Starting phenix.real_space_refine on Sun Sep 29 20:49:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxm_38753/09_2024/8xxm_38753.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxm_38753/09_2024/8xxm_38753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxm_38753/09_2024/8xxm_38753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxm_38753/09_2024/8xxm_38753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxm_38753/09_2024/8xxm_38753.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxm_38753/09_2024/8xxm_38753.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 1723 5.49 5 Mg 23 5.21 5 S 184 5.16 5 C 41782 2.51 5 N 14140 2.21 5 O 19079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76934 Number of models: 1 Model: "" Number of chains: 42 Chain: "Ln" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "S2" Number of atoms: 36538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1723, 36538 Classifications: {'DNA': 15, 'RNA': 1708} Modifications used: {'rna2p_pur': 147, 'rna2p_pyr': 131, 'rna3p_pur': 752, 'rna3p_pyr': 675} Link IDs: {'rna2p': 277, 'rna3p': 1445} Chain breaks: 3 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: "SA" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1741 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "SB" 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: "SD" 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: "SE" 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: "SF" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "SH" 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: "SI" 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: "SK" 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: "SL" 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: "SP" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "SQ" 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: "SR" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "SS" 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: "ST" 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: "SU" 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: "SV" 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: "SX" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Sa" 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: "Sc" 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: "Sd" 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: "Sg" 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: "SC" 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: "SG" 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: "SJ" 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: "SM" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 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: "SN" 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: "SO" 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: "SW" 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: "SY" 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: "SZ" 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: "Sb" 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: "Se" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Sf" 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: "CD" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3G" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "S2" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Unusual residues: {' MG': 22} Classifications: {'undetermined': 22} Link IDs: {None: 21} Chain: "Sa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Sf" 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 59100 SG CYSSa 23 88.893 171.237 110.673 1.00 8.74 S ATOM 59121 SG CYSSa 26 88.366 170.105 107.126 1.00 9.81 S ATOM 59504 SG CYSSa 74 90.653 168.104 109.357 1.00 9.43 S ATOM 59523 SG CYSSa 77 91.771 171.307 107.923 1.00 10.40 S ATOM 60415 SG CYSSd 21 152.792 164.519 72.241 1.00 13.76 S ATOM 60439 SG CYSSd 24 149.907 161.853 73.180 1.00 19.66 S ATOM 60560 SG CYSSd 39 149.633 165.573 74.111 1.00 15.58 S ATOM 60586 SG CYSSd 42 152.188 163.780 75.633 1.00 18.84 S Time building chain proxies: 31.96, per 1000 atoms: 0.42 Number of scatterers: 76934 At special positions: 0 Unit cell: (207.48, 256.424, 205.352, 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 184 16.00 P 1723 15.00 Mg 23 11.99 O 19079 8.00 N 14140 7.00 C 41782 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: 13.43 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNSa 201 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 26 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 74 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 77 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 23 " pdb=" ZNSd 101 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 39 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 42 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 21 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 24 " Number of angles added : 12 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9368 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 55 sheets defined 35.3% alpha, 16.9% beta 521 base pairs and 889 stacking pairs defined. Time for finding SS restraints: 26.07 Creating SS restraints... Processing helix chain 'Ln' and resid 2 through 24 Processing helix chain 'SA' and resid 11 through 22 Processing helix chain 'SA' and resid 34 through 36 No H-bonds generated for 'chain 'SA' and resid 34 through 36' Processing helix chain 'SA' and resid 50 through 67 Processing helix chain 'SA' and resid 70 through 72 No H-bonds generated for 'chain 'SA' and resid 70 through 72' Processing helix chain 'SA' and resid 80 through 94 removed outlier: 6.512A pdb=" N ALASA 86 " --> pdb=" O THRSA 82 " (cutoff:3.500A) Processing helix chain 'SA' and resid 130 through 140 Processing helix chain 'SA' and resid 167 through 186 Processing helix chain 'SA' and resid 198 through 202 Processing helix chain 'SA' and resid 206 through 223 removed outlier: 4.747A pdb=" N GLNSA 215 " --> pdb=" O GLUSA 211 " (cutoff:3.500A) Processing helix chain 'SB' and resid 57 through 63 Processing helix chain 'SB' and resid 106 through 114 removed outlier: 3.610A pdb=" N VALSB 114 " --> pdb=" O METSB 110 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 179 removed outlier: 3.893A pdb=" N ASNSB 179 " --> pdb=" O GLUSB 175 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.722A pdb=" N LYSSB 195 " --> pdb=" O ASPSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 202 through 204 No H-bonds generated for 'chain 'SB' and resid 202 through 204' Processing helix chain 'SB' and resid 224 through 233 removed outlier: 3.659A pdb=" N LEUSB 228 " --> pdb=" O GLUSB 224 " (cutoff:3.500A) Processing helix chain 'SD' and resid 6 through 29 Processing helix chain 'SD' and resid 54 through 60 Processing helix chain 'SD' and resid 63 through 78 Processing helix chain 'SD' and resid 93 through 96 Processing helix chain 'SD' and resid 97 through 112 Processing helix chain 'SD' and resid 114 through 128 Processing helix chain 'SD' and resid 162 through 166 Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 43 through 49 Processing helix chain 'SE' and resid 57 through 66 Processing helix chain 'SE' and resid 115 through 120 Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 247 through 263 Processing helix chain 'SF' and resid 18 through 22 Processing helix chain 'SF' and resid 32 through 38 Processing helix chain 'SF' and resid 42 through 46 Processing helix chain 'SF' and resid 67 through 77 removed outlier: 3.672A pdb=" N METSF 77 " --> pdb=" O THRSF 73 " (cutoff:3.500A) Processing helix chain 'SF' and resid 85 through 104 Processing helix chain 'SF' and resid 107 through 120 Processing helix chain 'SF' and resid 142 through 162 removed outlier: 3.615A pdb=" N ALASF 162 " --> pdb=" O ALASF 158 " (cutoff:3.500A) Processing helix chain 'SF' and resid 168 through 182 Processing helix chain 'SF' and resid 187 through 203 Processing helix chain 'SH' and resid 20 through 32 Processing helix chain 'SH' and resid 35 through 40 removed outlier: 4.106A pdb=" N GLNSH 39 " --> pdb=" O ASPSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 68 through 75 removed outlier: 3.604A pdb=" N ILESH 75 " --> pdb=" O SERSH 71 " (cutoff:3.500A) Processing helix chain 'SH' and resid 76 through 87 Processing helix chain 'SH' and resid 117 through 120 Processing helix chain 'SH' and resid 121 through 134 removed outlier: 3.699A pdb=" N VALSH 134 " --> pdb=" O LEUSH 130 " (cutoff:3.500A) Processing helix chain 'SH' and resid 169 through 181 Processing helix chain 'SI' and resid 25 through 27 No H-bonds generated for 'chain 'SI' and resid 25 through 27' Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 87 through 93 removed outlier: 3.750A pdb=" N VALSI 91 " --> pdb=" O ASNSI 87 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 132 through 138 removed outlier: 3.525A pdb=" N ILESI 136 " --> pdb=" O GLUSI 132 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASNSI 138 " --> pdb=" O GLUSI 134 " (cutoff:3.500A) Processing helix chain 'SI' and resid 142 through 154 Processing helix chain 'SI' and resid 160 through 169 Processing helix chain 'SI' and resid 178 through 183 Processing helix chain 'SI' and resid 192 through 206 Processing helix chain 'SK' and resid 4 through 18 Processing helix chain 'SK' and resid 41 through 55 Processing helix chain 'SK' and resid 72 through 84 Processing helix chain 'SL' and resid 47 through 52 Processing helix chain 'SP' and resid 21 through 27 Processing helix chain 'SP' and resid 29 through 37 Processing helix chain 'SP' and resid 38 through 47 Processing helix chain 'SP' and resid 50 through 66 Processing helix chain 'SP' and resid 