Starting phenix.real_space_refine on Mon Feb 19 19:12:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9p_35279/02_2024/8i9p_35279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9p_35279/02_2024/8i9p_35279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9p_35279/02_2024/8i9p_35279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9p_35279/02_2024/8i9p_35279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9p_35279/02_2024/8i9p_35279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9p_35279/02_2024/8i9p_35279.pdb" } resolution = 3.0 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1563 5.49 5 S 135 5.16 5 C 45009 2.51 5 N 14984 2.21 5 O 19106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CA TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 80799 Number of models: 1 Model: "" Number of chains: 35 Chain: "C1" Number of atoms: 27990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1307, 27990 Classifications: {'RNA': 1307} Modifications used: {'rna2p_pur': 148, 'rna2p_pyr': 89, 'rna3p_pur': 579, 'rna3p_pyr': 491} Link IDs: {'rna2p': 236, 'rna3p': 1070} Chain breaks: 9 Chain: "C2" Number of atoms: 5456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5456 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 29, 'rna2p_pyr': 22, 'rna3p_pur': 102, 'rna3p_pyr': 103} Link IDs: {'rna2p': 51, 'rna3p': 204} Chain breaks: 1 Chain: "CA" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2144 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain breaks: 2 Chain: "CB" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2140 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 20, 'TRANS': 248} Chain breaks: 1 Chain: "CC" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2159 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 35, 'TRANS': 222} Chain breaks: 3 Chain: "CE" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3673 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain breaks: 1 Chain: "CI" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1196 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "CJ" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3109 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 354} Chain breaks: 2 Chain: "CM" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1525 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "CR" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 3 Chain: "CU" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 924 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "LC" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2752 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 24, 'TRANS': 337} Chain: "LE" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1338 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 158} Chain breaks: 1 Chain: "LF" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1967 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "LG" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain breaks: 1 Chain: "LL" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "LM" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1037 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "LN" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1563 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "LO" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1618 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain: "LP" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1212 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Chain: "LQ" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "LS" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1433 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1014 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "LX" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 148 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Le" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1055 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lh" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "Li" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "Lj" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "Cc" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain breaks: 1 Chain: "Cd" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2768 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Ce" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1609 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ce" 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 73971 SG CYSLj 19 83.723 55.583 139.761 1.00 29.18 S ATOM 73999 SG CYSLj 22 84.966 57.338 142.846 1.00 33.04 S ATOM 74097 SG CYSLj 34 81.363 57.182 142.258 1.00 31.73 S ATOM 74114 SG CYSLj 37 83.495 59.480 140.054 1.00 23.75 S ATOM 79488 SG CYSCe 38 113.662 104.190 198.649 1.00 33.15 S Time building chain proxies: 31.23, per 1000 atoms: 0.39 Number of scatterers: 80799 At special positions: 0 Unit cell: (173.47, 176.605, 314.545, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 135 16.00 P 1563 15.00 O 19106 8.00 N 14984 7.00 C 45009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.28 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCe1000 " pdb="ZN ZNCe1000 " - pdb=" SG CYSCe 38 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " Number of angles added : 6 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11076 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 51 sheets defined 45.6% alpha, 12.7% beta 508 base pairs and 835 stacking pairs defined. Time for finding SS restraints: 24.52 Creating SS restraints... Processing helix chain 'CA' and resid 45 through 57 Processing helix chain 'CA' and resid 75 through 84 removed outlier: 3.681A pdb=" N GLUCA 79 " --> pdb=" O TYRCA 75 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYRCA 84 " --> pdb=" O LEUCA 80 " (cutoff:3.500A) Processing helix chain 'CA' and resid 143 through 147 removed outlier: 3.866A pdb=" N GLUCA 147 " --> pdb=" O ALACA 144 " (cutoff:3.500A) Processing helix chain 'CA' and resid 149 through 164 Processing helix chain 'CA' and resid 263 through 295 Processing helix chain 'CA' and resid 310 through 315 Processing helix chain 'CB' and resid 19 through 40 Processing helix chain 'CB' and resid 52 through 59 Processing helix chain 'CB' and resid 104 through 114 removed outlier: 3.504A pdb=" N TYRCB 108 " --> pdb=" O PROCB 104 " (cutoff:3.500A) Processing helix chain 'CB' and resid 119 through 123 Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 150 removed outlier: 3.518A pdb=" N HISCB 150 " --> pdb=" O LEUCB 146 " (cutoff:3.500A) Processing helix chain 'CB' and resid 159 through 161 No H-bonds generated for 'chain 'CB' and resid 159 through 161' Processing helix chain 'CB' and resid 162 through 167 Processing helix chain 'CB' and resid 168 through 173 Processing helix chain 'CB' and resid 216 through 229 removed outlier: 3.643A pdb=" N GLYCB 229 " --> pdb=" O ARGCB 225 " (cutoff:3.500A) Processing helix chain 'CB' and resid 251 through 271 removed outlier: 3.945A pdb=" N GLUCB 268 " --> pdb=" O ARGCB 264 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARGCB 269 " --> pdb=" O GLUCB 265 " (cutoff:3.500A) Processing helix chain 'CC' and resid 232 through 245 Processing helix chain 'CC' and resid 277 through 281 Processing helix chain 'CC' and resid 284 through 300 removed outlier: 3.523A pdb=" N ALACC 288 " --> pdb=" O SERCC 284 " (cutoff:3.500A) Processing helix chain 'CC' and resid 308 through 316 Processing helix chain 'CC' and resid 349 through 353 removed outlier: 3.634A pdb=" N LEUCC 352 " --> pdb=" O GLYCC 349 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SERCC 353 " --> pdb=" O TYRCC 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 349 through 353' Processing helix chain 'CC' and resid 363 through 373 removed outlier: 3.558A pdb=" N METCC 373 " --> pdb=" O GLUCC 369 " (cutoff:3.500A) Processing helix chain 'CC' and resid 398 through 413 Processing helix chain 'CE' and resid 119 through 130 Processing helix chain 'CE' and resid 135 through 147 Proline residue: CE 143 - end of helix Processing helix chain 'CE' and resid 160 through 176 Proline residue: CE 168 - end of helix Processing helix chain 'CE' and resid 179 through 183 removed outlier: 3.714A pdb=" N GLYCE 183 " --> pdb=" O PROCE 180 " (cutoff:3.500A) Processing helix chain 'CE' and resid 192 through 207 Processing helix chain 'CE' and resid 222 through 233 Processing helix chain 'CE' and resid 240 through 251 Processing helix chain 'CE' and resid 265 through 273 Processing helix chain 'CE' and resid 274 through 285 Processing helix chain 'CE' and resid 300 through 311 Processing helix chain 'CE' and resid 340 through 342 No H-bonds generated for 'chain 'CE' and resid 340 through 342' Processing helix chain 'CE' and resid 343 through 355 Processing helix chain 'CE' and resid 366 through 380 Processing helix chain 'CE' and resid 392 through 405 Processing helix chain 'CE' and resid 437 through 451 Processing helix chain 'CE' and resid 467 through 476 removed outlier: 3.814A pdb=" N ALACE 471 " --> pdb=" O LEUCE 467 " (cutoff:3.500A) Processing helix chain 'CE' and resid 486 through 490 removed outlier: 3.608A pdb=" N LYSCE 489 " --> pdb=" O PROCE 486 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILECE 490 " --> pdb=" O LYSCE 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'CE' and resid 486 through 490' Processing helix chain 'CE' and resid 493 through 504 Processing helix chain 'CE' and resid 504 through 524 Processing helix chain 'CE' and resid 532 through 536 Processing helix chain 'CE' and resid 537 through 546 Processing helix chain 'CI' and resid 200 through 211 removed outlier: 3.740A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 248 Processing helix chain 'CI' and resid 264 through 268 removed outlier: 3.787A pdb=" N VALCI 268 " --> pdb=" O PROCI 265 " (cutoff:3.500A) Processing helix chain 'CI' and resid 284 through 295 Processing helix chain 'CI' and resid 300 through 322 Processing helix chain 'CJ' and resid 11 through 15 removed outlier: 4.089A pdb=" N ASNCJ 15 " --> pdb=" O GLYCJ 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 11 through 15' Processing helix chain 'CJ' and resid 19 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 66 through 74 Processing helix chain 'CJ' and resid 76 through 97 Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 3.633A pdb=" N ASNCJ 111 " --> pdb=" O GLUCJ 107 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 123 through 131 removed outlier: 3.603A pdb=" N ILECJ 127 " --> pdb=" O LEUCJ 123 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 133 through 153 removed outlier: 3.728A pdb=" N ALACJ 137 " --> pdb=" O THRCJ 133 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 162 through 183 Processing helix chain 'CJ' and resid 224 through 250 Processing helix chain 'CJ' and resid 258 through 264 removed outlier: 3.651A pdb=" N ASPCJ 262 " --> pdb=" O ASPCJ 258 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 266 through 270 removed outlier: 3.622A pdb=" N ALACJ 270 " --> pdb=" O GLUCJ 267 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 379 through 390 removed outlier: 3.899A pdb=" N LEUCJ 383 " --> pdb=" O PROCJ 379 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 3.623A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) Processing helix chain 'CM' and resid 53 through 77 removed outlier: 3.535A pdb=" N TYRCM 57 " --> pdb=" O ARGCM 53 " (cutoff:3.500A) Processing helix chain 'CM' and resid 102 through 112 Processing helix chain 'CM' and resid 126 through 136 Processing helix chain 'CM' and resid 146 through 157 Processing helix chain 'CM' and resid 171 through 180 Processing helix chain 'CM' and resid 186 through 196 removed outlier: 3.655A pdb=" N LEUCM 190 " --> pdb=" O CYSCM 186 " (cutoff:3.500A) Processing helix chain 'CM' and resid 200 through 208 removed outlier: 3.701A pdb=" N ALACM 204 " --> pdb=" O ASNCM 200 " (cutoff:3.500A) Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.391A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) Processing helix chain 'CR' and resid 4 through 12 Processing helix chain 'CR' and resid 33 through 38 removed outlier: 3.691A pdb=" N LYSCR 37 " --> pdb=" O ASNCR 33 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SERCR 38 " --> pdb=" O ILECR 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'CR' and resid 33 through 38' Processing helix chain 'CR' and resid 44 through 53 Processing helix chain 'CR' and resid 166 through 178 Processing helix chain 'CR' and resid 188 through 203 removed outlier: 3.627A pdb=" N LYSCR 201 " --> pdb=" O ARGCR 197 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HISCR 202 " --> pdb=" O LEUCR 198 " (cutoff:3.500A) Processing helix chain 'CR' and resid 205 through 212 Processing helix chain 'CR' and resid 221 through 233 Processing helix chain 'CU' and resid 192 through 204 Processing helix chain 'CU' and resid 213 through 218 removed outlier: 4.263A pdb=" N HISCU 217 " --> pdb=" O PROCU 213 " (cutoff:3.500A) Processing helix chain 'CU' and resid 235 through 262 removed outlier: 3.609A pdb=" N ARGCU 239 " --> pdb=" O ASPCU 235 " (cutoff:3.500A) Processing helix chain 'CU' and resid 278 through 305 Processing helix chain 'LC' and resid 24 through 29 removed outlier: 3.523A pdb=" N PHELC 27 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALALC 29 " --> pdb=" O VALLC 26 " (cutoff:3.500A) Processing helix chain 'LC' and resid 32 through 44 Processing helix chain 'LC' and resid 115 through 131 removed outlier: 3.561A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) Processing helix chain 'LC' and resid 132 through 140 Processing helix chain 'LC' and resid 154 through 158 Processing helix chain 'LC' and resid 165 through 176 Processing helix chain 'LC' and resid 178 through 188 Processing helix chain 'LC' and resid 194 through 200 removed outlier: 3.847A pdb=" N LYSLC 197 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLYLC 