) REVERT: c 35 MET cc_start: 0.7904 (ptp) cc_final: 0.7625 (ptp) REVERT: G 156 TYR cc_start: 0.8471 (m-80) cc_final: 0.7904 (m-80) REVERT: G 224 ARG cc_start: 0.8235 (mmp80) cc_final: 0.8014 (mmp80) REVERT: M 61 TYR cc_start: 0.8415 (t80) cc_final: 0.7935 (t80) REVERT: M 107 SER cc_start: 0.8182 (m) cc_final: 0.7879 (p) REVERT: Z 90 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7691 (tm-30) REVERT: y 371 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6272 (tm) REVERT: i 75 LEU cc_start: 0.8838 (tp) cc_final: 0.8609 (tp) outliers start: 63 outliers final: 19 residues processed: 608 average time/residue: 1.6551 time to fit residues: 1331.9682 Evaluate side-chains 556 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 533 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 74 LYS Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 286 CYS Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain y residue 371 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 340 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 510 optimal weight: 6.9990 chunk 417 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 614 optimal weight: 6.9990 chunk 663 optimal weight: 8.9990 chunk 546 optimal weight: 0.0370 chunk 608 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 492 optimal weight: 20.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN H 162 GLN I 168 GLN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 ASN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN M 48 HIS O 20 GLN f 93 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 84190 Z= 0.253 Angle : 0.643 20.935 122263 Z= 0.332 Chirality : 0.040 0.279 15129 Planarity : 0.005 0.080 8827 Dihedral : 22.850 178.941 33843 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.26 % Favored : 92.66 % Rotamer: Outliers : 1.85 % Allowed : 13.27 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -1.17 (0.12), residues: 5000 helix: 0.49 (0.13), residues: 1695 sheet: -0.66 (0.18), residues: 854 loop : -1.75 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 8 HIS 0.005 0.001 HIS I 22 PHE 0.027 0.002 PHE C 236 TYR 0.031 0.001 TYR R 84 ARG 0.008 0.000 ARG f 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 565 time to evaluate : 4.572 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: A 10 MET cc_start: 0.8513 (tpt) cc_final: 0.8001 (tpt) REVERT: D 1 MET cc_start: 0.4763 (OUTLIER) cc_final: 0.3921 (ttt) REVERT: P 32 GLN cc_start: 0.8181 (pm20) cc_final: 0.7891 (pm20) REVERT: T 114 GLU cc_start: 0.8162 (pm20) cc_final: 0.7645 (pm20) REVERT: X 98 ASP cc_start: 0.8485 (m-30) cc_final: 0.8283 (m-30) REVERT: c 35 MET cc_start: 0.8070 (ptp) cc_final: 0.7855 (ptp) REVERT: C 242 ASP cc_start: 0.7882 (t0) cc_final: 0.7635 (t0) REVERT: G 156 TYR cc_start: 0.8460 (m-80) cc_final: 0.7908 (m-80) REVERT: Z 61 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6452 (tm-30) REVERT: Z 90 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7657 (tm-30) REVERT: Z 94 LYS cc_start: 0.8848 (tppp) cc_final: 0.8462 (mtmm) REVERT: y 321 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7416 (mp10) outliers start: 81 outliers final: 34 residues processed: 607 average time/residue: 1.6525 time to fit residues: 1328.3601 Evaluate side-chains 568 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 532 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain f residue 96 LYS Chi-restraints excluded: chain y residue 321 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 606 optimal weight: 0.0670 chunk 461 optimal weight: 0.2980 chunk 318 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 293 optimal weight: 0.0870 chunk 412 optimal weight: 20.0000 chunk 616 optimal weight: 6.9990 chunk 652 optimal weight: 50.0000 chunk 321 optimal weight: 10.0000 chunk 584 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 163 GLN E 214 ASN H 162 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN T 12 GLN T 142 ASN X 73 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 84190 Z= 0.144 Angle : 0.593 20.436 122263 Z= 0.304 Chirality : 0.037 0.254 15129 Planarity : 0.004 0.100 8827 Dihedral : 22.763 177.620 33843 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.14 % Favored : 92.82 % Rotamer: Outliers : 1.81 % Allowed : 15.37 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.08 % 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: -0.90 (0.12), residues: 5000 helix: 0.84 (0.13), residues: 1674 sheet: -0.64 (0.18), residues: 873 loop : -1.62 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP M 88 HIS 0.005 0.001 HIS E 138 PHE 0.021 0.001 PHE V 83 TYR 0.028 0.001 TYR R 84 ARG 0.006 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 595 time to evaluate : 4.516 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: A 10 MET cc_start: 0.8578 (tpt) cc_final: 0.8054 (tpp) REVERT: B 110 MET cc_start: 0.7680 (tpt) cc_final: 0.7382 (tpt) REVERT: D 1 MET cc_start: 0.4808 (OUTLIER) cc_final: 0.3928 (ttt) REVERT: P 32 GLN cc_start: 0.8148 (pm20) cc_final: 0.7891 (pm20) REVERT: P 83 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7717 (tpt) REVERT: S 1 MET cc_start: 0.4954 (mtm) cc_final: 0.4414 (mtp) REVERT: a 52 ASP cc_start: 0.7821 (m-30) cc_final: 0.7575 (m-30) REVERT: c 35 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7715 (ptp) REVERT: C 242 ASP cc_start: 0.7769 (t0) cc_final: 0.7481 (t0) REVERT: G 146 ASN cc_start: 0.8194 (t0) cc_final: 0.7839 (t0) REVERT: G 156 TYR cc_start: 0.8412 (m-80) cc_final: 0.7904 (m-80) REVERT: M 107 SER cc_start: 0.8160 (m) cc_final: 0.7915 (m) REVERT: O 88 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8535 (tm) REVERT: Z 61 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6469 (tm-30) REVERT: b 34 ASP cc_start: 0.8034 (m-30) cc_final: 0.7800 (m-30) REVERT: y 321 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: i 75 LEU cc_start: 0.8787 (tp) cc_final: 0.8507 (tp) outliers start: 79 outliers final: 25 residues processed: 633 average time/residue: 1.6873 time to fit residues: 1441.4488 Evaluate side-chains 567 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 537 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 83 MET Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain y residue 321 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 543 optimal weight: 8.9990 chunk 370 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 485 optimal weight: 30.0000 chunk 269 optimal weight: 9.9990 chunk 556 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 333 optimal weight: 0.0870 chunk 585 optimal weight: 10.0000 chunk 164 optimal weight: 50.0000 overall best weight: 5.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 43 ASN B 163 GLN E 214 ASN H 162 GLN I 138 ASN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 142 ASN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 HIS G 105 ASN M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 139 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 84190 Z= 0.274 Angle : 0.635 20.713 122263 Z= 0.326 Chirality : 0.040 0.280 15129 Planarity : 0.005 0.103 8827 Dihedral : 22.705 178.743 33843 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 2.43 % Allowed : 16.88 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.08 % 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: -0.87 (0.12), residues: 5000 helix: 0.81 (0.13), residues: 1688 sheet: -0.57 (0.18), residues: 862 loop : -1.60 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 17 HIS 0.006 0.001 HIS W 44 PHE 0.022 0.002 PHE X 105 TYR 0.030 0.001 TYR R 84 ARG 0.009 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 558 time to evaluate : 5.059 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: A 10 MET cc_start: 0.8590 (tpt) cc_final: 0.8177 (tpp) REVERT: D 1 MET cc_start: 0.4761 (OUTLIER) cc_final: 0.3859 (ttt) REVERT: P 32 GLN cc_start: 0.8247 (pm20) cc_final: 0.7956 (pm20) REVERT: S 1 MET cc_start: 0.5047 (mtm) cc_final: 0.4585 (mtp) REVERT: T 75 MET cc_start: 0.8764 (mmp) cc_final: 0.8416 (mmt) REVERT: T 114 GLU cc_start: 0.8216 (pm20) cc_final: 0.7535 (pm20) REVERT: U 102 THR cc_start: 0.7628 (t) cc_final: 0.7278 (m) REVERT: g 282 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: C 242 ASP cc_start: 0.7871 (t0) cc_final: 0.7583 (t0) REVERT: G 146 ASN cc_start: 0.8304 (t0) cc_final: 0.7911 (t0) REVERT: G 156 TYR cc_start: 0.8449 (m-80) cc_final: 0.7925 (m-80) REVERT: M 107 SER cc_start: 0.8368 (m) cc_final: 0.7981 (p) REVERT: Z 61 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6455 (tm-30) REVERT: Z 90 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7864 (tm-30) REVERT: Z 94 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8513 (mtmm) outliers start: 106 outliers final: 49 residues processed: 614 average time/residue: 