Starting phenix.real_space_refine on Sun Aug 24 17:36:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un0_42389/08_2025/8un0_42389_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un0_42389/08_2025/8un0_42389.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 { model { file = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2025/8un0_42389_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2025/8un0_42389_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2025/8un0_42389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2025/8un0_42389.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.068 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 P 61 5.49 5 Mg 4 5.21 5 S 138 5.16 5 C 13599 2.51 5 N 3772 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4319 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 512} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.22 Number of scatterers: 21860 At special positions: 0 Unit cell: (115.092, 129.168, 136.62, 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) S 138 16.00 P 61 15.00 Mg 4 11.99 O 4286 8.00 N 3772 7.00 C 13599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 841.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 17 sheets defined 50.9% alpha, 13.9% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.801A pdb=" N GLU A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.889A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.526A pdb=" N LEU A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.695A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.728A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 627 through 643 removed outlier: 4.070A pdb=" N GLY A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 666 through 689 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.796A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 695 " --> pdb=" O PHE A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 695' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.523A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 743 removed outlier: 3.616A pdb=" N GLY A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.664A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 762 through 770 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.524A pdb=" N TYR A 799 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.641A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.717A pdb=" N ARG B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.763A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.734A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 removed outlier: 4.015A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 removed outlier: 3.761A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.567A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.604A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.596A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.517A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.612A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.527A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.145A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.825A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.645A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.721A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.516A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.858A pdb=" N GLU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.764A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.698A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.582A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.540A pdb=" N GLN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.962A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.780A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.664A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 66 " --> pdb=" O GLY E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 66' Processing helix chain 'E' and resid 97 through 102 removed outlier: 6.870A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.719A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 149 removed outlier: 3.788A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.717A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.710A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.687A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.645A pdb=" N VAL E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.573A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.191A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 17 removed outlier: 4.370A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 removed outlier: 3.845A pdb=" N LYS F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.502A pdb=" N ARG F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 removed outlier: 4.360A pdb=" N PHE F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 17 Processing helix chain 'G' and resid 72 through 76 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.667A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 removed outlier: 3.866A pdb=" N PHE G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 11 through 16 removed outlier: 3.561A pdb=" N LEU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 21 removed outlier: 4.405A pdb=" N ASP H 