86 through 90 removed outlier: 3.682A pdb=" N VALSP 90 " --> pdb=" O PROSP 87 " (cutoff:3.500A) Processing helix chain 'SP' and resid 116 through 120 removed outlier: 3.794A pdb=" N PHESP 119 " --> pdb=" O LEUSP 116 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SERSP 120 " --> pdb=" O GLYSP 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 116 through 120' Processing helix chain 'SQ' and resid 40 through 42 No H-bonds generated for 'chain 'SQ' and resid 40 through 42' Processing helix chain 'SQ' and resid 47 through 52 removed outlier: 4.564A pdb=" N LEUSQ 51 " --> pdb=" O LEUSQ 47 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 59 Processing helix chain 'SQ' and resid 60 through 63 Processing helix chain 'SQ' and resid 77 through 99 Processing helix chain 'SQ' and resid 101 through 115 removed outlier: 3.928A pdb=" N LYSSQ 105 " --> pdb=" O ASPSQ 101 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 116 through 120 Processing helix chain 'SR' and resid 6 through 21 removed outlier: 3.523A pdb=" N TYRSR 21 " --> pdb=" O ILESR 17 " (cutoff:3.500A) Processing helix chain 'SR' and resid 27 through 38 Processing helix chain 'SR' and resid 43 through 63 removed outlier: 3.579A pdb=" N ARGSR 63 " --> pdb=" O LYSSR 59 " (cutoff:3.500A) Processing helix chain 'SR' and resid 70 through 82 Processing helix chain 'SR' and resid 99 through 109 Processing helix chain 'SS' and resid 25 through 32 Processing helix chain 'SS' and resid 37 through 48 Processing helix chain 'SS' and resid 60 through 73 removed outlier: 4.030A pdb=" N ASNSS 73 " --> pdb=" O THRSS 69 " (cutoff:3.500A) Processing helix chain 'SS' and resid 74 through 78 removed outlier: 3.950A pdb=" N LYSSS 78 " --> pdb=" O ARGSS 75 " (cutoff:3.500A) Processing helix chain 'SS' and resid 80 through 84 removed outlier: 3.736A pdb=" N LEUSS 84 " --> pdb=" O ASPSS 81 " (cutoff:3.500A) Processing helix chain 'SS' and resid 100 through 117 removed outlier: 3.733A pdb=" N ASPSS 104 " --> pdb=" O ALASS 100 " (cutoff:3.500A) Processing helix chain 'SS' and resid 119 through 127 removed outlier: 3.644A pdb=" N TRPSS 127 " --> pdb=" O LEUSS 123 " (cutoff:3.500A) Processing helix chain 'ST' and resid 10 through 25 Processing helix chain 'ST' and resid 51 through 67 Processing helix chain 'ST' and resid 71 through 79 Processing helix chain 'ST' and resid 96 through 110 Processing helix chain 'ST' and resid 124 through 144 Processing helix chain 'SU' and resid 28 through 46 removed outlier: 3.656A pdb=" N LEUSU 32 " --> pdb=" O ASNSU 28 " (cutoff:3.500A) Processing helix chain 'SU' and resid 94 through 103 removed outlier: 3.587A pdb=" N VALSU 98 " --> pdb=" O PROSU 94 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLNSU 100 " --> pdb=" O GLUSU 96 " (cutoff:3.500A) Processing helix chain 'SV' and resid 58 through 63 Processing helix chain 'SV' and resid 64 through 76 Processing helix chain 'SX' and resid 9 through 23 Processing helix chain 'SX' and resid 24 through 32 Processing helix chain 'SX' and resid 33 through 39 Processing helix chain 'SX' and resid 129 through 135 Processing helix chain 'Sa' and resid 46 through 49 Processing helix chain 'Sa' and resid 50 through 57 Processing helix chain 'Sa' and resid 74 through 81 Processing helix chain 'Sd' and resid 3 through 8 removed outlier: 4.364A pdb=" N TRPSd 8 " --> pdb=" O GLNSd 4 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 32 through 36 Processing helix chain 'Sd' and resid 40 through 46 removed outlier: 3.560A pdb=" N TYRSd 46 " --> pdb=" O CYSSd 42 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 46 through 51 Processing helix chain 'SC' and resid 64 through 72 Processing helix chain 'SC' and resid 78 through 84 Processing helix chain 'SC' and resid 90 through 98 removed outlier: 4.242A pdb=" N ILESC 94 " --> pdb=" O GLUSC 90 " (cutoff:3.500A) Processing helix chain 'SC' and resid 146 through 161 Processing helix chain 'SC' and resid 207 through 216 Processing helix chain 'SC' and resid 232 through 249 Processing helix chain 'SC' and resid 252 through 256 removed outlier: 3.558A pdb=" N TRPSC 256 " --> pdb=" O PROSC 253 " (cutoff:3.500A) Processing helix chain 'SC' and resid 264 through 269 removed outlier: 3.528A pdb=" N PHESC 269 " --> pdb=" O PROSC 265 " (cutoff:3.500A) Processing helix chain 'SC' and resid 269 through 277 Processing helix chain 'SG' and resid 20 through 28 removed outlier: 3.568A pdb=" N LEUSG 24 " --> pdb=" O ASPSG 20 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 145 Processing helix chain 'SG' and resid 181 through 234 removed outlier: 4.792A pdb=" N METSG 217 " --> pdb=" O LEUSG 213 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALASG 220 " --> pdb=" O ARGSG 216 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEUSG 234 " --> pdb=" O LYSSG 230 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 21 through 36 Processing helix chain 'SJ' and resid 39 through 62 removed outlier: 4.242A pdb=" N VALSJ 43 " --> pdb=" O ASNSJ 39 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 67 through 84 Processing helix chain 'SJ' and resid 93 through 99 Processing helix chain 'SJ' and resid 101 through 108 removed outlier: 3.864A pdb=" N PHESJ 105 " --> pdb=" O LYSSJ 101 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 109 through 117 Processing helix chain 'SJ' and resid 122 through 132 Processing helix chain 'SJ' and resid 171 through 184 Processing helix chain 'SM' and resid 12 through 29 removed outlier: 4.414A pdb=" N ALASM 17 " --> pdb=" O ASPSM 13 " (cutoff:3.500A) Processing helix chain 'SM' and resid 34 through 44 Processing helix chain 'SM' and resid 58 through 72 Processing helix chain 'SM' and resid 81 through 90 removed outlier: 3.672A pdb=" N LEUSM 85 " --> pdb=" O ASPSM 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLYSM 90 " --> pdb=" O GLYSM 86 " (cutoff:3.500A) Processing helix chain 'SM' and resid 119 through 132 Processing helix chain 'SN' and resid 29 through 44 Processing helix chain 'SN' and resid 46 through 57 Processing helix chain 'SN' and resid 62 through 67 removed outlier: 3.501A pdb=" N VALSN 66 " --> pdb=" O GLNSN 62 " (cutoff:3.500A) Processing helix chain 'SN' and resid 70 through 79 Processing helix chain 'SN' and resid 85 through 105 Processing helix chain 'SN' and resid 108 through 132 removed outlier: 3.653A pdb=" N LYSSN 112 " --> pdb=" O ASPSN 108 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHESN 113 " --> pdb=" O LYSSN 109 " (cutoff:3.500A) Processing helix chain 'SN' and resid 145 through 150 Processing helix chain 'SO' and resid 58 through 62 Processing helix chain 'SO' and resid 70 through 89 Processing helix chain 'SO' and resid 110 through 122 removed outlier: 4.180A pdb=" N SERSO 114 " --> pdb=" O PROSO 110 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 20 removed outlier: 3.824A pdb=" N ASPSW 9 " --> pdb=" O ASNSW 5 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 Processing helix chain 'SW' and resid 85 through 94 removed outlier: 3.703A pdb=" N TRPSW 89 " --> pdb=" O ASPSW 85 " (cutoff:3.500A) Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SY' and resid 36 through 49 Processing helix chain 'SY' and resid 78 through 85 Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 103 through 115 Processing helix chain 'SY' and resid 120 through 130 removed outlier: 4.818A pdb=" N GLYSY 128 " --> pdb=" O ASNSY 124 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 51 through 62 Processing helix chain 'SZ' and resid 63 through 65 No H-bonds generated for 'chain 'SZ' and resid 63 through 65' Processing helix chain 'SZ' and resid 69 through 77 Processing helix chain 'SZ' and resid 81 through 95 Processing helix chain 'Sb' and resid 11 through 18 Processing helix chain 'Se' and resid 10 through 16 Processing helix chain 'Se' and resid 30 through 43 removed outlier: 3.736A pdb=" N ARGSe 34 " --> pdb=" O GLYSe 30 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VALSe 43 " --> pdb=" O ASNSe 39 " (cutoff:3.500A) Processing helix chain 'Sf' and resid 123 through 127 removed outlier: 3.932A pdb=" N GLYSf 127 " --> pdb=" O ASPSf 124 " (cutoff:3.500A) Processing helix chain 'CD' and resid 113 through 118 removed outlier: 3.831A pdb=" N GLYCD 116 " --> pdb=" O PROCD 113 " (cutoff:3.500A) Processing helix chain '3G' and resid 251 through 260 Processing helix chain '3G' and resid 289 through 301 removed outlier: 3.585A pdb=" N SER3G 301 " --> pdb=" O ILE3G 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SA' and resid 38 through 41 removed outlier: 7.091A pdb=" N ILESA 48 " --> pdb=" O TYRSA 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SA' and resid 97 through 100 removed outlier: 6.812A pdb=" N VALSA 74 " --> pdb=" O THRSA 97 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILESA 99 " --> pdb=" O VALSA 74 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VALSA 76 " --> pdb=" O ILESA 99 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEUSA 122 " --> pdb=" O ILESA 145 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEUSA 147 " --> pdb=" O LEUSA 122 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VALSA 124 " --> pdb=" O LEUSA 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SB' and resid 43 through 50 removed outlier: 3.929A pdb=" N GLYSB 45 " --> pdb=" O VALSB 33 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNSB 95 " --> pdb=" O VALSB 91 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VALSB 91 " --> pdb=" O ASNSB 95 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEUSB 97 " --> pdb=" O GLUSB 89 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARGSB 65 " --> pdb=" O THRSB 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SB' and resid 69 through 70 removed outlier: 8.743A pdb=" N ARGSB 