1.6554 time to fit residues: 1351.7919 Evaluate side-chains 582 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 531 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain d residue 38 MET Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain e residue 25 LYS Chi-restraints excluded: chain f residue 96 LYS Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain i residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 219 optimal weight: 8.9990 chunk 587 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 383 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 653 optimal weight: 50.0000 chunk 542 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN E 214 ASN H 162 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 ASN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 139 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 84190 Z= 0.331 Angle : 0.669 20.835 122263 Z= 0.343 Chirality : 0.041 0.289 15129 Planarity : 0.005 0.102 8827 Dihedral : 22.735 178.771 33843 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.78 % Favored : 92.12 % Rotamer: Outliers : 2.31 % Allowed : 17.80 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -0.93 (0.12), residues: 5000 helix: 0.73 (0.13), residues: 1696 sheet: -0.54 (0.18), residues: 859 loop : -1.64 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 17 HIS 0.007 0.001 HIS W 44 PHE 0.023 0.002 PHE E 69 TYR 0.036 0.002 TYR R 84 ARG 0.015 0.001 ARG G 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 556 time to evaluate : 4.567 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: A 10 MET cc_start: 0.8634 (tpt) cc_final: 0.8221 (tpt) REVERT: D 1 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.3737 (ttt) REVERT: K 17 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6078 (mptt) REVERT: Q 116 ASP cc_start: 0.7430 (t0) cc_final: 0.7151 (t0) REVERT: S 1 MET cc_start: 0.4987 (mtm) cc_final: 0.4520 (mtp) REVERT: T 75 MET cc_start: 0.8731 (mmp) cc_final: 0.8322 (mmt) REVERT: V 51 LYS cc_start: 0.8995 (mttm) cc_final: 0.8725 (mttp) REVERT: g 282 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7301 (pp20) REVERT: C 242 ASP cc_start: 0.7940 (t0) cc_final: 0.7655 (t0) REVERT: G 146 ASN cc_start: 0.8317 (t0) cc_final: 0.7896 (t0) REVERT: G 156 TYR cc_start: 0.8484 (m-80) cc_final: 0.7987 (m-80) REVERT: J 73 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: M 107 SER cc_start: 0.8200 (m) cc_final: 0.7854 (m) REVERT: Z 90 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7779 (tm-30) REVERT: Z 94 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8416 (mtmm) REVERT: y 321 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7414 (mp10) REVERT: y 326 GLU cc_start: 0.7701 (tp30) cc_final: 0.6983 (tt0) outliers start: 101 outliers final: 60 residues processed: 612 average time/residue: 1.6346 time to fit residues: 1336.1413 Evaluate side-chains 596 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 531 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain d residue 38 MET Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain J residue 2 PRO Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain f residue 96 LYS Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain y residue 321 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 629 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 476 optimal weight: 9.9990 chunk 369 optimal weight: 20.0000 chunk 549 optimal weight: 0.6980 chunk 364 optimal weight: 3.9990 chunk 650 optimal weight: 80.0000 chunk 407 optimal weight: 7.9990 chunk 396 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN E 214 ASN H 162 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 GLN ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 ASN g 14 HIS C 272 HIS M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 139 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 84190 Z= 0.259 Angle : 0.646 20.653 122263 Z= 0.332 Chirality : 0.039 0.278 15129 Planarity : 0.005 0.101 8827 Dihedral : 22.734 178.485 33843 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.90 % Favored : 92.06 % Rotamer: Outliers : 2.47 % Allowed : 18.65 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -0.88 (0.12), residues: 5000 helix: 0.80 (0.13), residues: 1692 sheet: -0.57 (0.18), residues: 868 loop : -1.61 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 8 HIS 0.006 0.001 HIS f 139 