200 " --> pdb=" O LYSLC 197 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 219 Processing helix chain 'LC' and resid 221 through 226 removed outlier: 3.729A pdb=" N GLYLC 225 " --> pdb=" O GLULC 221 " (cutoff:3.500A) Processing helix chain 'LC' and resid 241 through 246 Processing helix chain 'LC' and resid 247 through 250 Processing helix chain 'LC' and resid 259 through 269 removed outlier: 4.174A pdb=" N TYRLC 269 " --> pdb=" O LEULC 265 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 292 Processing helix chain 'LC' and resid 293 through 298 Processing helix chain 'LC' and resid 322 through 330 Processing helix chain 'LC' and resid 332 through 339 Processing helix chain 'LC' and resid 355 through 363 Processing helix chain 'LE' and resid 115 through 123 Processing helix chain 'LE' and resid 138 through 144 Processing helix chain 'LE' and resid 156 through 176 removed outlier: 3.613A pdb=" N ALALE 160 " --> pdb=" O SERLE 156 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 184 Processing helix chain 'LE' and resid 194 through 198 Processing helix chain 'LF' and resid 15 through 78 Processing helix chain 'LF' and resid 102 through 112 Processing helix chain 'LF' and resid 126 through 136 Processing helix chain 'LF' and resid 146 through 158 Processing helix chain 'LF' and resid 171 through 180 removed outlier: 4.246A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) Processing helix chain 'LF' and resid 181 through 183 No H-bonds generated for 'chain 'LF' and resid 181 through 183' Processing helix chain 'LF' and resid 186 through 196 Processing helix chain 'LF' and resid 201 through 208 removed outlier: 3.539A pdb=" N LEULF 208 " --> pdb=" O ALALF 204 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 Processing helix chain 'LG' and resid 56 through 72 Processing helix chain 'LG' and resid 75 through 80 Processing helix chain 'LG' and resid 81 through 83 No H-bonds generated for 'chain 'LG' and resid 81 through 83' Processing helix chain 'LG' and resid 86 through 100 Processing helix chain 'LG' and resid 104 through 121 Processing helix chain 'LG' and resid 138 through 148 Processing helix chain 'LG' and resid 163 through 177 removed outlier: 4.725A pdb=" N PHELG 168 " --> pdb=" O GLULG 164 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEULG 169 " --> pdb=" O LEULG 165 " (cutoff:3.500A) Proline residue: LG 170 - end of helix Processing helix chain 'LG' and resid 185 through 193 removed outlier: 3.591A pdb=" N LEULG 189 " --> pdb=" O GLYLG 185 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 209 No H-bonds generated for 'chain 'LG' and resid 207 through 209' Processing helix chain 'LG' and resid 210 through 225 Processing helix chain 'LG' and resid 225 through 230 Processing helix chain 'LL' and resid 17 through 20 removed outlier: 3.612A pdb=" N ARGLL 20 " --> pdb=" O HISLL 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 20' Processing helix chain 'LL' and resid 27 through 46 Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 89 through 93 Processing helix chain 'LL' and resid 105 through 122 removed outlier: 3.804A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALALL 110 " --> pdb=" O GLULL 106 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 89 through 97 Processing helix chain 'LM' and resid 97 through 110 Processing helix chain 'LM' and resid 113 through 137 Processing helix chain 'LN' and resid 3 through 12 Processing helix chain 'LN' and resid 16 through 32 Processing helix chain 'LN' and resid 44 through 51 Processing helix chain 'LN' and resid 97 through 110 Processing helix chain 'LN' and resid 139 through 144 Processing helix chain 'LN' and resid 148 through 157 Proline residue: LN 154 - end of helix removed outlier: 3.626A pdb=" N LYSLN 157 " --> pdb=" O PROLN 154 " (cutoff:3.500A) Processing helix chain 'LN' and resid 158 through 162 Processing helix chain 'LN' and resid 165 through 172 Processing helix chain 'LN' and resid 177 through 181 removed outlier: 3.699A pdb=" N ASNLN 181 " --> pdb=" O HISLN 178 " (cutoff:3.500A) Processing helix chain 'LN' and resid 186 through 195 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 38 through 41 Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.958A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 88 Processing helix chain 'LO' and resid 94 through 103 Processing helix chain 'LO' and resid 111 through 115 removed outlier: 3.734A pdb=" N ASPLO 115 " --> pdb=" O PROLO 112 " (cutoff:3.500A) Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 140 through 148 Processing helix chain 'LO' and resid 152 through 190 Processing helix chain 'LO' and resid 193 through 202 Processing helix chain 'LP' and resid 10 through 12 No H-bonds generated for 'chain 'LP' and resid 10 through 12' Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 53 Processing helix chain 'LP' and resid 70 through 74 removed outlier: 3.751A pdb=" N GLYLP 73 " --> pdb=" O THRLP 70 " (cutoff:3.500A) Processing helix chain 'LP' and resid 85 through 106 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 82 removed outlier: 3.697A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 92 through 99 Processing helix chain 'LQ' and resid 134 through 144 Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LS' and resid 33 through 48 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 137 through 144 Processing helix chain 'LT' and resid 54 through 58 Processing helix chain 'LT' and resid 102 through 123 removed outlier: 3.522A pdb=" N LEULT 106 " --> pdb=" O ARGLT 102 " (cutoff:3.500A) Processing helix chain 'LX' and resid 13 through 29 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 101 No H-bonds generated for 'chain 'LY' and resid 99 through 101' Processing helix chain 'LY' and resid 111 through 134 Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 55 through 59 Processing helix chain 'Le' and resid 79 through 85 removed outlier: 3.790A pdb=" N VALLe 83 " --> pdb=" O ASNLe 79 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 44 Processing helix chain 'Lf' and resid 45 through 47 No H-bonds generated for 'chain 'Lf' and resid 45 through 47' Processing helix chain 'Lf' and resid 92 through 96 Processing helix chain 'Lh' and resid 8 through 15 removed outlier: 3.825A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 16 through 38 Processing helix chain 'Lh' and resid 44 through 75 removed outlier: 3.565A pdb=" N LYSLh 48 " --> pdb=" O ALALh 44 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 86 removed outlier: 3.525A pdb=" N ARGLh 86 " --> pdb=" O LEULh 83 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 98 through 103 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 43 through 58 removed outlier: 3.516A pdb=" N GLNLi 47 " --> pdb=" O SERLi 43 " (cutoff:3.500A) Processing helix chain 'Li' and resid 60 through 71 Processing helix chain 'Li' and resid 74 through 87 Processing helix chain 'Li' and resid 88 through 110 Processing helix chain 'Lj' and resid 50 through 56 Processing helix chain 'Lj' and resid 69 through 76 removed outlier: 3.528A pdb=" N ARGLj 73 " --> pdb=" O THRLj 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASNLj 76 " --> pdb=" O ARGLj 72 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 18 through 35 removed outlier: 3.543A pdb=" N ALACc 35 " --> pdb=" O ALACc 31 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 35 through 41 removed outlier: 4.194A pdb=" N ALACc 41 " --> pdb=" O GLNCc 37 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 43 through 60 removed outlier: 3.538A pdb=" N VALCc 47 " --> pdb=" O THRCc 43 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 63 through 77 Processing helix chain 'Cc' and resid 78 through 81 removed outlier: 3.769A pdb=" N LEUCc 81 " --> pdb=" O ILECc 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cc' and resid 78 through 81' Processing helix chain 'Cc' and resid 82 through 84 No H-bonds generated for 'chain 'Cc' and resid 82 through 84' Processing helix chain 'Cc' and resid 85 through 100 Processing helix chain 'Cc' and resid 108 through 127 removed outlier: 3.789A pdb=" N PHECc 112 " --> pdb=" O ARGCc 108 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N METCc 127 " --> pdb=" O SERCc 123 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 151 through 165 Processing helix chain 'Cc' and resid 190 through 209 removed outlier: 3.664A pdb=" N ARGCc 194 " --> pdb=" O PROCc 190 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VALCc 202 " --> pdb=" O LEUCc 198 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASPCc 203 " --> pdb=" O ASPCc 199 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 215 through 235 Processing helix chain 'Cc' and resid 238 through 250 Processing helix chain 'Cd' and resid 13 through 17 Processing helix chain 'Cd' and resid 20 through 53 Processing helix chain 'Cd' and resid 55 through 64 removed outlier: 3.652A pdb=" N LYSCd 59 " --> pdb=" O GLUCd 55 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 88 through 98 Processing helix chain 'Cd' and resid 181 through 187 Processing helix chain 'Cd' and resid 211 through 222 removed outlier: 3.531A pdb=" N ALACd 215 " --> pdb=" O ILECd 211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHECd 222 " --> pdb=" O ILECd 218 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 240 through 251 Processing helix chain 'Cd' and resid 318 through 331 removed outlier: 3.765A pdb=" N LEUCd 331 " --> pdb=" O SERCd 327 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 424 through 429 Processing helix chain 'Ce' and resid 3 through 13 Processing helix chain 'Ce' and resid 68 through 71 Processing helix chain 'Ce' and resid 73 through 76 Processing helix chain 'Ce' and resid 86 through 98 Processing helix chain 'Ce' and resid 102 through 134 Processing helix chain 'Ce' and resid 142 through 161 removed outlier: 3.982A pdb=" N LYSCe 161 " --> pdb=" O LEUCe 157 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 161 through 176 Processing helix chain 'Ce' and resid 187 through 195 Processing sheet with id=AA1, first strand: chain 'CA' and resid 62 through 64 removed outlier: 4.581A pdb=" N LEUCA 100 " --> pdb=" O ALACA 117 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYRCA 116 " --> pdb=" O PROCA 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'CA' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'CA' and resid 238 through 246 current: chain 'CA' and resid 139 through 142 Processing sheet with id=AA3, first strand: chain 'CB' and resid 46 through 48 removed outlier: 6.573A pdb=" N GLNCE 334 " --> pdb=" O VALCE 481 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYRCE 483 " --> pdb=" O GLNCE 334 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYRCE 336 " --> pdb=" O TYRCE 483 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLYCE 335 " --> pdb=" O LEUCE 460 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEUCE 462 " --> pdb=" O GLYCE 335 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VALCE 337 " --> pdb=" O LEUCE 462 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILECE 429 " --> pdb=" O LEUCE 459 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHECE 461 " --> pdb=" O ILECE 429 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLNCE 431 " --> pdb=" O PHECE 461 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYSCE 359 " --> pdb=" O TRPCE 428 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VALCE 430 " --> pdb=" O LYSCE 359 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILECE 361 " --> pdb=" O VALCE 430 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEUCE 385 " --> pdb=" O ILECE 412 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N THRCE 414 " --> pdb=" O LEUCE 385 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEUCE 387 " --> pdb=" O THRCE 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'CB' and resid 240 through 247 removed outlier: 5.667A pdb=" N ALACB 242 " --> pdb=" O LEUCB 66 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEUCB 66 " --> pdb=" O ALACB 242 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYSCB 244 " --> pdb=" O LEUCB 64 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEUCB 64 " --> pdb=" O LYSCB 244 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLYCB 246 " --> pdb=" O ILECB 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'CB' and resid 81 through 84 Processing sheet with id=AA6, first strand: chain 'CB' and resid 124 through 128 removed outlier: 7.360A pdb=" N VALCB 97 " --> pdb=" O GLYCB 125 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VALCB 127 " --> pdb=" O VALCB 97 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEUCB 99 " --> pdb=" O VALCB 127 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHECB 153 " --> pdb=" O ILECB 180 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VALCB 182 " --> pdb=" O PHECB 153 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALACB 155 " --> pdb=" O VALCB 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'CC' and resid 137 through 140 Processing sheet with id=AA8, first strand: chain 'CE' and resid 214 through 217 removed outlier: 6.545A pdb=" N GLYCE 215 " --> pdb=" O ILECE 238 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALACE 186 " --> pdb=" O LEUCE 237 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALACE 239 " --> pdb=" O ALACE 186 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VALCE 188 " --> pdb=" O ALACE 239 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEUCE 152 " --> pdb=" O ILECE 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'CI' and resid 213 through 220 removed outlier: 5.217A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'CI' and resid 252 through 253 Processing sheet with id=AB2, first strand: chain 'CJ' and resid 16 through 18 Processing sheet with id=AB3, first strand: chain 'CJ' and resid 185 through 190 removed outlier: 5.365A pdb=" N LEUCJ 185 " --> pdb=" O ASNCJ 200 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASNCJ 200 " --> pdb=" O LEUCJ 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'CJ' and resid 394 through 396 removed outlier: 6.521A pdb=" N THRCJ 371 " --> pdb=" O HISCJ 417 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILECJ 419 " --> pdb=" O THRCJ 371 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHECJ 373 " --> pdb=" O ILECJ 419 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLNCJ 418 " --> pdb=" O VALCJ 456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'CM' and resid 140 through 143 removed outlier: 4.699A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHECM 211 " --> pdb=" O GLYCM 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'CM' and resid 159 through 162 Processing sheet with id=AB7, first strand: chain 'LC' and resid 6 through 10 removed outlier: 4.990A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LC' and resid 63 through 65 Processing sheet with id=AB9, first strand: chain 'LC' and resid 150 through 153 Processing sheet with id=AC1, first strand: chain 'LC' and resid 190 through 191 Processing sheet with id=AC2, first strand: chain 'LE' and resid 92 through 98 removed outlier: 4.813A pdb=" N GLYLE 85 " --> pdb=" O PROLE 93 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THRLE 84 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEULE 72 " --> pdb=" O THRLE 84 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VALLE 107 " --> pdb=" O VALLE 57 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILELE 59 " --> pdb=" O THRLE 105 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THRLE 105 " --> pdb=" O ILELE 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LF' and resid 80 through 83 removed outlier: 3.527A pdb=" N HISLT 139 " --> pdb=" O ILELF 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LF' and resid 211 through 212 Processing sheet with id=AC5, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id=AC6, first strand: chain 'LG' and resid 136 through 137 Processing sheet with id=AC7, first strand: chain 'LL' and resid 22 through 24 Processing sheet with id=AC8, first strand: chain 'LL' and resid 57 through 59 Processing sheet with id=AC9, first strand: chain 'LL' and resid 123 through 125 Processing sheet with id=AD1, first strand: chain 'LM' and resid 13 through 14 Processing sheet with id=AD2, first strand: chain 'LM' and resid 52 through 58 removed outlier: 4.782A pdb=" N GLYLM 43 " --> pdb=" O PROLM 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLULM 32 " --> pdb=" O LEULM 40 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASPLM 42 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILELM 30 " --> pdb=" O ASPLM 42 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VALLM 19 " --> pdb=" O THRLM 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.117A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYRLN 127 " --> pdb=" O ASNLN 122 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASNLN 122 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYRLN 129 " --> pdb=" O TRPLN 120 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRPLN 120 " --> pdb=" O TYRLN 129 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLULN 131 " --> pdb=" O SERLN 118 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SERLN 118 " --> pdb=" O GLULN 131 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'LO' and resid 8 through 11 Processing sheet with id=AD5, first strand: chain 'LO' and resid 43 through 45 Processing sheet with id=AD6, first strand: chain 'LP' and resid 14 through 22 removed outlier: 3.578A pdb=" N TYRLP 21 " --> pdb=" O CYSLP 144 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N CYSLP 144 " --> pdb=" O TYRLP 21 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THRLP 151 " --> pdb=" O ILELP 114 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILELP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AD8, first strand: chain 'LQ' and resid 90 through 91 removed outlier: 6.344A pdb=" N VALLQ 90 " --> pdb=" O THRLQ 115 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VALLQ 108 " --> pdb=" O ALALQ 129 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEULQ 131 " --> pdb=" O VALLQ 108 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N VALLQ 110 " --> pdb=" O LEULQ 131 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N PHELQ 133 " --> pdb=" O VALLQ 110 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N ALALQ 112 " --> pdb=" O PHELQ 133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'LQ' and resid 90 through 91 removed outlier: 6.344A pdb=" N VALLQ 90 " --> pdb=" O THRLQ 115 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LS' and resid 56 through 63 removed outlier: 5.465A pdb=" N ILELS 58 " --> pdb=" O ARGLS 12 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARGLS 12 " --> pdb=" O ILELS 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LS' and resid 87 through 96 removed outlier: 6.723A pdb=" N ARGLS 80 " --> pdb=" O ILELS 123 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILELS 123 " --> pdb=" O ARGLS 80 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASPLS 82 " --> pdb=" O ILELS 121 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILELS 121 " --> pdb=" O ASPLS 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LT' and resid 83 through 92 removed outlier: 7.134A pdb=" N ALALT 71 " --> pdb=" O VALLT 67 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VALLT 67 " --> pdb=" O ALALT 71 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLYLT 73 " --> pdb=" O TYRLT 65 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYRLT 77 " --> pdb=" O THRLT 61 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THRLT 61 " --> pdb=" O TYRLT 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AE5, first strand: chain 'LY' and resid 78 through 81 removed outlier: 6.648A pdb=" N VALLY 78 " --> pdb=" O VALLY 72 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VALLY 72 " --> pdb=" O VALLY 78 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HISLY 80 " --> pdb=" O THRLY 70 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLNLY 56 " --> pdb=" O ILELY 105 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILELY 105 " --> pdb=" O GLNLY 56 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Le' and resid 73 through 77 removed outlier: 5.959A pdb=" N LYSLe 73 " --> pdb=" O ALALe 94 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLULe 96 " --> pdb=" O LYSLe 73 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHELe 75 " --> pdb=" O GLULe 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Le' and resid 127 through 130 Processing sheet with id=AE8, first strand: chain 'Lf' and resid 10 through 20 removed outlier: 5.493A pdb=" N HISLf 15 " --> pdb=" O LYSLf 33 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYSLf 33 " --> pdb=" O HISLf 15 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THRLf 29 " --> pdb=" O GLNLf 19 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LYSLf 28 " --> pdb=" O PHELf 87 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHELf 87 " --> pdb=" O LYSLf 28 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VALLf 82 " --> pdb=" O HISLf 77 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGLf 75 " --> pdb=" O ARGLf 84 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYSLf 86 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILELf 73 " --> pdb=" O LYSLf 86 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VALLf 54 " --> pdb=" O SERLf 99 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SERLf 99 " --> pdb=" O VALLf 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Lj' and resid 16 through 17 Processing sheet with id=AF1, first strand: chain 'Cc' and resid 172 through 175 Processing sheet with id=AF2, first strand: chain 'Cd' and resid 225 through 227 removed outlier: 6.650A pdb=" N LEUCd 256 " --> pdb=" O VALCd 271 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VALCd 271 " --> pdb=" O LEUCd 256 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VALCd 258 " --> pdb=" O LEUCd 269 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEUCd 269 " --> pdb=" O VALCd 258 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLNCd 260 " --> pdb=" O SERCd 267 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THRCd 284 " --> pdb=" O VALCd 404 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VALCd 404 " --> pdb=" O THRCd 284 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THRCd 286 " --> pdb=" O ARGCd 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Cd' and resid 310 through 314 removed outlier: 5.966A pdb=" N GLUCd 310 " --> pdb=" O VALCd 344 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEUCd 346 " --> pdb=" O GLUCd 310 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEUCd 312 " --> pdb=" O LEUCd 346 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASNCd 348 " --> pdb=" O LEUCd 312 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASNCd 314 " --> pdb=" O ASNCd 348 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Cd' and resid 310 through 314 removed outlier: 5.966A pdb=" N GLUCd 310 " --> pdb=" O VALCd 344 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEUCd 346 " --> pdb=" O GLUCd 310 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEUCd 312 " --> pdb=" O LEUCd 346 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASNCd 348 " --> pdb=" O LEUCd 312 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASNCd 314 " --> pdb=" O ASNCd 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Ce' and resid 18 through 20 Processing sheet with id=AF6, first strand: chain 'Ce' and resid 50 through 55 2104 hydrogen bonds defined for protein. 6066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1304 hydrogen bonds 2176 hydrogen bond angles 0 basepair planarities 508 basepair parallelities 835 stacking parallelities Total time for adding SS restraints: 49.58 Time building geometry restraints manager: 33.06 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: 12253 1.33 - 1.46: 32597 1.46 - 1.58: 37506 1.58 - 1.71: 3114 1.71 - 1.84: 224 Bond restraints: 85694 Sorted by residual: bond pdb=" N GLUCB 115 " pdb=" CA GLUCB 115 " ideal model delta sigma weight residual 1.457 1.489 -0.033 6.40e-03 2.44e+04 2.61e+01 bond pdb=" N ILECB 180 " pdb=" CA ILECB 180 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.08e+01 bond pdb=" N ILELF 83 " pdb=" CA ILELF 83 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.88e+01 bond pdb=" N VALLM 57 " pdb=" CA VALLM 57 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.75e+01 bond pdb=" N ILECB 159 " pdb=" CA ILECB 159 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.04e-02 9.25e+03 1.55e+01 ... (remaining 85689 not shown) Histogram of bond angle deviations from ideal: 94.51 - 104.19: 6512 104.19 - 113.88: 54178 113.88 - 123.56: 52934 123.56 - 133.25: 9522 133.25 - 142.94: 89 Bond angle restraints: 123235 Sorted by residual: angle pdb=" CA PROLO 193 " pdb=" N PROLO 193 " pdb=" CD PROLO 193 " ideal model delta sigma weight residual 112.00 100.01 11.99 1.40e+00 5.10e-01 7.34e+01 angle pdb=" CB METCJ 147 " pdb=" CG METCJ 147 " pdb=" SD METCJ 147 " ideal model delta sigma weight residual 112.70 135.84 -23.14 3.00e+00 1.11e-01 5.95e+01 angle pdb=" CA PROCM 210 " pdb=" N PROCM 210 " pdb=" CD PROCM 210 " ideal model delta sigma weight residual 112.00 101.73 10.27 1.40e+00 5.10e-01 5.38e+01 angle pdb=" CA GLULO 171 " pdb=" CB GLULO 171 " pdb=" CG GLULO 171 " ideal model delta sigma weight residual 114.10 127.95 -13.85 2.00e+00 2.50e-01 4.80e+01 angle pdb=" CA METCJ 147 " pdb=" CB METCJ 147 " pdb=" CG METCJ 147 " ideal model delta sigma weight residual 114.10 127.88 -13.78 2.00e+00 2.50e-01 4.75e+01 ... (remaining 123230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 49207 35.95 - 71.90: 4647 71.90 - 107.84: 476 107.84 - 143.79: 5 143.79 - 179.74: 12 Dihedral angle restraints: 54347 sinusoidal: 37270 harmonic: 17077 Sorted by residual: dihedral pdb=" O4' CC2 151 " pdb=" C1' CC2 151 " pdb=" N1 CC2 151 " pdb=" C2 CC2 151 " ideal model delta sinusoidal sigma weight residual 200.00 48.26 151.74 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' UC1 961 " pdb=" C1' UC1 961 " pdb=" N1 UC1 961 " pdb=" C2 UC1 961 " ideal model delta sinusoidal sigma weight residual -160.00 -8.44 -151.56 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' UC13158 " pdb=" C1' UC13158 " pdb=" N1 UC13158 " pdb=" C2 UC13158 " ideal model delta sinusoidal sigma weight residual 200.00 51.08 148.92 1 1.50e+01 4.44e-03 7.92e+01 ... (remaining 54344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 14148 0.115 - 0.230: 700 0.230 - 0.345: 27 0.345 - 0.459: 1 0.459 - 0.574: 1 Chirality restraints: 14877 Sorted by residual: chirality pdb=" CG LEULO 59 " pdb=" CB LEULO 59 " pdb=" CD1 LEULO 59 " pdb=" CD2 LEULO 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.24e+00 chirality pdb=" CA TYRLO 170 " pdb=" N TYRLO 170 " pdb=" C TYRLO 170 " pdb=" CB TYRLO 170 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PROLO 193 " pdb=" N PROLO 193 " pdb=" C PROLO 193 " pdb=" CB PROLO 193 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 14874 not shown) Planarity restraints: 9888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASPLO 192 " 0.095 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PROLO 193 " -0.231 5.00e-02 4.00e+02 pdb=" CA PROLO 193 " 0.065 5.00e-02 4.00e+02 pdb=" CD PROLO 193 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLUCd 194 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PROCd 195 " 0.203 5.00e-02 4.00e+02 pdb=" CA PROCd 195 " -0.061 5.00e-02 4.00e+02 pdb=" CD PROCd 195 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GC1 398 " -0.059 2.00e-02 2.50e+03 2.67e-02 2.14e+01 pdb=" N9 GC1 398 " 0.067 2.00e-02 2.50e+03 pdb=" C8 GC1 398 " 0.009 2.00e-02 2.50e+03 pdb=" N7 GC1 398 " -0.003 2.00e-02 2.50e+03 pdb=" C5 GC1 398 " -0.006 2.00e-02 2.50e+03 pdb=" C6 GC1 398 " -0.007 2.00e-02 2.50e+03 pdb=" O6 GC1 398 " -0.012 