213 " --> pdb=" O LEUSB 105 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VALSB 212 " --> pdb=" O VALSB 140 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VALSB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEUSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SD' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'SD' and resid 148 through 155 Processing sheet with id=AA7, first strand: chain 'SD' and resid 209 through 210 removed outlier: 3.676A pdb=" N SERSD 209 " --> pdb=" O ILESR 40 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILESR 40 " --> pdb=" O SERSD 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'SE' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'SE' and resid 121 through 125 removed outlier: 6.514A pdb=" N ASPSE 163 " --> pdb=" O ILESE 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILESE 169 " --> pdb=" O ASPSE 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 128 through 132 Processing sheet with id=AB2, first strand: chain 'SE' and resid 217 through 221 removed outlier: 6.588A pdb=" N VALSE 207 " --> pdb=" O ARGSE 198 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARGSE 198 " --> pdb=" O VALSE 207 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HISSE 209 " --> pdb=" O THRSE 196 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYSSE 230 " --> pdb=" O LYSSE 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSSE 233 " --> pdb=" O LYSSE 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SF' and resid 123 through 126 removed outlier: 7.794A pdb=" N ALASF 138 " --> pdb=" O ASNSc 45 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LYSSc 47 " --> pdb=" O ALASF 138 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASPSF 140 " --> pdb=" O LYSSc 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SH' and resid 47 through 52 removed outlier: 3.860A pdb=" N HISSH 91 " --> pdb=" O LYSSH 58 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VALSH 93 " --> pdb=" O ILESH 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SH' and resid 184 through 188 removed outlier: 6.330A pdb=" N ILESH 154 " --> pdb=" O ASNSH 186 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLUSH 188 " --> pdb=" O ILESH 154 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VALSH 156 " --> pdb=" O GLUSH 188 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARGSH 145 " --> pdb=" O LEUSH 153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHESW 50 " --> pdb=" O VALSH 146 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLUSW 49 " --> pdb=" O ASNSW 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 3 through 4 removed outlier: 4.231A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.452A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SI' and resid 62 through 67 removed outlier: 6.358A pdb=" N LEUSI 103 " --> pdb=" O ILESI 79 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VALSI 81 " --> pdb=" O ILESI 101 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILESI 101 " --> pdb=" O VALSI 81 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYSSI 100 " --> pdb=" O ILESI 175 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLYSI 187 " --> pdb=" O VALSI 62 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 187 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VALSI 189 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SERSI 66 " --> pdb=" O VALSI 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SK' and resid 20 through 24 Processing sheet with id=AC1, first strand: chain 'SL' and resid 72 through 79 removed outlier: 18.531A pdb=" N ILESL 72 " --> pdb=" O LEUSL 93 " (cutoff:3.500A) removed outlier: 15.093A pdb=" N LEUSL 93 " --> pdb=" O ILESL 72 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N SERSL 74 " --> pdb=" O ASPSL 91 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASPSL 91 " --> pdb=" O SERSL 74 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VALSL 76 " --> pdb=" O ARGSL 89 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VALSL 87 " --> pdb=" O THRSL 78 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHESL 140 " --> pdb=" O ASNSL 108 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SERSL 110 " --> pdb=" O PHESL 140 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VALSL 142 " --> pdb=" O SERSL 110 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HISSL 112 " --> pdb=" O VALSL 142 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LYSSL 144 " --> pdb=" O HISSL 112 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VALSL 142 " --> pdb=" O GLYSL 129 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLYSL 129 " --> pdb=" O VALSL 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SP' and resid 76 through 78 removed outlier: 5.904A pdb=" N VALSP 76 " --> pdb=" O GLYSP 95 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYRSP 97 " --> pdb=" O VALSP 76 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THRSP 78 " --> pdb=" O TYRSP 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SQ' and resid 10 through 16 removed outlier: 6.043A pdb=" N LEUSQ 31 " --> pdb=" O ILESQ 68 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VALSQ 70 " --> pdb=" O LEUSQ 31 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYSSQ 33 " --> pdb=" O VALSQ 70 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VALSQ 72 " --> pdb=" O LYSSQ 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SR' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'ST' and resid 81 through 83 Processing sheet with id=AC6, first strand: chain 'ST' and resid 113 through 115 Processing sheet with id=AC7, first strand: chain 'SU' and resid 54 through 55 Processing sheet with id=AC8, first strand: chain 'SU' and resid 59 through 65 Processing sheet with id=AC9, first strand: chain 'SV' and resid 15 through 17 Processing sheet with id=AD1, first strand: chain 'SV' and resid 32 through 39 removed outlier: 3.633A pdb=" N GLUSV 38 " --> pdb=" O GLNSV 49 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLNSV 49 " --> pdb=" O GLUSV 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'SX' and resid 46 through 58 removed outlier: 5.494A pdb=" N VALSX 51 " --> pdb=" O GLNSX 73 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLNSX 73 " --> pdb=" O VALSX 51 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHESX 120 " --> pdb=" O THRSX 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Sa' and resid 20 through 22 Processing sheet with id=AD4, first strand: chain 'Sa' and resid 36 through 43 Processing sheet with id=AD5, first strand: chain 'Sc' and resid 10 through 13 Processing sheet with id=AD6, first strand: chain 'Sd' and resid 30 through 31 Processing sheet with id=AD7, first strand: chain 'Sg' and resid 4 through 11 removed outlier: 4.974A pdb=" N METSg 5 " --> pdb=" O THRSg 313 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THRSg 313 " --> pdb=" O METSg 5 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEUSg 7 " --> pdb=" O GLNSg 311 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLNSg 311 " --> pdb=" O LEUSg 7 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLYSg 9 " --> pdb=" O VALSg 309 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VALSg 309 " --> pdb=" O GLYSg 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Sg' and resid 18 through 20 removed outlier: 6.364A pdb=" N LYSSg 44 " --> pdb=" O PROSg 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Sg' and resid 66 through 71 removed outlier: 6.479A pdb=" N GLYSg 81 " --> pdb=" O SERSg 67 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEUSg 79 " --> pdb=" O VALSg 69 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILESg 71 " --> pdb=" O PHESg 77 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHESg 77 " --> pdb=" O ILESg 71 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THRSg 86 " --> pdb=" O SERSg 82 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASPSg 91 " --> pdb=" O THRSg 97 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THRSg 97 " --> pdb=" O ASPSg 91 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Sg' and resid 108 through 113 removed outlier: 6.920A pdb=" N GLYSg 123 " --> pdb=" O LEUSg 109 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VALSg 111 " --> pdb=" O VALSg 121 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VALSg 121 " --> pdb=" O VALSg 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Sg' and resid 154 through 156 Processing sheet with id=AE3, first strand: chain 'Sg' and resid 195 through 200 removed outlier: 6.813A pdb=" N GLYSg 210 " --> pdb=" O ASNSg 196 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VALSg 198 " --> pdb=" O ALASg 208 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALASg 208 " --> pdb=" O VALSg 198 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLYSg 211 " --> pdb=" O GLNSg 215 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLNSg 215 " --> pdb=" O GLYSg 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Sg' and resid 236 through 240 removed outlier: 3.834A pdb=" N ALASg 238 " --> pdb=" O ALASg 251 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'SC' and resid 103 through 114 removed outlier: 5.284A pdb=" N ASPSC 104 " --> pdb=" O GLYSC 131 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLYSC 131 " --> pdb=" O ASPSC 104 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VALSC 106 " --> pdb=" O ALASC 129 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALASC 129 " --> pdb=" O VALSC 106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'SC' and resid 184 through 188 Processing sheet with id=AE7, first strand: chain 'SG' and resid 14 through 17 removed outlier: 6.668A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VALSG 114 " --> pdb=" O VALSG 50 