PHE 0.016 0.001 PHE E 69 TYR 0.036 0.001 TYR R 84 ARG 0.012 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 560 time to evaluate : 4.799 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: A 10 MET cc_start: 0.8639 (tpt) cc_final: 0.8253 (tpt) REVERT: D 1 MET cc_start: 0.4674 (OUTLIER) cc_final: 0.3725 (ttt) REVERT: K 17 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6074 (mptt) REVERT: Q 116 ASP cc_start: 0.7413 (t0) cc_final: 0.7145 (t0) REVERT: S 1 MET cc_start: 0.5000 (mtm) cc_final: 0.4581 (mtp) REVERT: T 75 MET cc_start: 0.8662 (mmp) cc_final: 0.8250 (mmt) REVERT: U 102 THR cc_start: 0.7718 (t) cc_final: 0.7428 (m) REVERT: V 51 LYS cc_start: 0.8994 (mttm) cc_final: 0.8730 (mttp) REVERT: g 5 MET cc_start: 0.8254 (mmm) cc_final: 0.8023 (mmp) REVERT: g 282 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: C 242 ASP cc_start: 0.7900 (t0) cc_final: 0.7588 (t0) REVERT: G 146 ASN cc_start: 0.8327 (t0) cc_final: 0.7910 (t0) REVERT: G 156 TYR cc_start: 0.8391 (m-80) cc_final: 0.7807 (m-80) REVERT: J 73 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: M 107 SER cc_start: 0.8173 (m) cc_final: 0.7918 (p) REVERT: O 86 LYS cc_start: 0.8820 (tppp) cc_final: 0.8606 (ttmt) REVERT: Z 61 GLU cc_start: 0.6581 (tm-30) cc_final: 0.6342 (tm-30) REVERT: Z 90 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7739 (tm-30) REVERT: Z 94 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8478 (mtmm) REVERT: y 321 GLN cc_start: 0.7868 (mp10) cc_final: 0.7393 (mp10) REVERT: y 326 GLU cc_start: 0.7628 (tp30) cc_final: 0.7064 (tt0) REVERT: i 75 LEU cc_start: 0.8794 (tp) cc_final: 0.8515 (tp) outliers start: 108 outliers final: 65 residues processed: 628 average time/residue: 1.6234 time to fit residues: 1370.5751 Evaluate side-chains 599 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 530 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain d residue 38 MET Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain J residue 2 PRO Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain Y residue 96 LEU Chi-restraints excluded: chain f residue 96 LYS Chi-restraints excluded: chain f residue 100 LEU Chi-restraints excluded: chain f residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 402 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 413 optimal weight: 7.9990 chunk 443 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 511 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN E 214 ASN H 162 GLN K 77 GLN g 14 HIS M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 139 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 84190 Z= 0.287 Angle : 0.660 20.667 122263 Z= 0.338 Chirality : 0.040 0.284 15129 Planarity : 0.005 0.102 8827 Dihedral : 22.719 178.593 33843 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.82 % Favored : 92.10 % Rotamer: Outliers : 2.40 % Allowed : 19.42 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -0.87 (0.12), residues: 5000 helix: 0.80 (0.13), residues: 1692 sheet: -0.53 (0.18), residues: 859 loop : -1.61 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 8 HIS 0.006 0.001 HIS f 139 PHE 0.019 0.002 PHE E 69 TYR 0.020 0.002 TYR R 84 ARG 0.013 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 549 time to evaluate : 4.523 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: A 10 MET cc_start: 0.8632 (tpt) cc_final: 0.8193 (tpt) REVERT: D 1 MET cc_start: 0.4688 (OUTLIER) cc_final: 0.3735 (ttt) REVERT: K 17 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6098 (mptt) REVERT: Q 116 ASP cc_start: 0.7459 (t0) cc_final: 0.7191 (t0) REVERT: S 1 MET cc_start: 0.4964 (mtm) cc_final: 0.4551 (mtp) REVERT: T 75 MET cc_start: 0.8644 (mmp) cc_final: 0.8274 (mmt) REVERT: U 102 THR cc_start: 0.7739 (t) cc_final: 0.7479 (m) REVERT: V 51 LYS cc_start: 0.9000 (mttm) cc_final: 0.8730 (mttp) REVERT: a 52 ASP cc_start: 0.7948 (m-30) cc_final: 0.7706 (m-30) REVERT: g 282 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: C 242 ASP cc_start: 0.7918 (t0) cc_final: 0.7628 (t0) REVERT: G 146 ASN cc_start: 0.8315 (t0) cc_final: 0.7902 (t0) REVERT: G 156 TYR cc_start: 0.8392 (m-80) cc_final: 0.7807 (m-80) REVERT: J 73 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: M 107 SER cc_start: 0.8111 (m) cc_final: 0.7812 (t) REVERT: W 4 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7159 (mmt) REVERT: y 326 GLU cc_start: 0.7590 (tp30) cc_final: 