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.898A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 removed outlier: 3.614A pdb=" N LEU H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 154 No H-bonds generated for 'chain 'H' and resid 152 through 154' Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.669A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 removed outlier: 3.516A pdb=" N VAL A 178 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 398 removed outlier: 5.930A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ALA A 370 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 removed outlier: 3.528A pdb=" N ILE A 814 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.038A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.455A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.832A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.121A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 221 through 222 removed outlier: 7.306A pdb=" N LYS D 221 " --> pdb=" O ILE D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.145A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 60 through 61 removed outlier: 3.675A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS G 162 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.837A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 237 " --> pdb=" O TYR F 249 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS F 138 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 177 through 181 removed outlier: 3.829A pdb=" N PHE F 169 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 61 through 62 removed outlier: 3.560A pdb=" N ILE G 88 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.589A pdb=" N LEU G 66 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 237 " --> pdb=" O TYR G 249 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.663A pdb=" N ARG H 61 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU H 3 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 4 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 67 through 70 removed outlier: 6.106A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS H 138 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.596A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2964 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7241 1.36 - 1.51: 5708 1.51 - 1.65: 9152 1.65 - 1.80: 99 1.80 - 1.95: 109 Bond restraints: 22309 Sorted by residual: bond pdb=" CA SER G 42 " pdb=" CB SER G 42 " ideal model delta sigma weight residual 1.529 1.457 0.073 1.63e-02 3.76e+03 1.99e+01 bond pdb=" N ASN B 272 " pdb=" CA ASN B 272 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.79e+00 bond pdb=" N MET G 75 " pdb=" CA MET G 75 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.26e-02 6.30e+03 9.35e+00 bond pdb=" N THR G 185 " pdb=" CA THR G 185 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.15e-02 7.56e+03 7.83e+00 bond pdb=" N ASN B 118 " pdb=" CA ASN B 118 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.37e-02 5.33e+03 7.68e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 29827 2.53 - 5.06: 478 5.06 - 7.59: 72 7.59 - 10.12: 20 10.12 - 12.65: 1 Bond angle restraints: 30398 Sorted by residual: angle pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" CD PRO A 535 " ideal model delta sigma weight residual 112.00 105.26 6.74 1.40e+00 5.10e-01 2.32e+01 angle pdb=" CA GLN E 119 " pdb=" CB GLN E 119 " pdb=" CG GLN E 119 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN A 363 " pdb=" CB GLN A 363 " pdb=" CG GLN A 363 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" C SER G 183 " pdb=" N GLN G 184 " pdb=" CA GLN G 184 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" C PHE A 299 " ideal model delta sigma weight residual 110.97 106.19 4.78 1.09e+00 8.42e-01 1.93e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.73: 12380 26.73 - 53.45: 1106 53.45 - 80.18: 136 80.18 - 106.90: 11 106.90 - 133.62: 2 Dihedral angle restraints: 13635 sinusoidal: 5895 harmonic: 7740 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 166.38 133.62 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" CA SER H 183 " pdb=" C SER H 183 " pdb=" N GLN H 184 " pdb=" CA GLN H 184 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLU G 109 " pdb=" C GLU G 109 " pdb=" N LYS G 110 " pdb=" CA LYS G 110 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3335 0.100 - 0.199: 194 0.199 - 0.299: 6 0.299 - 0.398: 0 0.398 - 0.498: 1 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE A 549 " pdb=" CA ILE A 549 " pdb=" CG1 ILE A 549 " pdb=" CG2 ILE A 549 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" CA LEU E 93 " pdb=" N LEU E 93 " pdb=" C LEU E 93 " pdb=" CB LEU E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE F 241 " pdb=" CA ILE F 241 " pdb=" CG1 ILE F 241 " pdb=" CG2 ILE F 241 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 198 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C GLU H 198 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU H 198 " 0.030 2.00e-02 2.50e+03 pdb=" N MET H 199 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 699 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO E 174 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.053 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 246 2.63 - 3.20: 17537 3.20 - 3.77: 34765 3.77 - 4.33: 46848 4.33 - 4.90: 77869 Nonbonded interactions: 177265 Sorted by model distance: nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.069 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.070 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR A 381 " pdb="MG MG A1201 " model vdw 2.075 2.170 ... (remaining 177260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.004 0.083 22309 Z= 0.224 Angle : 0.803 12.645 30398 Z= 0.452 Chirality : 0.048 0.498 3536 Planarity : 0.007 0.108 3723 Dihedral : 18.780 133.625 8597 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 0.56 % Allowed : 23.90 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.14), residues: 2623 helix: -1.49 (0.12), residues: 1195 sheet: -0.64 (0.22), residues: 519 loop : -1.03 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 61 TYR 0.016 0.002 TYR B 279 PHE 0.017 0.002 PHE G 169 TRP 0.062 0.002 TRP F 28 HIS 0.010 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00422 (22309) covalent geometry : angle 0.80271 (30398) hydrogen bonds : bond 0.18909 ( 1071) hydrogen bonds : angle 6.95054 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 322 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 345 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7975 (mppt) REVERT: F 149 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7444 (mmm-85) REVERT: H 117 LYS cc_start: 0.5768 (tptp) cc_final: 0.5456 (tptm) REVERT: H 199 MET cc_start: 0.3090 (mtm) cc_final: 0.2697 (mtp) outliers start: 13 outliers final: 1 residues processed: 329 average time/residue: 0.5812 time to fit residues: 219.6025 Evaluate side-chains 267 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 493 GLN A 573 GLN A 582 GLN A 595 GLN C 37 HIS C 241 HIS C 317 ASN D 308 ASN F 71 ASN G 246 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128914 restraints weight = 28684.946| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.11 r_work: 0.3355 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22309 Z= 0.246 Angle : 0.663 8.545 30398 Z= 0.343 Chirality : 0.044 0.194 3536 Planarity : 0.005 0.082 3723 Dihedral : 14.413 138.948 3454 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.33 % Allowed : 23.25 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.16), residues: 2623 helix: 0.00 (0.14), residues: 1221 sheet: -0.55 (0.23), residues: 506 loop : -0.71 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 52 TYR 0.021 0.002 TYR F 250 PHE 0.018 0.002 PHE A 632 TRP 0.020 0.002 TRP F 28 HIS 0.008 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00580 (22309) covalent geometry : angle 0.66333 (30398) hydrogen bonds : bond 0.04301 ( 1071) hydrogen bonds : angle 4.79186 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 274 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: D 95 LEU cc_start: 0.8927 (mt) cc_final: 0.8690 (mp) REVERT: E 65 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: E 194 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8256 (t-90) REVERT: E 269 GLN cc_start: 0.8185 (pm20) cc_final: 0.7940 (pm20) REVERT: F 68 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8699 (mmt) REVERT: F 88 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (mp) REVERT: G 49 GLN cc_start: 0.8099 (tt0) cc_final: 0.7830 (tm-30) REVERT: G 175 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6824 (mt) REVERT: H 1 MET cc_start: 0.4357 (ppp) cc_final: 0.4144 (tmt) REVERT: H 117 LYS cc_start: 0.5318 (tptp) cc_final: 0.4672 (mmmm) REVERT: H 254 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6366 (mmmt) outliers start: 100 outliers final: 42 residues processed: 339 average time/residue: 0.5737 time to fit residues: 222.7817 Evaluate side-chains 288 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS A 582 GLN B 182 GLN B 269 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130827 restraints weight = 28804.039| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.53 r_work: 0.3368 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22309 Z= 0.133 Angle : 0.559 8.487 30398 Z= 0.288 Chirality : 0.040 0.223 3536 Planarity : 0.004 0.075 3723 Dihedral : 14.207 138.232 3453 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.64 % Allowed : 24.42 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2623 helix: 0.62 (0.15), residues: 1235 sheet: -0.55 (0.22), residues: 511 loop : -0.48 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 210 TYR 0.015 0.001 TYR H 239 PHE 0.013 0.001 PHE A 558 TRP 0.013 0.001 TRP F 28 HIS 0.009 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00308 (22309) covalent geometry : angle 0.55862 (30398) hydrogen bonds : bond 0.03454 ( 1071) hydrogen bonds : angle 4.44207 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 275 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7847 (t80) cc_final: 0.6841 (t80) REVERT: A 306 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7927 (mttt) REVERT: A 592 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6354 (mm-30) REVERT: A 757 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7481 (tp) REVERT: A 804 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7449 (ptm160) REVERT: C 257 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: E 345 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7826 (mppt) REVERT: F 199 MET cc_start: 0.5350 (ppp) cc_final: 0.4355 (pp-130) REVERT: G 20 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8109 (tptt) REVERT: G 72 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7023 (tt) REVERT: G 88 ILE cc_start: 0.7994 (mm) cc_final: 0.7755 (mm) REVERT: H 117 LYS cc_start: 0.5075 (tptp) cc_final: 0.4584 (mmmm) REVERT: H 212 LEU cc_start: 0.8673 (mt) cc_final: 0.8324 (tm) REVERT: H 254 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6356 (mmmt) outliers start: 84 outliers final: 35 residues processed: 334 average time/residue: 0.5160 time to fit residues: 197.8882 Evaluate side-chains 279 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 3.9990 chunk 246 optimal weight: 0.0770 chunk 136 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 3 optimal weight: 0.0170 chunk 172 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS D 219 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.177031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133527 restraints weight = 28675.714| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.03 r_work: 0.3402 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22309 Z= 0.115 Angle : 0.533 7.937 30398 Z= 0.275 Chirality : 0.039 0.211 3536 Planarity : 0.004 0.072 3723 Dihedral : 14.051 139.171 3453 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.03 % Allowed : 25.19 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2623 helix: 0.99 (0.15), residues: 1231 sheet: -0.46 (0.22), residues: 507 loop : -0.34 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 210 TYR 0.014 0.001 TYR H 239 PHE 0.021 0.001 PHE G 2 TRP 0.012 0.001 TRP F 28 HIS 0.009 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00260 (22309) covalent geometry : angle 0.53342 (30398) hydrogen bonds : bond 0.03086 ( 1071) hydrogen bonds : angle 4.21853 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 265 time to evaluate : 0.833 Fit side-chains REVERT: A 592 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6297 (mm-30) REVERT: A 757 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7339 (tp) REVERT: A 804 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7584 (ptm160) REVERT: B 298 ASN cc_start: 0.8529 (m110) cc_final: 0.8324 (m-40) REVERT: E 65 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: E 112 LEU cc_start: 0.8320 (mm) cc_final: 0.8050 (mt) REVERT: E 345 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7820 (mppt) REVERT: F 199 MET cc_start: 0.5533 (ppp) cc_final: 0.4509 (pp-130) REVERT: G 20 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8107 (tptt) REVERT: G 53 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6638 (mmt-90) REVERT: G 61 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7897 (ppp80) REVERT: G 72 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7247 (tt) REVERT: G 88 ILE cc_start: 0.8009 (mm) cc_final: 0.7780 (mm) REVERT: G 116 MET cc_start: 0.7631 (mmm) cc_final: 0.7372 (tpp) REVERT: H 117 LYS cc_start: 0.5199 (tptp) cc_final: 0.4597 (mmmm) REVERT: H 139 MET cc_start: 0.3863 (mmp) cc_final: 0.3227 (ppp) REVERT: H 212 LEU cc_start: 0.8673 (mt) cc_final: 0.8325 (tm) REVERT: H 254 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6247 (mmmt) outliers start: 93 outliers final: 42 residues processed: 336 average time/residue: 0.5264 time to fit residues: 203.1534 Evaluate side-chains 295 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 238 optimal weight: 50.0000 chunk 29 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 197 optimal weight: 0.0270 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 71 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134024 restraints weight = 28585.982| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.05 r_work: 0.3422 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22309 Z= 0.109 Angle : 0.533 8.250 30398 Z= 0.273 Chirality : 0.039 0.179 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.949 139.778 3453 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.64 % Allowed : 26.80 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2623 helix: 1.21 (0.15), residues: 1235 sheet: -0.45 (0.22), residues: 510 loop : -0.26 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 210 TYR 0.015 0.001 TYR E 343 PHE 0.024 0.001 PHE G 2 TRP 0.011 0.001 TRP F 28 HIS 0.007 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00249 (22309) covalent geometry : angle 0.53344 (30398) hydrogen bonds : bond 0.02889 ( 1071) hydrogen bonds : angle 4.08666 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 267 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 592 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6292 (mm-30) REVERT: A 804 ARG cc_start: 0.7805 (ptm160) cc_final: 0.7584 (ptm160) REVERT: E 65 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: E 345 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7806 (mppt) REVERT: F 199 MET cc_start: 0.5546 (ppp) cc_final: 0.4543 (pp-130) REVERT: G 53 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6555 (mmt-90) REVERT: G 72 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7143 (tt) REVERT: G 116 MET cc_start: 0.7673 (mmm) cc_final: 0.7379 (tpp) REVERT: H 117 LYS cc_start: 0.4960 (tptp) cc_final: 0.4414 (mmmm) REVERT: H 212 LEU cc_start: 0.8655 (mt) cc_final: 0.8285 (tm) outliers start: 84 outliers final: 46 residues processed: 331 average time/residue: 0.5441 time to fit residues: 206.6549 Evaluate side-chains 293 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 0.0970 chunk 254 optimal weight: 8.9990 chunk 239 optimal weight: 30.0000 