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VALSG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'SG' and resid 72 through 77 Processing sheet with id=AE9, first strand: chain 'SG' and resid 160 through 162 Processing sheet with id=AF1, first strand: chain 'SJ' and resid 140 through 141 Processing sheet with id=AF2, first strand: chain 'SM' and resid 32 through 33 removed outlier: 3.790A pdb=" N ALASM 32 " --> pdb=" O VALSM 110 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALSM 110 " --> pdb=" O ALASM 32 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'SO' and resid 52 through 57 removed outlier: 7.262A pdb=" N LEUSO 93 " --> pdb=" O GLYSO 127 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILESO 129 " --> pdb=" O LEUSO 93 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILESO 95 " --> pdb=" O ILESO 129 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASPSO 131 " --> pdb=" O ILESO 95 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEUSO 97 " --> pdb=" O ASPSO 131 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'SW' and resid 80 through 81 removed outlier: 5.638A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'SY' and resid 6 through 15 removed outlier: 6.261A pdb=" N ILESY 7 " --> pdb=" O LEUSY 28 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEUSY 28 " --> pdb=" O ILESY 7 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THRSY 9 " --> pdb=" O ASPSY 26 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASPSY 26 " --> pdb=" O THRSY 9 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYSSY 11 " --> pdb=" O VALSY 24 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THRSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHESY 60 " --> pdb=" O THRSY 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'SZ' and resid 97 through 99 Processing sheet with id=AF7, first strand: chain 'Sb' and resid 44 through 47 removed outlier: 3.605A pdb=" N ARGSb 80 " --> pdb=" O ASPSb 34 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Sb' and resid 54 through 55 removed outlier: 6.932A pdb=" N VALSb 54 " --> pdb=" O LEUSb 63 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Sf' and resid 138 through 141 Processing sheet with id=AG1, first strand: chain '3G' and resid 265 through 272 removed outlier: 5.443A pdb=" N ILE3G 265 " --> pdb=" O SER3G 286 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER3G 286 " --> pdb=" O ILE3G 265 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG3G 267 " --> pdb=" O PHE3G 284 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE3G 284 " --> pdb=" O ARG3G 267 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYR3G 269 " --> pdb=" O PHE3G 282 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE3G 282 " --> pdb=" O TYR3G 269 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA3G 271 " --> pdb=" O LYS3G 280 " (cutoff:3.500A) 1625 hydrogen bonds defined for protein. 4596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1289 hydrogen bonds 1988 hydrogen bond angles 0 basepair planarities 521 basepair parallelities 889 stacking parallelities Total time for adding SS restraints: 61.31 Time building geometry restraints manager: 16.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11314 1.33 - 1.45: 30937 1.45 - 1.58: 35920 1.58 - 1.70: 3444 1.70 - 1.83: 282 Bond restraints: 81897 Sorted by residual: bond pdb=" CA TRPSX 22 " pdb=" C TRPSX 22 " ideal model delta sigma weight residual 1.522 1.482 0.041 1.40e-02 5.10e+03 8.51e+00 bond pdb=" CB VALSJ 3 " pdb=" CG1 VALSJ 3 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.53e+00 bond pdb=" CG1 ILESV 32 " pdb=" CD1 ILESV 32 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.20e+00 bond pdb=" CB METSF 88 " pdb=" CG METSF 88 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.13e+00 bond pdb=" CA ASNSI 99 " pdb=" CB ASNSI 99 " ideal model delta sigma weight residual 1.531 1.601 -0.070 3.12e-02 1.03e+03 5.03e+00 ... (remaining 81892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 116611 2.80 - 5.59: 1803 5.59 - 8.39: 250 8.39 - 11.18: 47 11.18 - 13.98: 10 Bond angle restraints: 118721 Sorted by residual: angle pdb=" C ILESB 150 " pdb=" N ARGSB 151 " pdb=" CA ARGSB 151 " ideal model delta sigma weight residual 121.54 134.80 -13.26 1.91e+00 2.74e-01 4.82e+01 angle pdb=" C LEUSR 114 " pdb=" CA LEUSR 114 " pdb=" CB LEUSR 114 " ideal model delta sigma weight residual 115.79 109.06 6.73 1.19e+00 7.06e-01 3.20e+01 angle pdb=" C ARGSG 216 " pdb=" N METSG 217 " pdb=" CA METSG 217 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" CA METSG 217 " pdb=" CB METSG 217 " pdb=" CG METSG 217 " ideal model delta sigma weight residual 114.10 124.78 -10.68 2.00e+00 2.50e-01 2.85e+01 angle pdb=" C LYSSD 214 " pdb=" CA LYSSD 214 " pdb=" CB LYSSD 214 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.15e+00 7.56e-01 2.84e+01 ... (remaining 118716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 47167 35.99 - 71.99: 4489 71.99 - 107.98: 511 107.98 - 143.98: 7 143.98 - 179.97: 17 Dihedral angle restraints: 52191 sinusoidal: 37660 harmonic: 14531 Sorted by residual: dihedral pdb=" CA ALASX 126 " pdb=" C ALASX 126 " pdb=" N ASNSX 127 " pdb=" CA ASNSX 127 " ideal model delta harmonic sigma weight residual -180.00 -118.92 -61.08 0 5.00e+00 4.00e-02 1.49e+02 dihedral pdb=" O4' CS21139 " pdb=" C1' CS21139 " pdb=" N1 CS21139 " pdb=" C2 CS21139 " ideal model delta sinusoidal sigma weight residual 200.00 20.03 179.97 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' US2 427 " pdb=" C1' US2 427 " pdb=" N1 US2 427 " pdb=" C2 US2 427 " ideal model delta sinusoidal sigma weight residual -160.00 18.91 -178.91 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 52188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 13127 0.078 - 0.156: 1313 0.156 - 0.234: 157 0.234 - 0.312: 28 0.312 - 0.390: 4 Chirality restraints: 14629 Sorted by residual: chirality pdb=" CB VALSY 54 " pdb=" CA VALSY 54 " pdb=" CG1 VALSY 54 " pdb=" CG2 VALSY 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C1' GS21780 " pdb=" O4' GS21780 " pdb=" C2' GS21780 " pdb=" N9 GS21780 " both_signs ideal model delta sigma weight residual False 2.46 2.09 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILESQ 42 " pdb=" CA ILESQ 42 " pdb=" CG1 ILESQ 42 " pdb=" CG2 ILESQ 42 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 14626 not shown) Planarity restraints: 8727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CS21756 " -0.002 2.00e-02 2.50e+03 3.60e-02 2.91e+01 pdb=" N1 CS21756 " 0.002 2.00e-02 2.50e+03 pdb=" C2 CS21756 " -0.086 2.00e-02 2.50e+03 pdb=" O2 CS21756 " 0.061 2.00e-02 2.50e+03 pdb=" N3 CS21756 " -0.005 2.00e-02 2.50e+03 pdb=" C4 CS21756 " -0.000 2.00e-02 2.50e+03 pdb=" N4 CS21756 " 0.005 2.00e-02 2.50e+03 pdb=" C5 CS21756 " 0.016 2.00e-02 2.50e+03 pdb=" C6 CS21756 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHESC 236 " -0.041 2.00e-02 2.50e+03 3.96e-02 2.74e+01 pdb=" CG PHESC 236 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 PHESC 236 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHESC 236 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHESC 236 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHESC 236 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHESC 236 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GS2 841 " -0.003 2.00e-02 2.50e+03 2.94e-02 2.60e+01 pdb=" N9 GS2 841 " -0.004 2.00e-02 2.50e+03 pdb=" C8 GS2 841 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GS2 841 " -0.004 2.00e-02 2.50e+03 pdb=" C5 GS2 841 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GS2 841 " 0.040 2.00e-02 2.50e+03 pdb=" O6 GS2 841 " -0.024 2.00e-02 2.50e+03 pdb=" N1 GS2 841 " -0.020 2.00e-02 2.50e+03 pdb=" C2 GS2 841 " 0.076 2.00e-02 2.50e+03 pdb=" N2 GS2 841 " -0.042 2.00e-02 2.50e+03 pdb=" N3 GS2 841 " -0.003 2.00e-02 2.50e+03 pdb=" C4 GS2 841 " -0.015 2.00e-02 2.50e+03 ... (remaining 8724 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 2143 2.64 - 3.21: 62505 3.21 - 3.77: 145146 3.77 - 4.34: 194323 4.34 - 4.90: 276416 Nonbonded interactions: 680533 Sorted by model distance: nonbonded pdb=" O2' CS21488 " pdb=" OP2 GS21490 " model vdw 2.081 3.040 nonbonded pdb=" OP2 AS2 449 " pdb="MG MGS21907 " model vdw 2.087 2.170 nonbonded pdb=" OP1 GS21166 " pdb="MG MGS21914 " model vdw 2.090 2.170 nonbonded pdb=" OP1 AS21832 " pdb="MG MGS21921 " model vdw 2.102 2.170 nonbonded pdb=" OP2 GS21387 " pdb="MG MGS21915 " model vdw 2.106 2.170 ... (remaining 680528 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.350 Check model and map are aligned: 0.450 Set scattering table: 0.540 Process input model: 187.710 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.005 0.089 81897 Z= 0.323 Angle : 0.886 13.980 118721 Z= 0.460 Chirality : 0.049 0.390 14629 Planarity : 0.007 0.087 8727 Dihedral : 22.157 179.969 42823 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.18 % Favored : 92.58 % Rotamer: Outliers : 0.02 % Allowed : 0.71 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % 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: -2.18 (0.11), residues: 4988 helix: -0.90 (0.11), residues: 1652 sheet: -0.91 (0.17), residues: 858 loop : -2.01 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPSF 23 HIS 0.010 0.002 HISSB 208 PHE 0.091 0.002 PHESC 236 TYR 0.063 0.002 TYRSG 28 ARG 0.016 0.001 ARGSc 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 806 time to evaluate : 4.519 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: SA 166 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7981 (ttmm) REVERT: SH 43 LEU cc_start: 0.6576 (pt) cc_final: 0.6374 (pt) REVERT: SK 57 TYR cc_start: 0.7636 (m-10) cc_final: 0.7384 (m-10) REVERT: ST 126 GLN cc_start: 0.7090 (tp40) cc_final: 0.6885 (tp-100) REVERT: SC 254 ASP cc_start: 