2.00e-02 2.50e+03 pdb=" N1 GC1 398 " -0.005 2.00e-02 2.50e+03 pdb=" C2 GC1 398 " -0.002 2.00e-02 2.50e+03 pdb=" N2 GC1 398 " 0.011 2.00e-02 2.50e+03 pdb=" N3 GC1 398 " 0.005 2.00e-02 2.50e+03 pdb=" C4 GC1 398 " 0.003 2.00e-02 2.50e+03 ... (remaining 9885 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 6174 2.73 - 3.27: 70956 3.27 - 3.81: 153918 3.81 - 4.36: 191683 4.36 - 4.90: 276747 Nonbonded interactions: 699478 Sorted by model distance: nonbonded pdb=" O2' UC13138 " pdb=" OG1 THRLS 172 " model vdw 2.185 2.440 nonbonded pdb=" O ILECd 207 " pdb=" OG1 THRCd 231 " model vdw 2.189 2.440 nonbonded pdb=" N7 AC13112 " pdb=" O2 UC13232 " model vdw 2.192 3.120 nonbonded pdb=" OG1 THRCR 50 " pdb=" O ASNCR 69 " model vdw 2.215 2.440 nonbonded pdb=" OP2 GC2 103 " pdb=" O2' AC2 105 " model vdw 2.223 2.440 ... (remaining 699473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 16.950 Check model and map are aligned: 0.950 Set scattering table: 0.550 Process input model: 210.670 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 0.139 85694 Z= 0.331 Angle : 0.905 23.141 123235 Z= 0.521 Chirality : 0.051 0.574 14877 Planarity : 0.007 0.134 9888 Dihedral : 22.027 179.741 43271 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 1.13 % Allowed : 28.39 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.14 (0.10), residues: 5764 helix: -0.30 (0.10), residues: 2444 sheet: -0.47 (0.20), residues: 692 loop : -1.18 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPCC 396 HIS 0.019 0.001 HISCM 192 PHE 0.059 0.002 PHELP 47 TYR 0.044 0.002 TYRLF 142 ARG 0.018 0.001 ARGCd 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 863 time to evaluate : 5.085 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: CB 22 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7464 (tp40) REVERT: CB 33 HIS cc_start: 0.9201 (t70) cc_final: 0.8929 (t-90) REVERT: CB 104 PRO cc_start: 0.7431 (OUTLIER) cc_final: 0.7156 (Cg_exo) REVERT: CB 211 ASN cc_start: 0.8088 (p0) cc_final: 0.7775 (p0) REVERT: CB 264 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.8432 (mtm110) REVERT: CE 437 ASP cc_start: 0.8508 (t0) cc_final: 0.8007 (t70) REVERT: CJ 164 MET cc_start: 0.6209 (ppp) cc_final: 0.5352 (pp-130) REVERT: CM 64 GLN cc_start: 0.8830 (mp10) cc_final: 0.8596 (mm-40) REVERT: CR 10 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8088 (ttp80) REVERT: LC 56 LYS cc_start: 0.6414 (mtmm) cc_final: 0.5934 (pttm) REVERT: LE 64 ARG cc_start: 0.7893 (ptm160) cc_final: 0.7523 (ptm160) REVERT: LF 39 ARG cc_start: 0.8081 (ttp-170) cc_final: 0.7816 (ttp-110) REVERT: LG 52 MET cc_start: 0.2873 (pmt) cc_final: -0.0104 (tmt) REVERT: LG 109 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7634 (mttp) REVERT: LO 48 PHE cc_start: 0.8202 (t80) cc_final: 0.7963 (t80) REVERT: LO 62 MET cc_start: 0.5956 (tpt) cc_final: 0.5687 (mmt) REVERT: LQ 78 ARG cc_start: 0.8645 (ttp80) cc_final: 0.7889 (ttp-110) REVERT: LS 140 ILE cc_start: 0.9479 (mm) cc_final: 0.9185 (mt) REVERT: LT 52 MET cc_start: 0.4011 (ppp) cc_final: 0.3574 (ppp) REVERT: Le 84 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8112 (mm-30) REVERT: Li 107 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7961 (mtt90) REVERT: Cd 58 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8151 (mp10) outliers start: 57 outliers final: 24 residues processed: 900 average time/residue: 1.6916 time to fit residues: 1993.4093 Evaluate side-chains 726 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 700 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 46 TYR Chi-restraints excluded: chain CA residue 244 ILE Chi-restraints excluded: chain CB residue 104 PRO Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 327 PHE Chi-restraints excluded: chain CJ residue 30 LEU Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 10 ARG Chi-restraints excluded: chain CR residue 134 GLN Chi-restraints excluded: chain CR residue 164 SER Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 33 ILE Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LQ residue 92 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 114 VAL Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain Cc residue 175 ILE Chi-restraints excluded: chain Cc residue 176 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 2.9990 chunk 551 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 570 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 246 GLN CA 286 GLN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN CI 209 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN ** CR 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 246 GLN LC 264 GLN LC 284 GLN LE 172 ASN LF 64 GLN LF 77 GLN LG 82 GLN LO 124 GLN LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS Lf 79 ASN ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 115 HIS Cc 152 GLN Cd 315 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 85694 Z= 0.312 Angle : 0.626 13.419 123235 Z= 0.321 Chirality : 0.040 0.428 14877 Planarity : 0.006 0.079 9888 Dihedral : 22.057 175.427 30968 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 4.78 % Allowed : 25.72 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5764 helix: 0.67 (0.10), residues: 2473 sheet: -0.34 (0.19), residues: 694 loop : -0.90 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPLN 120 HIS 0.012 0.001 HISCM 192 PHE 0.027 0.002 PHECE 165 TYR 0.025 0.002 TYRLO 170 ARG 0.008 0.001 ARGCB 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 729 time to evaluate : 5.253 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: CA 98 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8537 (mtpt) REVERT: CA 126 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6951 (tt) REVERT: CA 270 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: CB 22 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7795 (tp40) REVERT: CB 105 GLN cc_start: 0.8875 (pt0) cc_final: 0.8661 (pt0) REVERT: CB 121 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7700 (ttp-170) REVERT: CB 138 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8793 (ttpp) REVERT: CB 149 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: CE 128 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8555 (mp0) REVERT: CE 134 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7980 (mtt) REVERT: CE 289 ASP cc_start: 0.7605 (t0) cc_final: 0.7241 (t0) REVERT: CE 437 ASP cc_start: 0.8485 (t0) cc_final: 0.8069 (t70) REVERT: CM 64 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8733 (mm-40) REVERT: CM 69 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9004 (mp) REVERT: CM 246 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6651 (tpt170) REVERT: CR 21 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6907 (m-40) REVERT: CU 261 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5933 (tp30) REVERT: LC 301 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7378 (ptp90) REVERT: LC 306 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: LG 52 MET cc_start: 0.2853 (pmt) cc_final: -0.0132 (tmm) REVERT: LG 209 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: LG 210 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8019 (p0) REVERT: LL 66 ASN cc_start: 0.8348 (m-40) cc_final: 0.8069 (m-40) REVERT: LN 9 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: LO 48 PHE cc_start: 0.8483 (t80) cc_final: 0.7756 (t80) REVERT: LO 62 MET cc_start: 0.6300 (tpt) cc_final: 0.6095 (mmt) REVERT: LO 89 MET cc_start: 0.8631 (mtm) cc_final: 0.8294 (ptp) REVERT: LO 146 GLU cc_start: 0.8444 (mp0) cc_final: 0.7741 (mp0) REVERT: LO 157 ARG cc_start: 0.8956 (mpt-90) cc_final: 0.8728 (mpt-90) REVERT: LQ 78 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8080 (mtm-85) REVERT: LS 137 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7955 (ttm-80) REVERT: LT 52 MET cc_start: 0.4087 (ppp) cc_final: 0.3211 (ppp) REVERT: LY 114 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7293 (tpt90) REVERT: Le 84 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7957 (mm-30) REVERT: Lh 70 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: Lh 77 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7823 (t0) REVERT: Cc 100 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: Cc 219 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7975 (ttm-80) REVERT: Cd 296 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8823 (mmmt) REVERT: Cd 369 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8028 (mt-10) REVERT: Cd 417 ASP cc_start: 0.7773 (t0) cc_final: 0.7433 (t0) REVERT: Ce 135 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7353 (mm-30) outliers start: 240 outliers final: 93 residues processed: 903 average time/residue: 1.6588 time to fit residues: 1978.0175 Evaluate side-chains 788 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 673 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 126 LEU Chi-restraints excluded: chain CA residue 133 LEU Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 138 LYS Chi-restraints excluded: chain CB residue 141 GLU Chi-restraints excluded: chain CB residue 149 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 166 ASN Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CE residue 134 MET Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 240 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 240 VAL Chi-restraints excluded: chain CI residue 327 PHE Chi-restraints excluded: chain CJ residue 89 LYS Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 135 ILE Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 21 ASN Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CR residue 235 LEU Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 301 ARG Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 143 LEU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 158 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LP residue 161 GLU Chi-restraints excluded: chain LQ residue 92 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 114 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 64 ILE Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 89 ASN Chi-restraints excluded: chain LS residue 100 VAL Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LS residue 161 THR Chi-restraints excluded: chain LT residue 74 VAL Chi-restraints excluded: chain LY residue 66 GLU Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 7 VAL Chi-restraints excluded: chain Lh residue 14 SER Chi-restraints excluded: chain Lh residue 70 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 77 ASN Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 7 SER Chi-restraints excluded: chain Cc residue 100 GLU Chi-restraints excluded: chain Cc residue 208 VAL Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 279 VAL Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Ce residue 13 GLN Chi-restraints excluded: chain Ce residue 135 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 550 optimal weight: 0.0020 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 662 optimal weight: 0.6980 chunk 715 optimal weight: 0.6980 chunk 589 optimal weight: 0.0770 chunk 656 optimal weight: 0.6980 chunk 225 optimal weight: 20.0000 chunk 531 optimal weight: 7.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 178 HIS CA 246 GLN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN CJ 102 ASN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN ** CU 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 172 ASN LE 196 HIS LF 77 GLN LF 163 ASN LF 240 HIS LG 82 GLN LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS Lh 37 GLN Cc 152 GLN Cd 20 ASN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 185 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 85694 Z= 0.134 Angle : 0.536 14.695 123235 Z= 0.273 Chirality : 0.035 0.345 14877 Planarity : 0.004 0.070 9888 Dihedral : 21.988 179.851 30944 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 3.78 % Allowed : 26.94 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 5764 helix: 1.18 (0.10), residues: 2473 sheet: -0.23 (0.19), residues: 708 loop : -0.72 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCJ 208 HIS 0.010 0.001 HISCM 192 PHE 0.025 0.001 PHECA 238 TYR 0.016 0.001 TYRLF 142 ARG 0.008 0.000 ARGCC 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 728 time to evaluate : 5.077 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: CA 126 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6867 (tt) REVERT: CA 312 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6113 (ptp-110) REVERT: CB 22 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7716 (tp40) REVERT: CB 121 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (ttp-170) REVERT: CB 209 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7960 (mm) REVERT: CB 264 ARG cc_start: 0.8520 (mtm110) cc_final: 0.8089 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7267 (mp0) REVERT: CE 128 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8527 (mp0) REVERT: CE 437 ASP cc_start: 0.8383 (t0) cc_final: 0.7992 (t70) REVERT: CI 208 SER cc_start: 0.9416 (OUTLIER) cc_final: 0.9051 (p) REVERT: CI 311 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8912 (pm20) REVERT: CM 64 GLN cc_start: 0.8958 (mp10) cc_final: 0.8712 (mm-40) REVERT: CM 69 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8991 (mp) REVERT: CM 94 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5904 (ppp80) REVERT: CM 246 ARG cc_start: 0.6887 (tpt170) cc_final: 0.6596 (tpt170) REVERT: CR 18 ARG cc_start: 0.7722 (ttt180) cc_final: 0.7500 (ttt90) REVERT: CU 261 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5960 (tp30) REVERT: LC 56 LYS cc_start: 0.6502 (mtmm) cc_final: 0.6240 (ptmm) REVERT: LC 306 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: LE 172 ASN cc_start: 0.8906 (m-40) cc_final: 0.8631 (m-40) REVERT: LF 61 TYR cc_start: 0.8998 (m-10) cc_final: 0.8442 (m-80) REVERT: LG 52 MET cc_start: 0.2911 (OUTLIER) cc_final: -0.0116 (tmt) REVERT: LG 209 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: LG 210 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7932 (p0) REVERT: LL 66 ASN cc_start: 0.8316 (m-40) cc_final: 0.8002 (m-40) REVERT: LL 120 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8384 (mtmt) REVERT: LN 9 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: LO 89 MET cc_start: 0.8422 (mtm) cc_final: 0.8192 (ptp) REVERT: LO 146 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: LO 157 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8757 (mpt-90) REVERT: LS 137 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8044 (ttm-80) REVERT: LT 52 MET cc_start: 0.3875 (ppp) cc_final: 0.2957 (ppp) REVERT: LY 114 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7308 (tpt90) REVERT: Le 84 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7920 (mm-30) REVERT: Lh 77 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7843 (t0) REVERT: Cc 188 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8397 (tttp) REVERT: Cc 219 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7914 (ttm-80) REVERT: Cd 369 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7931 (mt-10) REVERT: Cd 417 ASP cc_start: 0.7650 (t0) cc_final: 0.7279 (t0) REVERT: Ce 13 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: Ce 135 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7687 (mm-30) REVERT: Ce 176 GLN cc_start: 0.9072 (mt0) cc_final: 0.8831 (mm-40) outliers start: 190 outliers final: 68 residues processed: 866 average time/residue: 1.6911 time to fit residues: 1934.4799 Evaluate side-chains 770 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 681 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 126 LEU Chi-restraints excluded: chain CA residue 136 SER Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CA residue 312 ARG Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 134 MET Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 94 ARG Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain CU residue 288 LYS Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LF residue 135 ILE Chi-restraints excluded: chain LG residue 52 MET Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 183 ILE Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 227 GLU Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 104 LEU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 157 ARG Chi-restraints excluded: chain LO residue 158 LEU Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LP residue 161 GLU Chi-restraints excluded: chain LQ residue 92 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 1 MET Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 77 ASN Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 208 VAL Chi-restraints excluded: chain Ce residue 13 GLN Chi-restraints excluded: chain Ce residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 0.8980 chunk 497 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 chunk 73 optimal weight: 50.0000 chunk 316 optimal weight: 7.9990 chunk 444 optimal weight: 0.7980 chunk 664 optimal weight: 7.9990 chunk 703 optimal weight: 0.2980 chunk 347 optimal weight: 0.2980 chunk 629 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 246 GLN CA 286 GLN CC 166 ASN CC 170 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 485 HIS ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN CR 216 ASN ** CU 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 264 GLN LF 77 GLN LG 82 GLN ** LO 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 152 GLN Cd 20 ASN Cd 65 GLN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 85694 Z= 0.141 Angle : 0.523 13.904 123235 Z= 0.266 Chirality : 0.035 0.381 14877 Planarity : 0.004 0.065 9888 Dihedral : 21.889 177.041 30937 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.86 % Allowed : 27.19 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 5764 helix: 1.45 (0.10), residues: 2479 sheet: -0.09 (0.19), residues: 700 loop : -0.61 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPCJ 208 HIS 0.010 0.001 HISCM 192 PHE 0.030 0.001 PHELP 47 TYR 0.026 0.001 TYRLO 169 ARG 0.017 0.000 ARGCA 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 719 time to evaluate : 5.086 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: CA 80 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8974 (tt) REVERT: CA 126 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6803 (tt) REVERT: CA 177 ASP cc_start: 0.8157 (p0) cc_final: 0.7902 (p0) REVERT: CB 22 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7662 (tp40) REVERT: CB 121 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8023 (ttp-170) REVERT: CB 264 ARG cc_start: 0.8392 (mtm110) cc_final: 0.8088 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7239 (mp0) REVERT: CE 128 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8522 (mp0) REVERT: CE 134 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7935 (mtt) REVERT: CE 437 ASP cc_start: 0.8362 (t0) cc_final: 0.7978 (t70) REVERT: CI 208 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.9061 (p) REVERT: CI 311 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: CJ 77 LEU cc_start: 0.5699 (mm) cc_final: 0.5494 (tp) REVERT: CM 64 GLN cc_start: 0.8974 (mp10) cc_final: 0.8668 (mm-40) REVERT: CM 69 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9004 (mp) REVERT: CM 94 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5915 (ppp80) REVERT: CM 246 ARG cc_start: 0.6989 (tpt170) cc_final: 0.6719 (tpt170) REVERT: CU 234 GLU cc_start: 0.8119 (mp0) cc_final: 0.7713 (mp0) REVERT: CU 261 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6342 (tp30) REVERT: LC 56 LYS cc_start: 0.6510 (mtmm) cc_final: 0.6223 (ptmm) REVERT: LC 306 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: LE 172 ASN cc_start: 0.8876 (m-40) cc_final: 0.8645 (m-40) REVERT: LG 52 MET cc_start: 0.2937 (OUTLIER) cc_final: -0.0108 (tmt) REVERT: LG 209 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: LG 210 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7935 (p0) REVERT: LL 66 ASN cc_start: 0.8320 (m-40) cc_final: 0.8014 (m-40) REVERT: LL 120 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8466 (mtmt) REVERT: LN 9 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: LO 48 PHE cc_start: 0.8548 (t80) cc_final: 0.8226 (t80) REVERT: LO 62 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5729 (tpt) REVERT: LO 146 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: LO 169 TYR cc_start: 0.9016 (t80) cc_final: 0.8720 (t80) REVERT: LO 172 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8860 (mtm-85) REVERT: LO 196 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8518 (p) REVERT: LS 137 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8016 (ttm-80) REVERT: LT 52 MET cc_start: 0.3889 (ppp) cc_final: 0.2957 (ppp) REVERT: LY 36 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7687 (ttmm) REVERT: LY 114 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7349 (tpt90) REVERT: Le 84 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7926 (mm-30) REVERT: Lh 77 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7721 (t0) REVERT: Cc 188 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8447 (tttp) REVERT: Cc 214 ASP cc_start: 0.8823 (m-30) cc_final: 0.8413 (m-30) REVERT: Cc 219 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7898 (ttm-80) REVERT: Cd 42 GLU cc_start: 0.8163 (tp30) cc_final: 0.7925 (mp0) REVERT: Cd 417 ASP cc_start: 0.7752 (t0) cc_final: 0.7291 (t0) REVERT: Ce 13 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: Ce 155 LYS cc_start: 0.8623 (mttt) cc_final: 0.8365 (mttm) REVERT: Ce 176 GLN cc_start: 0.9066 (mt0) cc_final: 0.8848 (mm-40) outliers start: 194 outliers final: 80 residues processed: 859 average time/residue: 1.6306 time to fit residues: 1856.1072 Evaluate side-chains 776 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 673 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 80 LEU Chi-restraints excluded: chain CA residue 126 LEU Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 134 MET Chi-restraints excluded: chain CE residue 328 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 240 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CJ residue 256 LYS Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 94 ARG Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain CU residue 288 LYS Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 52 MET Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 183 ILE Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 227 GLU Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 104 LEU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 172 ARG Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LP residue 161 GLU Chi-restraints excluded: chain LQ residue 99 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 156 LEU Chi-restraints excluded: chain LS residue 1 MET Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 126 LYS Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 77 ASN Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 260 GLN Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Cd residue 419 VAL Chi-restraints excluded: chain Ce residue 13 GLN Chi-restraints excluded: chain Ce residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 0.5980 chunk 399 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 523 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 chunk 600 optimal weight: 3.9990 chunk 486 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 359 optimal weight: 0.4980 chunk 631 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 246 GLN CA 279 HIS CA 286 GLN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN LF 77 GLN LG 82 GLN ** LM 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 124 GLN LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 42 GLN Cc 152 GLN Cc 212 ASN Cd 20 ASN Cd 65 GLN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 85694 Z= 0.167 Angle : 0.531 16.266 123235 Z= 0.269 Chirality : 0.035 0.357 14877 Planarity : 0.004 0.063 9888 Dihedral : 21.838 179.891 30934 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 4.10 % Allowed : 27.27 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5764 helix: 1.56 (0.10), residues: 2475 sheet: -0.03 (0.20), residues: 691 loop : -0.53 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPCJ 208 HIS 0.008 0.001 HISCM 192 PHE 0.031 0.001 PHELP 47 TYR 0.025 0.001 TYRLO 169 ARG 0.007 0.000 ARGCd 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 716 time to evaluate : 5.114 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: CA 80 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9025 (tt) REVERT: CA 98 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8485 (mtpt) REVERT: CA 270 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: CA 312 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.6071 (ptp-110) REVERT: CB 22 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7583 (tp40) REVERT: CB 121 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7982 (ttp-170) REVERT: CB 265 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7253 (mp0) REVERT: CB 294 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6576 (t80) REVERT: CC 307 LYS cc_start: 0.7713 (tptp) cc_final: 0.7444 (tptp) REVERT: CE 437 ASP cc_start: 0.8379 (t0) cc_final: 0.7981 (t70) REVERT: CI 208 SER cc_start: 0.9425 (OUTLIER) cc_final: 0.9074 (p) REVERT: CI 311 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: CJ 77 LEU cc_start: 0.5806 (mm) cc_final: 0.5560 (tp) REVERT: CM 64 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8734 (mm110) REVERT: CM 69 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9026 (mp) REVERT: CM 94 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.5961 (ppp80) REVERT: CM 246 ARG cc_start: 0.6971 (tpt170) cc_final: 0.6712 (tpt170) REVERT: CU 234 GLU cc_start: 0.8070 (mp0) cc_final: 0.7732 (mp0) REVERT: CU 261 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6359 (tp30) REVERT: LC 25 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7966 (mmpt) REVERT: LC 99 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7615 (ttm110) REVERT: LC 306 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: LE 172 ASN cc_start: 0.8877 (m-40) cc_final: 0.8658 (m-40) REVERT: LF 39 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7862 (ttp-110) REVERT: LF 127 LYS cc_start: 0.7528 (tmtm) cc_final: 0.7257 (tmtt) REVERT: LG 52 MET cc_start: 0.2825 (OUTLIER) cc_final: -0.0000 (tmt) REVERT: LG 209 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: LG 210 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7850 (p0) REVERT: LL 106 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: LL 120 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8416 (mtmt) REVERT: LM 108 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8386 (mtp85) REVERT: LN 9 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: LO 48 PHE cc_start: 0.8523 (t80) cc_final: 0.8181 (t80) REVERT: LO 62 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5701 (tpt) REVERT: LO 146 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: LO 169 TYR cc_start: 0.9073 (t80) cc_final: 0.8849 (t80) REVERT: LO 196 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8719 (p) REVERT: LS 137 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7988 (ttm-80) REVERT: LT 52 MET cc_start: 0.3933 (ppp) cc_final: 0.3061 (ppp) REVERT: LY 36 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7768 (ttmm) REVERT: LY 114 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7273 (tpt90) REVERT: Le 84 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7984 (mm-30) REVERT: Lh 77 ASN cc_start: 0.7978 (m-40) cc_final: 0.7702 (t0) REVERT: Cc 73 GLU cc_start: 0.8298 (tt0) cc_final: 0.8079 (tt0) REVERT: Cc 171 GLU cc_start: 0.8074 (pm20) cc_final: 0.7754 (pt0) REVERT: Cc 188 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8464 (tttp) REVERT: Cc 219 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7919 (ttm-80) REVERT: Cd 417 