0.7086 (tt0) REVERT: i 75 LEU cc_start: 0.8797 (tp) cc_final: 0.8519 (tp) outliers start: 105 outliers final: 67 residues processed: 616 average time/residue: 1.6149 time to fit residues: 1334.0391 Evaluate side-chains 602 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 530 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain d residue 38 MET Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain J residue 2 PRO Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain Y residue 96 LEU Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain f residue 100 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 139 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 591 optimal weight: 0.7980 chunk 623 optimal weight: 8.9990 chunk 568 optimal weight: 0.8980 chunk 606 optimal weight: 8.9990 chunk 364 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 476 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 547 optimal weight: 9.9990 chunk 573 optimal weight: 10.0000 chunk 604 optimal weight: 4.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 163 GLN E 214 ASN H 12 ASN H 162 GLN K 77 GLN ** g 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 139 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 84190 Z= 0.203 Angle : 0.640 20.483 122263 Z= 0.328 Chirality : 0.038 0.268 15129 Planarity : 0.005 0.105 8827 Dihedral : 22.716 178.299 33843 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.80 % Favored : 92.16 % Rotamer: Outliers : 1.99 % Allowed : 20.38 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -0.82 (0.12), residues: 5000 helix: 0.85 (0.13), residues: 1688 sheet: -0.53 (0.18), residues: 869 loop : -1.57 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 8 HIS 0.030 0.001 HIS f 139 PHE 0.014 0.001 PHE W 50 TYR 0.022 0.001 TYR f 140 ARG 0.013 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 556 time to evaluate : 4.608 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: A 10 MET cc_start: 0.8600 (tpt) cc_final: 0.8126 (tpp) REVERT: D 1 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.3753 (ttt) REVERT: Q 96 TYR cc_start: 0.8908 (m-80) cc_final: 0.8530 (m-80) REVERT: Q 116 ASP cc_start: 0.7410 (t0) cc_final: 0.7152 (t0) REVERT: S 1 MET cc_start: 0.5008 (mtm) cc_final: 0.4575 (mtp) REVERT: T 75 MET cc_start: 0.8599 (mmp) cc_final: 0.8255 (mmt) REVERT: U 102 THR cc_start: 0.7746 (t) cc_final: 0.7455 (m) REVERT: V 51 LYS cc_start: 0.8997 (mttm) cc_final: 0.8740 (mttp) REVERT: g 247 TRP cc_start: 0.6783 (m-10) cc_final: 0.6326 (m-10) REVERT: g 282 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: C 242 ASP cc_start: 0.7865 (t0) cc_final: 0.7561 (t0) REVERT: G 146 ASN cc_start: 0.8337 (t0) cc_final: 0.7927 (t0) REVERT: G 156 TYR cc_start: 0.8367 (m-80) cc_final: 0.7765 (m-80) REVERT: J 73 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: M 35 ILE cc_start: 0.9118 (tp) cc_final: 0.8883 (mm) REVERT: M 107 SER cc_start: 0.8097 (m) cc_final: 0.7738 (m) REVERT: O 86 LYS cc_start: 0.8790 (tppp) cc_final: 0.8583 (ttmt) REVERT: W 4 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7161 (mmt) REVERT: Z 51 ASP cc_start: 0.8267 (p0) cc_final: 0.8034 (OUTLIER) REVERT: Z 90 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7768 (tm-30) REVERT: Z 94 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8566 (mtmm) REVERT: y 321 GLN cc_start: 0.7877 (mp10) cc_final: 0.7439 (mp10) REVERT: y 326 GLU cc_start: 0.7527 (tp30) cc_final: 0.7045 (tt0) REVERT: i 75 LEU cc_start: 0.8762 (tp) cc_final: 0.8493 (tp) outliers start: 87 outliers final: 60 residues processed: 612 average time/residue: 1.6059 time to fit residues: 1323.7435 Evaluate side-chains 607 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 544 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain d residue 38 MET Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 108 VAL Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain J residue 2 PRO Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain f residue 96 LYS Chi-restraints excluded: chain f residue 100 LEU Chi-restraints excluded: chain f residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 398 optimal weight: 4.9990 chunk 641 optimal weight: 0.0570 chunk 391 optimal weight: 4.9990 chunk 304 optimal weight: 0.2980 chunk 445 optimal weight: 0.0980 chunk 672 optimal weight: 7.9990 chunk 618 optimal weight: 7.9990 chunk 535 