0.8206 (p0) cc_final: 0.7997 (p0) REVERT: SJ 135 ILE cc_start: 0.9035 (mp) cc_final: 0.8656 (mp) REVERT: SN 105 ASN cc_start: 0.8354 (m-40) cc_final: 0.8046 (m110) REVERT: SN 110 ASP cc_start: 0.7302 (t70) cc_final: 0.7080 (t70) REVERT: SO 68 GLU cc_start: 0.6826 (pm20) cc_final: 0.6213 (pt0) REVERT: Sf 99 LYS cc_start: 0.2961 (tptt) cc_final: 0.2700 (tptt) outliers start: 1 outliers final: 0 residues processed: 807 average time/residue: 0.7622 time to fit residues: 1046.6166 Evaluate side-chains 686 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 559 optimal weight: 50.0000 chunk 502 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 519 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 315 optimal weight: 8.9990 chunk 386 optimal weight: 9.9990 chunk 602 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 177 GLN SB 179 ASN SD 101 GLN SF 95 HIS SF 203 ASN SH 68 GLN SH 91 HIS SH 165 ASN SI 88 ASN ** SI 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 167 GLN SK 28 HIS SL 19 ASN SP 35 GLN SP 46 ASN SQ 80 GLN ** SQ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 10 GLN SV 35 ASN SX 61 GLN Sa 8 ASN Sa 25 ASN ** Sc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 267 GLN SC 277 HIS ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 110 ASN SY 94 HIS Sf 139 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 81897 Z= 0.289 Angle : 0.675 15.095 118721 Z= 0.346 Chirality : 0.041 0.310 14629 Planarity : 0.006 0.075 8727 Dihedral : 23.216 179.872 32393 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.88 % Favored : 92.90 % Rotamer: Outliers : 1.43 % Allowed : 9.77 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.62 (0.11), residues: 4988 helix: 0.02 (0.12), residues: 1661 sheet: -1.00 (0.17), residues: 893 loop : -1.88 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPSF 23 HIS 0.008 0.001 HISSX 110 PHE 0.047 0.002 PHESC 236 TYR 0.029 0.002 TYRSS 40 ARG 0.009 0.001 ARGSb 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 723 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 10 MET cc_start: 0.7550 (mmm) cc_final: 0.7128 (mmt) REVERT: SA 166 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8164 (ttmm) REVERT: SD 72 VAL cc_start: 0.8685 (t) cc_final: 0.8426 (m) REVERT: SI 6 ASP cc_start: 0.8007 (p0) cc_final: 0.7794 (p0) REVERT: SI 88 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.7129 (m-40) REVERT: SK 1 MET cc_start: 0.6632 (mmp) cc_final: 0.6388 (mmp) REVERT: SR 96 ILE cc_start: 0.7365 (mm) cc_final: 0.7123 (mm) REVERT: ST 126 GLN cc_start: 0.7119 (tp40) cc_final: 0.6876 (tp-100) REVERT: SV 21 ASN cc_start: 0.7230 (t0) cc_final: 0.7029 (t0) REVERT: Sc 35 MET cc_start: 0.7154 (mmm) cc_final: 0.6951 (mtp) REVERT: SC 254 ASP cc_start: 0.8169 (p0) cc_final: 0.7948 (p0) REVERT: SO 68 GLU cc_start: 0.7151 (pm20) cc_final: 0.6555 (pt0) outliers start: 62 outliers final: 38 residues processed: 746 average time/residue: 0.7713 time to fit residues: 975.9421 Evaluate side-chains 715 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 676 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 11 LYS Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SD residue 58 VAL Chi-restraints excluded: chain SE residue 105 THR Chi-restraints excluded: chain SF residue 88 MET Chi-restraints excluded: chain SH residue 68 GLN Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 88 ASN Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 124 THR Chi-restraints excluded: chain SX residue 34 THR Chi-restraints excluded: chain SX residue 119 ARG Chi-restraints excluded: chain Sa residue 25 ASN Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 57 SER Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SJ residue 104 ASP Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 145 THR Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 126 ILE Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain CD residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 334 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 501 optimal weight: 0.9990 chunk 409 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 603 optimal weight: 0.7980 chunk 651 optimal weight: 7.9990 chunk 537 optimal weight: 0.9990 chunk 598 optimal weight: 0.0980 chunk 205 optimal weight: 3.9990 chunk 483 optimal weight: 0.3980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 177 GLN SH 68 GLN SI 88 ASN SI 168 GLN SK 28 HIS SL 19 ASN SP 46 ASN SP 103 ASN ** SQ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 87 GLN ST 63 HIS ST 137 GLN SX 61 GLN SX 77 ASN ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 13 GLN ** SO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 94 HIS Se 15 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 81897 Z= 0.155 Angle : 0.599 14.753 118721 Z= 0.307 Chirality : 0.037 0.283 14629 Planarity : 0.005 0.070 8727 Dihedral : 23.134 179.787 32393 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.60 % Favored : 93.22 % Rotamer: Outliers : 1.59 % Allowed : 13.10 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.30 (0.11), residues: 4988 helix: 0.42 (0.13), residues: 1668 sheet: -0.90 (0.17), residues: 866 loop : -1.78 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPSg 43 HIS 0.006 0.001 HISSY 94 PHE 0.028 0.001 PHESC 236 TYR 0.021 0.001 TYRSC 248 ARG 0.010 0.000 ARGSc 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 740 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SA 166 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8142 (ttmm) REVERT: SD 72 VAL cc_start: 0.8584 (t) cc_final: 0.8294 (m) REVERT: SP 66 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6958 (pp20) REVERT: SQ 87 SER cc_start: 0.8261 (t) cc_final: 0.7812 (t) REVERT: SR 96 ILE cc_start: 0.7357 (mm) cc_final: 0.7098 (mm) REVERT: ST 126 GLN cc_start: 0.7043 (tp40) cc_final: 0.6836 (tp-100) REVERT: SC 254 ASP cc_start: 0.8119 (p0) cc_final: 0.7893 (p0) REVERT: SN 105 ASN cc_start: 0.8377 (m-40) cc_final: 0.8175 (m110) REVERT: SN 110 ASP cc_start: 0.7215 (t70) cc_final: 0.6902 (t70) REVERT: SO 68 GLU cc_start: 0.7120 (pm20) cc_final: 0.6489 (pt0) outliers start: 69 outliers final: 39 residues processed: 778 average time/residue: 0.7556 time to fit residues: 999.2869 Evaluate side-chains 718 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 679 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 11 LYS Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 48 TYR Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SP residue 60 LEU Chi-restraints excluded: chain SQ residue 9 SER Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 48 ASN Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain ST residue 124 THR Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SX residue 34 THR Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 247 THR Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 83 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SZ residue 59 CYS Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain 3G residue 257 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 595 optimal weight: 6.9990 chunk 453 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 66 optimal weight: 40.0000 chunk 287 optimal weight: 6.9990 chunk 405 optimal weight: 5.9990 chunk 605 optimal weight: 4.9990 chunk 640 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 573 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 113 GLN SB 177 GLN ** SB 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 179 GLN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 168 GLN SK 28 HIS SL 19 ASN ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 46 ASN ** SQ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 48 ASN SS 87 GLN SS 134 GLN ST 91 HIS ** Sc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 65 GLN SG 202 ASN SJ 154 GLN SO 32 HIS SO 103 ASN ** SO 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 26 GLN Sb 49 HIS Sb 65 GLN Se 58 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.104 81897 Z= 0.591 Angle : 0.829 12.469 118721 Z= 0.418 Chirality : 0.051 0.323 14629 Planarity : 0.007 0.109 8727 Dihedral : 23.162 179.132 32393 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer: Outliers : 3.17 % Allowed : 15.40 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.41 (0.11), residues: 4988 helix: 0.33 (0.12), residues: 1666 sheet: -0.97 (0.17), residues: 889 loop : -1.85 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPSF 23 HIS 0.014 0.002 HISSX 110 PHE 0.034 0.003 PHESC 236 TYR 0.033 0.002 TYRSC 248 ARG 0.009 0.001 ARGSJ 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 680 time to evaluate : 4.