ASP cc_start: 0.7778 (t0) cc_final: 0.7329 (t0) REVERT: Ce 155 LYS cc_start: 0.8633 (mttt) cc_final: 0.8371 (mttm) outliers start: 206 outliers final: 98 residues processed: 861 average time/residue: 1.6767 time to fit residues: 1925.6547 Evaluate side-chains 785 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 661 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 46 TYR Chi-restraints excluded: chain CA residue 80 LEU Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CA residue 312 ARG Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 141 GLU Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 294 TYR Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 257 ASP Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 333 GLU Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 240 VAL Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CJ residue 175 PHE Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CJ residue 256 LYS Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 94 ARG Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain LC residue 99 ARG Chi-restraints excluded: chain LC residue 109 LYS Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 174 ILE Chi-restraints excluded: chain LG residue 52 MET Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 227 GLU Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 106 GLU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 108 ARG Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 92 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 92 LEU Chi-restraints excluded: chain LQ residue 99 LEU Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 1 MET Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 64 ILE Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 100 VAL Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 126 LYS Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 76 LYS Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 260 GLN Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Ce residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 8.9990 chunk 633 optimal weight: 0.5980 chunk 139 optimal weight: 6.9990 chunk 413 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 704 optimal weight: 9.9990 chunk 584 optimal weight: 0.0270 chunk 326 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 369 optimal weight: 6.9990 overall best weight: 2.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 246 GLN CA 286 GLN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN LC 264 GLN LF 77 GLN LG 82 GLN LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS Cc 152 GLN Cd 20 ASN Cd 65 GLN Cd 233 HIS ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 185 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 85694 Z= 0.287 Angle : 0.590 13.892 123235 Z= 0.299 Chirality : 0.039 0.358 14877 Planarity : 0.005 0.063 9888 Dihedral : 21.848 179.240 30933 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.03 % Rotamer: Outliers : 4.38 % Allowed : 27.65 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 5764 helix: 1.45 (0.10), residues: 2477 sheet: -0.09 (0.19), residues: 692 loop : -0.55 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPLN 120 HIS 0.008 0.001 HISCM 192 PHE 0.034 0.002 PHELP 47 TYR 0.031 0.002 TYRLO 170 ARG 0.010 0.001 ARGCB 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 677 time to evaluate : 5.111 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: CA 80 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9045 (tt) REVERT: CA 98 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: CA 270 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: CA 312 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6007 (ptp-110) REVERT: CB 22 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7650 (tp40) REVERT: CB 121 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8048 (ttp-170) REVERT: CB 138 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8957 (ttpp) REVERT: CB 264 ARG cc_start: 0.8502 (mtm110) cc_final: 0.7937 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7283 (mp0) REVERT: CC 338 MET cc_start: 0.2061 (tpt) cc_final: 0.1802 (tpt) REVERT: CE 128 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: CE 289 ASP cc_start: 0.7610 (t0) cc_final: 0.7310 (t0) REVERT: CE 437 ASP cc_start: 0.8401 (t0) cc_final: 0.8002 (t70) REVERT: CI 208 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.9092 (p) REVERT: CJ 77 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5598 (tp) REVERT: CJ 89 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6852 (mtpp) REVERT: CJ 224 PHE cc_start: 0.6088 (m-80) cc_final: 0.5638 (m-10) REVERT: CJ 227 MET cc_start: 0.6091 (ttt) cc_final: 0.5835 (ttm) REVERT: CM 64 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: CM 69 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9037 (mp) REVERT: CM 94 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6030 (ppp80) REVERT: CM 153 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8311 (mm) REVERT: CU 234 GLU cc_start: 0.8058 (mp0) cc_final: 0.7750 (mp0) REVERT: CU 261 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6111 (tp30) REVERT: LC 99 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7691 (ttm110) REVERT: LC 301 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7361 (ptp90) REVERT: LC 306 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: LE 172 ASN cc_start: 0.8904 (m-40) cc_final: 0.8680 (m-40) REVERT: LF 39 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7905 (ttp-110) REVERT: LG 52 MET cc_start: 0.2784 (pmt) cc_final: -0.0098 (tmt) REVERT: LG 100 TYR cc_start: 0.8773 (m-80) cc_final: 0.8530 (m-80) REVERT: LG 184 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8840 (ttpp) REVERT: LG 209 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: LG 210 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7734 (p0) REVERT: LL 106 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: LL 120 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8423 (mtmt) REVERT: LM 108 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8405 (mtp85) REVERT: LN 9 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: LO 48 PHE cc_start: 0.8612 (t80) cc_final: 0.8278 (t80) REVERT: LO 62 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5770 (tpt) REVERT: LO 146 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: LS 137 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7896 (ttm-80) REVERT: LT 52 MET cc_start: 0.3970 (ppp) cc_final: 0.3117 (ppp) REVERT: LY 114 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7401 (tpt90) REVERT: Le 84 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8008 (mm-30) REVERT: Lh 70 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: Lh 77 ASN cc_start: 0.8028 (m-40) cc_final: 0.7743 (t0) REVERT: Cc 188 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8532 (tttp) REVERT: Cc 219 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7938 (ttm-80) REVERT: Cd 396 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7283 (mtm180) REVERT: Cd 417 ASP cc_start: 0.7814 (t0) cc_final: 0.7514 (t0) outliers start: 220 outliers final: 100 residues processed: 840 average time/residue: 1.6703 time to fit residues: 1848.9227 Evaluate side-chains 794 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 663 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 41 SER Chi-restraints excluded: chain CA residue 80 LEU Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CA residue 312 ARG Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 138 LYS Chi-restraints excluded: chain CB residue 141 GLU Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 128 GLU Chi-restraints excluded: chain CE residue 240 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 381 ASP Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 219 VAL Chi-restraints excluded: chain CI residue 240 VAL Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 77 LEU Chi-restraints excluded: chain CJ residue 89 LYS Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CJ residue 277 ASN Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 94 ARG Chi-restraints excluded: chain CM residue 132 MET Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 12 SER Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 138 GLU Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CR residue 234 LEU Chi-restraints excluded: chain CR residue 235 LEU Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain LC residue 8 THR Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 83 THR Chi-restraints excluded: chain LC residue 99 ARG Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 216 GLU Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 301 ARG Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 80 VAL Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 227 GLU Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 106 GLU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 108 ARG Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 92 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 171 LYS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 89 ASN Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 7 VAL Chi-restraints excluded: chain Lh residue 70 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 76 LYS Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 7 SER Chi-restraints excluded: chain Cc residue 208 VAL Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Cd residue 396 ARG Chi-restraints excluded: chain Ce residue 13 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 401 optimal weight: 0.9990 chunk 514 optimal weight: 0.8980 chunk 398 optimal weight: 2.9990 chunk 592 optimal weight: 1.9990 chunk 393 optimal weight: 0.4980 chunk 701 optimal weight: 5.9990 chunk 439 optimal weight: 1.9990 chunk 427 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 129 GLN CA 246 GLN CA 286 GLN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN LF 77 GLN LG 82 GLN ** LO 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS Cc 152 GLN Cd 20 ASN Cd 65 GLN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 176 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 85694 Z= 0.194 Angle : 0.554 16.786 123235 Z= 0.279 Chirality : 0.036 0.370 14877 Planarity : 0.004 0.062 9888 Dihedral : 21.833 178.054 30932 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.29 % Rotamer: Outliers : 3.52 % Allowed : 28.49 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5764 helix: 1.56 (0.10), residues: 2472 sheet: -0.07 (0.19), residues: 702 loop : -0.51 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLN 120 HIS 0.007 0.001 HISCM 192 PHE 0.031 0.001 PHELP 47 TYR 0.021 0.001 TYRLF 142 ARG 0.008 0.000 ARGCI 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 679 time to evaluate : 5.153 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: CA 98 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8522 (mtpt) REVERT: CA 270 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: CB 22 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7589 (tp40) REVERT: CB 121 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8064 (ttp-170) REVERT: CB 138 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8911 (ttpp) REVERT: CB 264 ARG cc_start: 0.8452 (mtm110) cc_final: 0.7904 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7239 (mp0) REVERT: CE 128 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: CE 289 ASP cc_start: 0.7575 (t0) cc_final: 0.7276 (t0) REVERT: CE 437 ASP cc_start: 0.8408 (t0) cc_final: 0.8005 (t70) REVERT: CI 208 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.9086 (p) REVERT: CI 311 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8951 (pm20) REVERT: CJ 224 PHE cc_start: 0.5973 (m-80) cc_final: 0.5544 (m-10) REVERT: CM 64 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8704 (mm-40) REVERT: CM 69 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9041 (mp) REVERT: CM 94 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5980 (ppp80) REVERT: CM 246 ARG cc_start: 0.6866 (tpt170) cc_final: 0.6661 (tpt170) REVERT: CU 234 GLU cc_start: 0.8036 (mp0) cc_final: 0.7758 (mp0) REVERT: CU 261 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.6033 (tp30) REVERT: LC 99 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7602 (ttm110) REVERT: LC 301 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7171 (ptp90) REVERT: LC 306 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: LE 172 ASN cc_start: 0.8885 (m-40) cc_final: 0.8663 (m-40) REVERT: LF 39 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7730 (ttp-110) REVERT: LG 52 MET cc_start: 0.2788 (pmt) cc_final: -0.0069 (tmt) REVERT: LG 184 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8840 (ttpp) REVERT: LG 209 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: LG 210 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7719 (p0) REVERT: LL 106 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: LL 120 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8454 (mtmt) REVERT: LM 108 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8398 (mtp85) REVERT: LN 9 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: LO 48 PHE cc_start: 0.8601 (t80) cc_final: 0.8287 (t80) REVERT: LO 62 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5423 (tpt) REVERT: LO 146 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: LO 157 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8826 (mpt-90) REVERT: LS 137 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7884 (ttm-80) REVERT: LT 52 MET cc_start: 0.3834 (ppp) cc_final: 0.3020 (ppp) REVERT: LY 114 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7379 (tpt90) REVERT: Lf 56 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7824 (ptm-80) REVERT: Lh 17 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7706 (tmtm) REVERT: Lh 77 ASN cc_start: 0.8013 (m-40) cc_final: 0.7735 (t0) REVERT: Cc 73 GLU cc_start: 0.8308 (tt0) cc_final: 0.8073 (tt0) REVERT: Cc 188 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8530 (tttp) REVERT: Cc 219 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7981 (ttm-80) REVERT: Cd 42 GLU cc_start: 0.8182 (tp30) cc_final: 0.7918 (mp0) REVERT: Cd 94 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7688 (ttp80) REVERT: Cd 396 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7238 (mtm180) REVERT: Cd 417 ASP cc_start: 0.7788 (t0) cc_final: 0.7514 (t0) REVERT: Ce 13 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8049 (tt0) outliers start: 177 outliers final: 98 residues processed: 806 average time/residue: 1.6744 time to fit residues: 1778.6519 Evaluate side-chains 778 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 651 time to evaluate : 4.