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 202 GLN E 214 ASN H 162 GLN K 77 GLN X 23 HIS g 14 HIS g 196 ASN M 48 HIS O 20 GLN W 56 HIS ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 139 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 84190 Z= 0.152 Angle : 0.618 20.130 122263 Z= 0.316 Chirality : 0.037 0.252 15129 Planarity : 0.004 0.101 8827 Dihedral : 22.661 178.470 33843 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.60 % Favored : 92.36 % Rotamer: Outliers : 1.58 % Allowed : 20.86 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -0.74 (0.12), residues: 5000 helix: 0.94 (0.13), residues: 1689 sheet: -0.50 (0.18), residues: 875 loop : -1.55 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 8 HIS 0.007 0.001 HIS f 139 PHE 0.014 0.001 PHE E 99 TYR 0.019 0.001 TYR S 95 ARG 0.015 0.000 ARG i 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 572 time to evaluate : 4.605 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: A 10 MET cc_start: 0.8613 (tpt) cc_final: 0.8132 (tpt) REVERT: B 229 MET cc_start: 0.8184 (tpp) cc_final: 0.7861 (mmm) REVERT: D 1 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.3838 (ttt) REVERT: S 1 MET cc_start: 0.5093 (mtm) cc_final: 0.4685 (mtp) REVERT: U 102 THR cc_start: 0.7598 (t) cc_final: 0.7294 (m) REVERT: V 51 LYS cc_start: 0.8984 (mttm) cc_final: 0.8759 (mmtp) REVERT: g 247 TRP cc_start: 0.6664 (m-10) cc_final: 0.6263 (m-10) REVERT: g 282 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7305 (pp20) REVERT: C 242 ASP cc_start: 0.7720 (t0) cc_final: 0.7377 (t0) REVERT: G 146 ASN cc_start: 0.8310 (t0) cc_final: 0.7893 (t0) REVERT: G 156 TYR cc_start: 0.8351 (m-80) cc_final: 0.7780 (m-80) REVERT: J 73 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: M 107 SER cc_start: 0.8200 (m) cc_final: 0.7797 (t) REVERT: N 4 MET cc_start: 0.8336 (ttt) cc_final: 0.8024 (tmm) REVERT: Z 51 ASP cc_start: 0.8343 (p0) cc_final: 0.8053 (p0) REVERT: Z 62 VAL cc_start: 0.9127 (t) cc_final: 0.8888 (t) REVERT: Z 90 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7745 (tm-30) REVERT: Z 94 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8555 (mtmm) REVERT: f 136 PHE cc_start: 0.9028 (p90) cc_final: 0.8716 (p90) REVERT: y 321 GLN cc_start: 0.7861 (mp10) cc_final: 0.7349 (mp10) REVERT: y 326 GLU cc_start: 0.7497 (tp30) cc_final: 0.7014 (tt0) REVERT: i 75 LEU cc_start: 0.8756 (tp) cc_final: 0.8493 (tp) outliers start: 69 outliers final: 45 residues processed: 619 average time/residue: 1.6061 time to fit residues: 1336.0009 Evaluate side-chains 589 residues out of total 4373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 541 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain Q residue 29 ASN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain g residue 18 VAL Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain f residue 100 LEU Chi-restraints excluded: chain f residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 675 random chunks: chunk 425 optimal weight: 0.8980 chunk 570 optimal weight: 8.9990 chunk 164 optimal weight: 50.0000 chunk 493 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 536 optimal weight: 30.0000 chunk 224 optimal weight: 9.9990 chunk 550 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 163 GLN E 214 ASN H 162 GLN K 77 GLN g 14 HIS M 48 HIS O 20 GLN ** Z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048734 restraints weight = 240688.259| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.52 r_work: 0.2726 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 84190 Z= 0.326 Angle : 0.680 20.434 122263 Z= 0.347 Chirality : 0.041 0.284 15129 Planarity : 0.005 0.108 8827 Dihedral : 22.607 178.355 33843 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.92 % Favored : 92.00 % Rotamer: Outliers : 1.53 % Allowed : 21.30 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.23 % Twisted Proline : 1.00 % Twisted General : 0.10 % 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: -0.80 (0.12), residues: 5000 helix: 0.85 (0.13), residues: 1692 sheet: -0.48 (0.18), residues: 870 loop : -1.58 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 33 HIS 0.009 0.001 HIS f 139 PHE 0.020 0.002 PHE E 69 TYR 0.025 0.002 TYR G 28 ARG 0.012 0.001 ARG f 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23164.51 seconds wall clock time: 399 minutes 36.98 seconds (23976.98 seconds total)