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SA 11 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8154 (mtmm) REVERT: SA 166 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8239 (ttmm) REVERT: SD 72 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8696 (m) REVERT: SK 3 MET cc_start: 0.8752 (ppp) cc_final: 0.8463 (ptm) REVERT: SS 72 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: SV 21 ASN cc_start: 0.7661 (t0) cc_final: 0.7415 (t0) REVERT: Sc 23 SER cc_start: 0.8227 (p) cc_final: 0.7979 (p) REVERT: SC 254 ASP cc_start: 0.8302 (p0) cc_final: 0.8067 (p0) REVERT: SO 68 GLU cc_start: 0.7317 (pm20) cc_final: 0.6858 (pt0) REVERT: SO 103 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6613 (m-40) REVERT: Sf 89 LYS cc_start: 0.4368 (mppt) cc_final: 0.4150 (ttpp) outliers start: 138 outliers final: 90 residues processed: 768 average time/residue: 0.7567 time to fit residues: 988.6962 Evaluate side-chains 752 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 658 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 11 LYS Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 81 ASN Chi-restraints excluded: chain SA residue 125 THR Chi-restraints excluded: chain SA residue 193 HIS Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SD residue 72 VAL Chi-restraints excluded: chain SD residue 84 VAL Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 98 ASN Chi-restraints excluded: chain SE residue 105 THR Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SF residue 87 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 164 GLU Chi-restraints excluded: chain SK residue 9 ILE Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SP residue 60 LEU Chi-restraints excluded: chain SQ residue 9 SER Chi-restraints excluded: chain SQ residue 12 VAL Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 51 LEU Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 48 ASN Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SS residue 31 THR Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 60 THR Chi-restraints excluded: chain SS residue 72 GLN Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 55 THR Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SX residue 50 ILE Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sc residue 17 VAL Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sd residue 53 ILE Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain Sg residue 268 ASP Chi-restraints excluded: chain SC residue 64 THR Chi-restraints excluded: chain SC residue 76 LYS Chi-restraints excluded: chain SC residue 104 ASP Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SJ residue 84 ILE Chi-restraints excluded: chain SJ residue 86 VAL Chi-restraints excluded: chain SJ residue 104 ASP Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SO residue 126 ILE Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 4 THR Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SZ residue 59 CYS Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 8 LEU Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Sb residue 54 VAL Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain CD residue 133 VAL Chi-restraints excluded: chain 3G residue 257 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 533 optimal weight: 8.9990 chunk 363 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 477 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 546 optimal weight: 0.8980 chunk 442 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 575 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 113 GLN SF 83 ASN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SH 165 ASN SK 7 ASN SK 28 HIS ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 48 ASN ST 126 GLN ST 137 GLN ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 202 ASN SN 138 ASN SO 103 ASN SY 63 HIS SY 94 HIS SZ 106 GLN Sb 51 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 81897 Z= 0.211 Angle : 0.627 12.612 118721 Z= 0.322 Chirality : 0.039 0.296 14629 Planarity : 0.005 0.072 8727 Dihedral : 23.142 179.556 32393 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.64 % Favored : 93.20 % Rotamer: Outliers : 2.34 % Allowed : 17.47 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.16 (0.12), residues: 4988 helix: 0.65 (0.13), residues: 1660 sheet: -0.93 (0.17), residues: 890 loop : -1.73 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPSF 23 HIS 0.007 0.001 HISSY 94 PHE 0.020 0.001 PHESC 236 TYR 0.027 0.002 TYRSC 248 ARG 0.010 0.000 ARGSO 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 689 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 13 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7965 (tt) REVERT: Ln 15 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7339 (mtt180) REVERT: SA 166 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8195 (ttmm) REVERT: SA 174 MET cc_start: 0.8289 (mmm) cc_final: 0.8038 (mmm) REVERT: SB 202 GLN cc_start: 0.8369 (tp40) cc_final: 0.8167 (tp40) REVERT: SD 72 VAL cc_start: 0.8781 (t) cc_final: 0.8550 (m) REVERT: SD 206 ASP cc_start: 0.8323 (p0) cc_final: 0.8096 (p0) REVERT: SS 70 ILE cc_start: 0.8239 (tp) cc_final: 0.7996 (tp) REVERT: SS 72 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: SV 2 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7574 (mm110) REVERT: SV 51 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7941 (mtpp) REVERT: SC 254 ASP cc_start: 0.8197 (p0) cc_final: 0.7978 (p0) REVERT: SC 266 TYR cc_start: 0.8804 (m-10) cc_final: 0.8601 (m-10) REVERT: SN 110 ASP cc_start: 0.7188 (t70) cc_final: 0.6887 (t70) REVERT: SO 68 GLU cc_start: 0.7275 (pm20) cc_final: 0.6807 (pt0) outliers start: 102 outliers final: 62 residues processed: 758 average time/residue: 0.7572 time to fit residues: 978.3551 Evaluate side-chains 720 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 655 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 13 LEU Chi-restraints excluded: chain Ln residue 15 ARG Chi-restraints excluded: chain SA residue 193 HIS Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SB residue 183 GLU Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SK residue 9 ILE Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 51 LEU Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 48 ASN Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 72 GLN Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SX residue 34 THR Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain Sg residue 261 LEU Chi-restraints excluded: chain SC residue 64 THR Chi-restraints excluded: chain SC residue 76 LYS Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SG residue 179 LEU Chi-restraints excluded: chain SJ residue 104 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SN residue 83 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain 3G residue 257 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 215 optimal weight: 0.8980 chunk 577 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 376 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 641 optimal weight: 3.9990 chunk 532 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 336 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SH 165 ASN ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 46 ASN ** SQ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 48 ASN SS 134 GLN ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 103 ASN SO 113 GLN SY 63 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 81897 Z= 0.165 Angle : 0.599 16.275 118721 Z= 0.307 Chirality : 0.037 0.293 14629 Planarity : 0.004 0.071 8727 Dihedral : 23.020 179.982 32393 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.82 % Favored : 93.02 % Rotamer: Outliers : 2.23 % Allowed : 18.25 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.99 (0.12), residues: 4988 helix: 0.82 (0.13), residues: 1664 sheet: -0.82 (0.17), residues: 883 loop : -1.66 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPSF 23 HIS 0.006 0.001 HISSg 188 PHE 0.018 0.001 PHESC 236 TYR 0.024 0.001 TYRSP 17 ARG 0.008 0.000 ARGSb 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 698 time to evaluate : 4.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 13 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7947 (tt) REVERT: Ln 15 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: SA 11 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7969 (mtmm) REVERT: SA 166 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8198 (ttmm) REVERT: SB 202 GLN cc_start: 0.8377 (tp40) cc_final: 0.8162 (tp40) REVERT: SD 72 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8533 (m) REVERT: SD 206 ASP cc_start: 0.8175 (p0) cc_final: 0.7892 (p0) REVERT: SH 76 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6818 (tm-30) REVERT: SP 37 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: SS 70 ILE cc_start: 0.8251 (tp) cc_final: 0.8023 (tp) REVERT: SS 72 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: SS 87 GLN cc_start: 0.8413 (mp10) cc_final: 0.8116 (mp10) REVERT: SU 21 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8503 (ttm170) REVERT: SV 21 ASN cc_start: 0.7377 (t0) cc_final: 0.7153 (t0) REVERT: SV 50 PHE cc_start: 0.7314 (p90) cc_final: 0.6960 (p90) REVERT: SC 254 ASP cc_start: 0.8193 (p0) cc_final: 0.7967 (p0) REVERT: SN 110 ASP cc_start: 0.7226 (t70) cc_final: 0.6932 (t70) REVERT: SO 68 GLU cc_start: 0.7198 (pm20) cc_final: 0.6750 (pt0) outliers start: 97 outliers final: 65 residues processed: 763 average time/residue: 0.7769 time to fit residues: 1009.0148 Evaluate side-chains 738 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 668 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 13 LEU Chi-restraints excluded: chain Ln residue 15 ARG Chi-restraints excluded: chain SA residue 125 THR Chi-restraints excluded: chain SA residue 193 HIS Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SB residue 183 GLU Chi-restraints excluded: chain SD residue 72 VAL Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 48 TYR Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SK residue 9 ILE Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 60 LEU Chi-restraints excluded: chain SQ residue 12 VAL Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 55 VAL Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 48 ASN Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 72 GLN Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SJ residue 21 GLU Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 4 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain CD residue 133 VAL Chi-restraints excluded: chain 3G residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 618 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 468 optimal weight: 0.4980 chunk 362 optimal weight: 0.0870 chunk 539 optimal weight: 0.9980 chunk 358 optimal weight: 0.8980 chunk 639 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 chunk 389 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 overall best weight: 1.