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 41 SER Chi-restraints excluded: chain CA residue 46 TYR Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 138 LYS Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 233 VAL Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 166 ASN Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 236 LEU Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 128 GLU Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 240 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 381 ASP Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 240 VAL Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CJ residue 175 PHE Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 94 ARG Chi-restraints excluded: chain CM residue 132 MET Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 138 GLU Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain LC residue 8 THR Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 99 ARG Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 301 ARG Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 80 VAL Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 226 LYS Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 227 GLU Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 106 GLU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 108 ARG Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 157 ARG Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 171 LYS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 17 LYS Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 76 LYS Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 7 SER Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 260 GLN Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Cd residue 396 ARG Chi-restraints excluded: chain Ce residue 13 GLN Chi-restraints excluded: chain Ce residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.3980 chunk 280 optimal weight: 6.9990 chunk 419 optimal weight: 0.4980 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 446 optimal weight: 4.9990 chunk 478 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 551 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 246 GLN CA 286 GLN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN ** CM 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN LF 77 GLN LG 82 GLN ** LO 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN LP 37 ASN LP 42 GLN Cc 152 GLN Cd 20 ASN Cd 65 GLN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 176 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 85694 Z= 0.165 Angle : 0.540 15.899 123235 Z= 0.272 Chirality : 0.035 0.372 14877 Planarity : 0.004 0.061 9888 Dihedral : 21.800 179.275 30932 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 3.26 % Allowed : 29.11 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 5764 helix: 1.64 (0.10), residues: 2475 sheet: -0.03 (0.20), residues: 698 loop : -0.44 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCJ 208 HIS 0.007 0.001 HISCM 192 PHE 0.041 0.001 PHELP 47 TYR 0.023 0.001 TYRLF 142 ARG 0.008 0.000 ARGCA 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 684 time to evaluate : 5.046 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: CA 98 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8506 (mtpt) REVERT: CA 152 LEU cc_start: 0.8146 (mt) cc_final: 0.7898 (mt) REVERT: CA 177 ASP cc_start: 0.8288 (p0) cc_final: 0.8085 (p0) REVERT: CA 270 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: CB 22 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7577 (tp40) REVERT: CB 121 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8214 (ttm170) REVERT: CB 264 ARG cc_start: 0.8453 (mtm110) cc_final: 0.7927 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7246 (mp0) REVERT: CE 128 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: CE 289 ASP cc_start: 0.7601 (t0) cc_final: 0.7301 (t0) REVERT: CE 437 ASP cc_start: 0.8367 (t0) cc_final: 0.7984 (t70) REVERT: CE 533 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8911 (p) REVERT: CI 208 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.9086 (p) REVERT: CI 322 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8341 (mp0) REVERT: CJ 89 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6851 (mtpp) REVERT: CM 64 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8701 (mm-40) REVERT: CM 69 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9035 (mp) REVERT: CU 234 GLU cc_start: 0.8002 (mp0) cc_final: 0.7740 (mp0) REVERT: CU 261 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.6006 (tp30) REVERT: LC 99 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7565 (ttm110) REVERT: LC 306 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: LE 172 ASN cc_start: 0.8888 (m-40) cc_final: 0.8649 (m-40) REVERT: LF 39 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7723 (ttm110) REVERT: LG 52 MET cc_start: 0.2624 (pmt) cc_final: 0.0179 (tmt) REVERT: LG 184 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8830 (ttpp) REVERT: LG 209 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: LG 210 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7725 (p0) REVERT: LL 106 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: LL 120 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8464 (mtmt) REVERT: LM 42 ASP cc_start: 0.8671 (t0) cc_final: 0.8468 (t0) REVERT: LM 108 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8406 (mtp85) REVERT: LN 9 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: LO 48 PHE cc_start: 0.8630 (t80) cc_final: 0.8343 (t80) REVERT: LO 62 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5437 (tpt) REVERT: LO 146 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: LP 3 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7804 (ttp80) REVERT: LP 55 LYS cc_start: 0.8575 (mppt) cc_final: 0.8349 (mppt) REVERT: LS 137 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7910 (ttm-80) REVERT: LT 52 MET cc_start: 0.3822 (ppp) cc_final: 0.3021 (ppp) REVERT: LY 36 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7737 (ttmm) REVERT: LY 114 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7346 (tpt90) REVERT: Lh 77 ASN cc_start: 0.7991 (m-40) cc_final: 0.7725 (t0) REVERT: Lh 100 GLU cc_start: 0.7646 (tt0) cc_final: 0.7364 (tt0) REVERT: Cc 73 GLU cc_start: 0.8313 (tt0) cc_final: 0.8069 (tt0) REVERT: Cc 171 GLU cc_start: 0.8004 (pm20) cc_final: 0.7731 (pt0) REVERT: Cc 188 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8535 (tttp) REVERT: Cc 214 ASP cc_start: 0.8793 (m-30) cc_final: 0.8467 (m-30) REVERT: Cc 219 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7901 (ttm-80) REVERT: Cd 42 GLU cc_start: 0.8211 (tp30) cc_final: 0.7936 (mp0) REVERT: Cd 93 LYS cc_start: 0.7859 (tppp) cc_final: 0.7633 (mmpt) REVERT: Cd 417 ASP cc_start: 0.7751 (t0) cc_final: 0.7530 (t0) REVERT: Ce 13 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7970 (tt0) outliers start: 164 outliers final: 101 residues processed: 802 average time/residue: 1.7041 time to fit residues: 1820.1236 Evaluate side-chains 777 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 652 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 41 SER Chi-restraints excluded: chain CA residue 46 TYR Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 65 THR Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 233 VAL Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 236 LEU Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 128 GLU Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 271 GLU Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 381 ASP Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CJ residue 89 LYS Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CJ residue 175 PHE Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 12 SER Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 128 SER Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 230 ILE Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 83 THR Chi-restraints excluded: chain LC residue 99 ARG Chi-restraints excluded: chain LC residue 109 LYS Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 273 LYS Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 80 VAL Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 70 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 227 GLU Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 106 GLU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 108 ARG Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 157 ARG Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 92 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LQ residue 99 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 171 LYS Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 109 ASP Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Le residue 131 VAL Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 7 VAL Chi-restraints excluded: chain Lh residue 53 ARG Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 176 THR Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Ce residue 13 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 0.9990 chunk 672 optimal weight: 8.9990 chunk 613 optimal weight: 0.0980 chunk 653 optimal weight: 2.9990 chunk 393 optimal weight: 0.0980 chunk 284 optimal weight: 0.9980 chunk 513 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 590 optimal weight: 3.9990 chunk 618 optimal weight: 0.7980 chunk 651 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 129 GLN CA 246 GLN CA 286 GLN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN LF 77 GLN LG 82 GLN LL 13 HIS ** LO 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS Li 42 GLN Cd 20 ASN Cd 65 GLN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 176 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 85694 Z= 0.141 Angle : 0.535 17.714 123235 Z= 0.269 Chirality : 0.034 0.396 14877 Planarity : 0.004 0.061 9888 Dihedral : 21.780 177.576 30932 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 29.60 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 5764 helix: 1.71 (0.10), residues: 2471 sheet: -0.01 (0.19), residues: 707 loop : -0.42 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLS 78 HIS 0.007 0.001 HISCM 192 PHE 0.044 0.001 PHELP 47 TYR 0.023 0.001 TYRLF 142 ARG 0.009 0.000 ARGCI 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 655 time to evaluate : 4.996 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: CA 98 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8484 (mtpt) REVERT: CA 152 LEU cc_start: 0.8099 (mt) cc_final: 0.7846 (mt) REVERT: CA 270 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: CB 22 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7588 (tp40) REVERT: CB 121 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8235 (ttm170) REVERT: CB 264 ARG cc_start: 0.8467 (mtm110) cc_final: 0.8030 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7283 (mp0) REVERT: CC 299 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6499 (mtp180) REVERT: CE 128 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: CE 280 GLN cc_start: 0.8504 (mt0) cc_final: 0.8290 (mt0) REVERT: CE 437 ASP cc_start: 0.8346 (t0) cc_final: 0.7954 (t70) REVERT: CE 533 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8884 (p) REVERT: CI 208 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9079 (p) REVERT: CM 64 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8711 (mm-40) REVERT: CM 69 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9032 (mp) REVERT: CR 21 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6912 (m-40) REVERT: CU 261 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.6035 (tp30) REVERT: CU 275 MET cc_start: 0.5229 (tpp) cc_final: 0.3908 (ttp) REVERT: LC 99 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7531 (ttm110) REVERT: LC 306 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: LE 172 ASN cc_start: 0.8855 (m-40) cc_final: 0.8626 (m-40) REVERT: LF 39 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7711 (ttm110) REVERT: LG 52 MET cc_start: 0.2659 (OUTLIER) cc_final: 0.0154 (tmt) REVERT: LG 184 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8818 (ttpp) REVERT: LG 209 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: LG 210 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7893 (p0) REVERT: LL 106 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: LL 120 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8463 (mtmt) REVERT: LM 108 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8443 (mtp85) REVERT: LN 9 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: LO 48 PHE cc_start: 0.8631 (t80) cc_final: 0.8233 (t80) REVERT: LO 62 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5395 (tpt) REVERT: LO 146 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: LO 169 TYR cc_start: 0.9089 (t80) cc_final: 0.8808 (t80) REVERT: LP 3 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7814 (ttp80) REVERT: LS 137 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: LT 52 MET cc_start: 0.3760 (ppp) cc_final: 0.2987 (ppp) REVERT: LT 91 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7703 (m) REVERT: LY 36 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7741 (ttmm) REVERT: LY 114 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7286 (tpt90) REVERT: Lh 77 ASN cc_start: 0.8036 (m-40) cc_final: 0.7769 (t0) REVERT: Lh 100 GLU cc_start: 0.7629 (tt0) cc_final: 0.7347 (tt0) REVERT: Cc 73 GLU cc_start: 0.8310 (tt0) cc_final: 0.8072 (tt0) REVERT: Cc 171 GLU cc_start: 0.7994 (pm20) cc_final: 0.7736 (pt0) REVERT: Cc 188 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8532 (tttp) REVERT: Cc 219 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7844 (ttm-80) REVERT: Cd 42 GLU cc_start: 0.8173 (tp30) cc_final: 0.7906 (mp0) REVERT: Cd 93 LYS cc_start: 0.7815 (tppp) cc_final: 0.7579 (mmpt) REVERT: Ce 13 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: Ce 135 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7648 (mm-30) outliers start: 149 outliers final: 88 residues processed: 765 average time/residue: 1.6920 time to fit residues: 1710.3778 Evaluate side-chains 756 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 640 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 46 TYR Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 233 VAL Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 186 ILE Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CC residue 299 ARG Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 128 GLU Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 240 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 381 ASP Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CJ residue 175 PHE Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 12 SER Chi-restraints excluded: chain CR residue 21 ASN Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 138 GLU Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 230 ILE Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain CU residue 277 ARG Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 99 ARG Chi-restraints excluded: chain LC residue 109 LYS Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 273 LYS Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 80 VAL Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 52 MET Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 106 GLU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 108 ARG Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 92 ILE Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LP residue 161 GLU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 171 LYS Chi-restraints excluded: chain LS residue 13 HIS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 91 VAL Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 7 VAL Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 176 THR Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Ce residue 13 GLN Chi-restraints excluded: chain Ce residue 83 LEU Chi-restraints excluded: chain Ce residue 135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 2.9990 chunk 691 optimal weight: 5.9990 chunk 422 optimal weight: 0.1980 chunk 328 optimal weight: 0.0770 chunk 480 optimal weight: 0.7980 chunk 725 optimal weight: 3.9990 chunk 667 optimal weight: 7.9990 chunk 577 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 446 optimal weight: 6.9990 chunk 354 optimal weight: 4.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 246 GLN CA 286 GLN CC 144 ASN CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN CR 136 GLN LF 77 GLN LG 82 GLN ** LO 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN LP 37 ASN LP 42 GLN Li 42 GLN Cd 20 ASN Cd 65 GLN ** Ce 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 85694 Z= 0.225 Angle : 0.571 18.159 123235 Z= 0.286 Chirality : 0.037 0.428 14877 Planarity : 0.005 0.074 9888 Dihedral : 21.765 179.380 30932 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.87 % Favored : 96.11 % Rotamer: Outliers : 2.81 % Allowed : 29.82 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5764 helix: 1.61 (0.10), residues: 2475 sheet: -0.03 (0.19), residues: 703 loop : -0.43 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPCI 285 HIS 0.006 0.001 HISCM 192 PHE 0.039 0.002 PHELP 47 TYR 0.025 0.001 TYRLF 142 ARG 0.010 0.000 ARGCI 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11528 Ramachandran restraints generated. 5764 Oldfield, 0 Emsley, 5764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 633 time to evaluate : 5.453 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: CA 98 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8537 (mtpt) REVERT: CA 270 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: CB 22 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7609 (tp40) REVERT: CB 121 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: CB 138 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8951 (ttpp) REVERT: CB 264 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8026 (ttp-110) REVERT: CB 265 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7350 (mp0) REVERT: CC 299 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6493 (mtp180) REVERT: CE 128 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: CE 289 ASP cc_start: 0.7620 (t0) cc_final: 0.7323 (t0) REVERT: CE 437 ASP cc_start: 0.8369 (t0) cc_final: 0.7963 (t70) REVERT: CI 208 SER cc_start: 0.9445 (OUTLIER) cc_final: 0.9092 (p) REVERT: CI 322 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8303 (mp0) REVERT: CM 64 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8695 (mm-40) REVERT: CM 69 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9028 (mp) REVERT: CM 153 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (mm) REVERT: CR 21 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6912 (m-40) REVERT: CU 275 MET cc_start: 0.5461 (tpp) cc_final: 0.4587 (tpp) REVERT: LC 99 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7620 (ttm110) REVERT: LC 306 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: LE 172 ASN cc_start: 0.8916 (m-40) cc_final: 0.8699 (m-40) REVERT: LF 39 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7730 (ttm110) REVERT: LG 52 MET cc_start: 0.2620 (pmt) cc_final: 0.0127 (tmt) REVERT: LG 109 LYS cc_start: 0.8585 (mtpp) cc_final: 0.7903 (mttp) REVERT: LG 184 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8844 (ttpp) REVERT: LG 209 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: LG 210 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7860 (p0) REVERT: LL 106 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: LL 120 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8438 (mtmt) REVERT: LM 108 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8397 (mtp85) REVERT: LN 9 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: LO 48 PHE cc_start: 0.8653 (t80) cc_final: 0.8248 (t80) REVERT: LO 62 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.5428 (tpt) REVERT: LO 146 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: LO 169 TYR cc_start: 0.9114 (t80) cc_final: 0.8823 (t80) REVERT: LS 137 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7920 (ttm-80) REVERT: LT 52 MET cc_start: 0.3848 (ppp) cc_final: 0.3068 (ppp) REVERT: LT 91 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7674 (m) REVERT: LY 82 GLU cc_start: 0.8289 (tt0) cc_final: 0.7884 (pt0) REVERT: LY 101 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8985 (p) REVERT: LY 114 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7389 (tpt90) REVERT: Lh 17 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7737 (tmtm) REVERT: Lh 77 ASN cc_start: 0.8004 (m-40) cc_final: 0.7725 (t0) REVERT: Lh 100 GLU cc_start: 0.7686 (tt0) cc_final: 0.7403 (tt0) REVERT: Cc 171 GLU cc_start: 0.8016 (pm20) cc_final: 0.7753 (pt0) REVERT: Cc 188 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8541 (tttp) REVERT: Cc 219 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7786 (ttm-80) REVERT: Cd 93 LYS cc_start: 0.7861 (tppp) cc_final: 0.7629 (mmpt) REVERT: Ce 13 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: Ce 135 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7542 (mm-30) outliers start: 141 outliers final: 88 residues processed: 736 average time/residue: 1.7230 time to fit residues: 1667.8193 Evaluate side-chains 729 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 612 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 98 LYS Chi-restraints excluded: chain CA residue 186 ASP Chi-restraints excluded: chain CA residue 239 VAL Chi-restraints excluded: chain CA residue 270 GLU Chi-restraints excluded: chain CA residue 290 LEU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 121 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 138 LYS Chi-restraints excluded: chain CB residue 163 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 233 VAL Chi-restraints excluded: chain CC residue 135 ARG Chi-restraints excluded: chain CC residue 152 ASP Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 186 ILE Chi-restraints excluded: chain CC residue 268 LYS Chi-restraints excluded: chain CC residue 280 ARG Chi-restraints excluded: chain CC residue 299 ARG Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 128 GLU Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 240 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 381 ASP Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 526 SER Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CI residue 208 SER Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CJ residue 144 CYS Chi-restraints excluded: chain CJ residue 175 PHE Chi-restraints excluded: chain CJ residue 213 LYS Chi-restraints excluded: chain CM residue 64 GLN Chi-restraints excluded: chain CM residue 69 ILE Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 153 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 163 ASN Chi-restraints excluded: chain CM residue 241 ILE Chi-restraints excluded: chain CR residue 12 SER Chi-restraints excluded: chain CR residue 21 ASN Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 38 SER Chi-restraints excluded: chain CR residue 138 GLU Chi-restraints excluded: chain CR residue 211 ARG Chi-restraints excluded: chain CU residue 210 LYS Chi-restraints excluded: chain CU residue 226 THR Chi-restraints excluded: chain CU residue 230 ILE Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 276 VAL Chi-restraints excluded: chain CU residue 277 ARG Chi-restraints excluded: chain LC residue 54 SER Chi-restraints excluded: chain LC residue 99 ARG Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 306 GLU Chi-restraints excluded: chain LC residue 335 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 80 VAL Chi-restraints excluded: chain LF residue 98 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 209 GLU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 229 VAL Chi-restraints excluded: chain LL residue 106 GLU Chi-restraints excluded: chain LL residue 120 LYS Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 108 ARG Chi-restraints excluded: chain LN residue 9 GLU Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 166 SER Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 6 SER Chi-restraints excluded: chain LO residue 62 MET Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 116 LYS Chi-restraints excluded: chain LO residue 128 VAL Chi-restraints excluded: chain LO residue 146 GLU Chi-restraints excluded: chain LO residue 154 VAL Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 116 HIS Chi-restraints excluded: chain LP residue 161 GLU Chi-restraints excluded: chain LQ residue 92 LEU Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 171 LYS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 137 ARG Chi-restraints excluded: chain LS residue 159 ILE Chi-restraints excluded: chain LT residue 91 VAL Chi-restraints excluded: chain LT residue 114 GLU Chi-restraints excluded: chain LY residue 101 SER Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Le residue 103 SER Chi-restraints excluded: chain Lf residue 7 HIS Chi-restraints excluded: chain Lh residue 7 VAL Chi-restraints excluded: chain Lh residue 17 LYS Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 79 ARG Chi-restraints excluded: chain Cc residue 7 SER Chi-restraints excluded: chain Cd residue 226 THR Chi-restraints excluded: chain Cd residue 327 SER Chi-restraints excluded: chain Ce residue 13 GLN Chi-restraints excluded: chain Ce residue 83 LEU Chi-restraints excluded: chain Ce residue 135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 0.7980 chunk 615 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 532 optimal weight: 7.9990 chunk 85 optimal weight: 50.0000 chunk 160 optimal weight: 6.9990 chunk 578 optimal weight: 50.0000 chunk 242 optimal weight: 0.9980 chunk 593 optimal weight: 2.9990 chunk 73 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 34 GLN CA 246 GLN CA 286 GLN ** CB 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 166 ASN CC 286 ASN ** CE 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 280 GLN ** CM 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 133 GLN LF 77 GLN ** LG 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 82 GLN ** LO 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN LP 37 ASN LP 42 GLN LS 122 HIS Cd 20 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.169995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129046 restraints weight = 95378.473| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.92 r_work: 0.2884 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 85694 Z= 0.367 Angle : 0.649 18.106 123235 Z= 0.327 Chirality : 0.042 0.428 14877 Planarity : 0.006 0.086 9888 Dihedral : 21.853 178.012 30932 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.98 % Rotamer: Outliers : 2.85 % Allowed : 29.76 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5764 helix: 1.41 (0.10), residues: 2468 sheet: -0.09 (0.19), residues: 704 loop : -0.52 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPCI 285 HIS 0.010 0.001 HISLh 115 PHE 0.052 0.002 PHELP 47 TYR 0.032 0.002 TYRLF 142 ARG 0.009 0.001 ARGCI 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25663.55 seconds wall clock time: 448 minutes 2.88 seconds (26882.88 seconds total)