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 177 GLN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SH 165 ASN ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 51 ASN ST 137 GLN SU 81 GLN ** Sc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 103 ASN SO 113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 81897 Z= 0.226 Angle : 0.617 15.339 118721 Z= 0.315 Chirality : 0.038 0.287 14629 Planarity : 0.005 0.071 8727 Dihedral : 22.956 179.647 32393 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.92 % Favored : 92.92 % Rotamer: Outliers : 2.57 % Allowed : 18.41 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.94 (0.12), residues: 4988 helix: 0.89 (0.13), residues: 1658 sheet: -0.78 (0.18), residues: 875 loop : -1.65 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPSF 23 HIS 0.007 0.001 HISSH 126 PHE 0.017 0.001 PHESC 236 TYR 0.025 0.001 TYRSC 248 ARG 0.010 0.000 ARGSO 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 676 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 13 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7997 (tt) REVERT: Ln 15 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7358 (mtt180) REVERT: SA 11 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7997 (mtmm) REVERT: SB 172 MET cc_start: 0.7832 (mtt) cc_final: 0.7566 (mtt) REVERT: SB 202 GLN cc_start: 0.8378 (tp40) cc_final: 0.8174 (tp40) REVERT: SD 72 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8620 (m) REVERT: SD 206 ASP cc_start: 0.8154 (p0) cc_final: 0.7866 (p0) REVERT: SH 76 GLN cc_start: 0.7351 (tm-30) cc_final: 0.6965 (tm-30) REVERT: SI 168 GLN cc_start: 0.7747 (tp40) cc_final: 0.7546 (tp-100) REVERT: SP 37 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: SR 96 ILE cc_start: 0.7695 (mm) cc_final: 0.7406 (mm) REVERT: SS 70 ILE cc_start: 0.8130 (tp) cc_final: 0.7874 (tp) REVERT: SU 21 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8517 (ttm170) REVERT: SV 21 ASN cc_start: 0.7337 (t0) cc_final: 0.7112 (t0) REVERT: Sc 31 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: Sg 41 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6376 (mt) REVERT: SC 254 ASP cc_start: 0.8206 (p0) cc_final: 0.7967 (p0) REVERT: SG 120 ASP cc_start: 0.8127 (p0) cc_final: 0.7772 (p0) REVERT: SO 68 GLU cc_start: 0.7232 (pm20) cc_final: 0.6826 (pt0) REVERT: Se 40 ARG cc_start: 0.8303 (ttp80) cc_final: 0.8061 (mtm110) outliers start: 112 outliers final: 81 residues processed: 757 average time/residue: 0.7543 time to fit residues: 970.1959 Evaluate side-chains 737 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 650 time to evaluate : 4.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 13 LEU Chi-restraints excluded: chain Ln residue 15 ARG Chi-restraints excluded: chain SA residue 11 LYS Chi-restraints excluded: chain SA residue 125 THR Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 91 VAL Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SB residue 183 GLU Chi-restraints excluded: chain SD residue 72 VAL Chi-restraints excluded: chain SD residue 84 VAL Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 60 GLU Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SE residue 210 VAL Chi-restraints excluded: chain SH residue 148 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SK residue 9 ILE Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SQ residue 12 VAL Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 55 VAL Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 48 ASN Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sg residue 41 ILE Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain Sg residue 261 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SC residue 262 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SG residue 179 LEU Chi-restraints excluded: chain SG residue 219 GLU Chi-restraints excluded: chain SJ residue 21 GLU Chi-restraints excluded: chain SJ residue 104 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SN residue 83 ASP Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 4 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 133 VAL Chi-restraints excluded: chain 3G residue 257 GLU Chi-restraints excluded: chain 3G residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 395 optimal weight: 8.9990 chunk 255 optimal weight: 0.0570 chunk 381 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 406 optimal weight: 2.9990 chunk 435 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 502 optimal weight: 0.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 113 GLN SB 43 ASN SF 83 ASN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SH 165 ASN SK 7 ASN ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 113 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 81897 Z= 0.327 Angle : 0.672 14.521 118721 Z= 0.342 Chirality : 0.041 0.297 14629 Planarity : 0.005 0.072 8727 Dihedral : 22.973 179.973 32393 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.36 % Rotamer: Outliers : 3.01 % Allowed : 18.32 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.96 (0.12), residues: 4988 helix: 0.88 (0.13), residues: 1655 sheet: -0.79 (0.17), residues: 882 loop : -1.66 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPSF 23 HIS 0.007 0.001 HISSX 110 PHE 0.020 0.002 PHESJ 147 TYR 0.034 0.002 TYRSC 248 ARG 0.010 0.001 ARGSc 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 660 time to evaluate : 4.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 13 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8002 (tt) REVERT: Ln 15 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7375 (mtt180) REVERT: SA 11 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8015 (mtmm) REVERT: SH 76 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7165 (tm-30) REVERT: SP 37 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7359 (m-10) REVERT: SR 96 ILE cc_start: 0.7794 (mm) cc_final: 0.7456 (mm) REVERT: SS 70 ILE cc_start: 0.8155 (tp) cc_final: 0.7914 (tp) REVERT: SV 21 ASN cc_start: 0.7416 (t0) cc_final: 0.7161 (t0) REVERT: Sg 5 MET cc_start: 0.6131 (mmm) cc_final: 0.5446 (tpt) REVERT: SC 254 ASP cc_start: 0.8304 (p0) cc_final: 0.8069 (p0) REVERT: SO 68 GLU cc_start: 0.7266 (pm20) cc_final: 0.6895 (pt0) REVERT: SO 113 GLN cc_start: 0.7655 (mm110) cc_final: 0.7434 (mm-40) REVERT: SZ 55 TYR cc_start: 0.7528 (t80) cc_final: 0.7052 (t80) REVERT: Se 40 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8104 (mtm110) outliers start: 131 outliers final: 99 residues processed: 747 average time/residue: 0.7517 time to fit residues: 962.8178 Evaluate side-chains 746 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 643 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 13 LEU Chi-restraints excluded: chain Ln residue 15 ARG Chi-restraints excluded: chain SA residue 11 LYS Chi-restraints excluded: chain SA residue 125 THR Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 91 VAL Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SB residue 183 GLU Chi-restraints excluded: chain SD residue 84 VAL Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 60 GLU Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 105 THR Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SE residue 210 VAL Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SH residue 75 ILE Chi-restraints excluded: chain SH residue 148 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SQ residue 9 SER Chi-restraints excluded: chain SQ residue 12 VAL Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 51 LEU Chi-restraints excluded: chain SQ residue 55 VAL Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain SS residue 136 THR Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sc residue 66 ARG Chi-restraints excluded: chain Sg residue 41 ILE Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain Sg residue 261 LEU Chi-restraints excluded: chain Sg residue 268 ASP Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 64 THR Chi-restraints excluded: chain SC residue 76 LYS Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SC residue 262 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SG residue 179 LEU Chi-restraints excluded: chain SG residue 219 GLU Chi-restraints excluded: chain SJ residue 21 GLU Chi-restraints excluded: chain SJ residue 86 VAL Chi-restraints excluded: chain SJ residue 104 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SO residue 126 ILE Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 4 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Sb residue 43 ILE Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 133 VAL Chi-restraints excluded: chain 3G residue 257 GLU Chi-restraints excluded: chain 3G residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 581 optimal weight: 4.9990 chunk 612 optimal weight: 0.9980 chunk 558 optimal weight: 2.9990 chunk 595 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 467 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 538 optimal weight: 2.9990 chunk 563 optimal weight: 0.6980 chunk 593 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 113 GLN SB 177 GLN SF 83 ASN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 51 ASN ST 137 GLN ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 81897 Z= 0.195 Angle : 0.621 15.355 118721 Z= 0.317 Chirality : 0.038 0.285 14629 Planarity : 0.005 0.070 8727 Dihedral : 22.982 179.645 32393 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.82 % Favored : 93.04 % Rotamer: Outliers : 2.37 % Allowed : 18.92 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.91 (0.12), residues: 4988 helix: 0.90 (0.13), residues: 1657 sheet: -0.78 (0.17), residues: 886 loop : -1.62 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRPSF 23 HIS 0.007 0.001 HISSY 94 PHE 0.016 0.001 PHESC 236 TYR 0.033 0.002 TYRSK 12 ARG 0.008 0.000 ARGSc 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 662 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 13 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7993 (tt) REVERT: Ln 15 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: SA 11 LYS cc_start: 0.8258 (mtmm) cc_final: 0.8018 (mtmm) REVERT: SF 27 ASP cc_start: 0.7015 (p0) cc_final: 0.6443 (p0) REVERT: SH 76 GLN cc_start: 0.7400 (tm-30) cc_final: 0.7109 (tm-30) REVERT: SP 37 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: SR 96 ILE cc_start: 0.7852 (mm) cc_final: 0.7569 (mm) REVERT: SS 70 ILE cc_start: 0.8093 (tp) cc_final: 0.7855 (tp) REVERT: SU 21 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8537 (ttm170) REVERT: SC 254 ASP cc_start: 0.8261 (p0) cc_final: 0.8027 (p0) REVERT: SO 51 GLU cc_start: 0.7183 (mp0) cc_final: 0.6780 (mp0) REVERT: SO 68 GLU cc_start: 0.7218 (pm20) cc_final: 0.6849 (pt0) REVERT: Se 40 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8068 (mtm110) outliers start: 103 outliers final: 87 residues processed: 732 average time/residue: 0.7605 time to fit residues: 949.9903 Evaluate side-chains 733 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 643 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 13 LEU Chi-restraints excluded: chain Ln residue 15 ARG Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 125 THR Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 91 VAL Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SB residue 183 GLU Chi-restraints excluded: chain SD residue 84 VAL Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 105 THR Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SE residue 210 VAL Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SH residue 75 ILE Chi-restraints excluded: chain SH residue 148 LEU Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 120 VAL Chi-restraints excluded: chain SL residue 124 ASP Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SQ residue 9 SER Chi-restraints excluded: chain SQ residue 12 VAL Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 55 VAL Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sc residue 66 ARG Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 64 THR Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SG residue 219 GLU Chi-restraints excluded: chain SJ residue 21 GLU Chi-restraints excluded: chain SJ residue 86 VAL Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SM residue 66 GLU Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SY residue 4 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Sb residue 43 ILE Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 133 VAL Chi-restraints excluded: chain 3G residue 257 GLU Chi-restraints excluded: chain 3G residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 391 optimal weight: 5.9990 chunk 629 optimal weight: 7.9990 chunk 384 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 437 optimal weight: 3.9990 chunk 660 optimal weight: 30.0000 chunk 607 optimal weight: 2.9990 chunk 525 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 406 optimal weight: 0.3980 chunk 322 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 113 GLN ** SB 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 165 ASN ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 81897 Z= 0.388 Angle : 0.706 16.221 118721 Z= 0.359 Chirality : 0.043 0.305 14629 Planarity : 0.005 0.074 8727 Dihedral : 22.984 179.803 32393 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.84 % Favored : 91.98 % Rotamer: Outliers : 2.44 % Allowed : 19.10 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4988 helix: 0.79 (0.13), residues: 1654 sheet: -0.85 (0.17), residues: 902 loop : -1.64 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPSF 23 HIS 0.011 0.001 HISSg 188 PHE 0.023 0.002 PHESJ 147 TYR 0.042 0.002 TYRSZ 55 ARG 0.011 0.001 ARGSc 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9976 Ramachandran restraints generated. 4988 Oldfield, 0 Emsley, 4988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 646 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 13 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8063 (tt) REVERT: Ln 15 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7393 (mtt180) REVERT: SA 11 LYS cc_start: 0.8353 (mtmm) cc_final: 0.8122 (mtmm) REVERT: SF 27 ASP cc_start: 0.7064 (p0) cc_final: 0.6526 (p0) REVERT: SH 76 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7193 (tm-30) REVERT: SP 37 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7364 (m-10) REVERT: SR 96 ILE cc_start: 0.7864 (mm) cc_final: 0.7532 (mm) REVERT: SS 70 ILE cc_start: 0.8152 (tp) cc_final: 0.7902 (tp) REVERT: SX 14 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8055 (ttp-170) REVERT: Sc 23 SER cc_start: 0.8124 (p) cc_final: 0.7861 (p) REVERT: SC 254 ASP cc_start: 0.8323 (p0) cc_final: 0.8089 (p0) REVERT: SO 68 GLU cc_start: 0.7292 (pm20) cc_final: 0.6881 (pt0) outliers start: 106 outliers final: 92 residues processed: 718 average time/residue: 0.7521 time to fit residues: 924.8286 Evaluate side-chains 739 residues out of total 4352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 643 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 13 LEU Chi-restraints excluded: chain Ln residue 15 ARG Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 125 THR Chi-restraints excluded: chain SA residue 209 GLU Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 88 THR Chi-restraints excluded: chain SB residue 91 VAL Chi-restraints excluded: chain SB residue 170 GLU Chi-restraints excluded: chain SB residue 183 GLU Chi-restraints excluded: chain SD residue 84 VAL Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 105 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SE residue 210 VAL Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SH residue 75 ILE Chi-restraints excluded: chain SH residue 148 LEU Chi-restraints excluded: chain SI residue 92 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SK residue 40 VAL Chi-restraints excluded: chain SL residue 19 ASN Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 60 LEU Chi-restraints excluded: chain SQ residue 9 SER Chi-restraints excluded: chain SQ residue 12 VAL Chi-restraints excluded: chain SQ residue 29 ASN Chi-restraints excluded: chain SQ residue 51 LEU Chi-restraints excluded: chain SQ residue 55 VAL Chi-restraints excluded: chain SQ residue 56 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 116 ASP Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 50 ILE Chi-restraints excluded: chain SS residue 85 ASN Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SX residue 14 ARG Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sc residue 66 ARG Chi-restraints excluded: chain Sg residue 41 ILE Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 104 HIS Chi-restraints excluded: chain Sg residue 105 THR Chi-restraints excluded: chain Sg residue 261 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain SC residue 64 THR Chi-restraints excluded: chain SC residue 76 LYS Chi-restraints excluded: chain SC residue 102 LEU Chi-restraints excluded: chain SC residue 137 VAL Chi-restraints excluded: chain SC residue 240 THR Chi-restraints excluded: chain SC residue 262 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SG residue 139 SER Chi-restraints excluded: chain SG residue 179 LEU Chi-restraints excluded: chain SG residue 219 GLU Chi-restraints excluded: chain SJ residue 21 GLU Chi-restraints excluded: chain SJ residue 86 VAL Chi-restraints excluded: chain SJ residue 104 ASP Chi-restraints excluded: chain SJ residue 112 THR Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 4 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 34 ASP Chi-restraints excluded: chain Sb residue 46 VAL Chi-restraints excluded: chain Se residue 19 VAL Chi-restraints excluded: chain Se residue 59 SER Chi-restraints excluded: chain CD residue 100 LEU Chi-restraints excluded: chain CD residue 133 VAL Chi-restraints excluded: chain 3G residue 257 GLU Chi-restraints excluded: chain 3G residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 663 random chunks: chunk 417 optimal weight: 0.9990 chunk 560 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 484 optimal weight: 0.0030 chunk 77 optimal weight: 50.0000 chunk 146 optimal weight: 6.9990 chunk 526 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 540 optimal weight: 10.0000 chunk 66 optimal weight: 40.0000 chunk 97 optimal weight: 4.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 113 GLN SH 165 ASN ** SL 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 51 ASN ST 137 GLN ** Sc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 113 GLN SY 94 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076122 restraints weight = 164139.246| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.52 r_work: 0.2770 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 81897 Z= 0.214 Angle : 0.631 16.636 118721 Z= 0.323 Chirality : 0.038 0.290 14629 Planarity : 0.005 0.070 8727 Dihedral : 22.981 179.874 32393 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.88 % Favored : 92.98 % Rotamer: Outliers : 2.16 % Allowed : 19.54 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.12), residues: 4988 helix: 0.84 (0.13), residues: 1658 sheet: -0.83 (0.17), residues: 892 loop : -1.59 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRPSF 23 HIS 0.011 0.001 HISSg 188 PHE 0.016 0.001 PHESC 236 TYR 0.032 0.002 TYRSK 12 ARG 0.013 0.000 ARGSc 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17781.05 seconds wall clock time: 309 minutes 16.07 seconds (18556.07 seconds total)