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 166 optimal weight: 0.0170 chunk 148 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS D 219 ASN E 22 GLN F 246 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.173870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128786 restraints weight = 28667.101| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.58 r_work: 0.3364 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22309 Z= 0.191 Angle : 0.590 8.356 30398 Z= 0.301 Chirality : 0.042 0.180 3536 Planarity : 0.004 0.070 3723 Dihedral : 14.031 141.764 3453 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.46 % Allowed : 26.80 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2623 helix: 1.14 (0.15), residues: 1235 sheet: -0.47 (0.22), residues: 516 loop : -0.27 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 52 TYR 0.014 0.001 TYR H 239 PHE 0.026 0.001 PHE G 2 TRP 0.009 0.001 TRP F 28 HIS 0.005 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00459 (22309) covalent geometry : angle 0.59031 (30398) hydrogen bonds : bond 0.03357 ( 1071) hydrogen bonds : angle 4.16231 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 252 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8006 (mttt) REVERT: A 500 GLN cc_start: 0.6452 (mp10) cc_final: 0.6232 (mp10) REVERT: A 757 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 804 ARG cc_start: 0.7736 (ptm160) cc_final: 0.7522 (ptm160) REVERT: C 320 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8243 (mm) REVERT: E 65 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: G 20 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8179 (tptt) REVERT: G 53 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6625 (mmt-90) REVERT: G 72 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7112 (tt) REVERT: H 117 LYS cc_start: 0.4997 (tptp) cc_final: 0.4466 (mmmm) outliers start: 103 outliers final: 51 residues processed: 333 average time/residue: 0.4938 time to fit residues: 189.2693 Evaluate side-chains 294 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 237 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 221 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 161 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 255 optimal weight: 0.1980 chunk 134 optimal weight: 6.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.175654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130626 restraints weight = 28543.181| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.17 r_work: 0.3388 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22309 Z= 0.124 Angle : 0.558 9.272 30398 Z= 0.285 Chirality : 0.040 0.193 3536 Planarity : 0.004 0.076 3723 Dihedral : 13.982 140.866 3453 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.55 % Allowed : 27.49 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.17), residues: 2623 helix: 1.27 (0.15), residues: 1236 sheet: -0.44 (0.22), residues: 514 loop : -0.19 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 210 TYR 0.015 0.001 TYR E 343 PHE 0.028 0.001 PHE G 2 TRP 0.011 0.001 TRP F 28 HIS 0.006 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00293 (22309) covalent geometry : angle 0.55754 (30398) hydrogen bonds : bond 0.02986 ( 1071) hydrogen bonds : angle 4.07620 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 258 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 592 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: A 725 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: A 757 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7411 (tp) REVERT: C 320 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8237 (mm) REVERT: E 65 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: E 298 GLU cc_start: 0.8439 (tp30) cc_final: 0.8064 (tp30) REVERT: E 345 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7812 (mppt) REVERT: F 149 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7620 (mmm-85) REVERT: F 199 MET cc_start: 0.5373 (ppp) cc_final: 0.4568 (pp-130) REVERT: G 20 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8131 (tptt) REVERT: G 53 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6533 (mmt-90) REVERT: G 72 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7117 (tt) REVERT: H 117 LYS cc_start: 0.5041 (tptp) cc_final: 0.4512 (mmmm) outliers start: 82 outliers final: 51 residues processed: 326 average time/residue: 0.4999 time to fit residues: 187.9178 Evaluate side-chains 301 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 65 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 208 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS D 219 ASN E 22 GLN E 71 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN G 49 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131675 restraints weight = 28419.058| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.44 r_work: 0.3386 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22309 Z= 0.123 Angle : 0.574 17.435 30398 Z= 0.290 Chirality : 0.040 0.182 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.945 140.825 3453 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.16 % Allowed : 27.75 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2623 helix: 1.33 (0.15), residues: 1234 sheet: -0.43 (0.22), residues: 515 loop : -0.15 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 52 TYR 0.012 0.001 TYR H 239 PHE 0.027 0.001 PHE G 2 TRP 0.010 0.001 TRP F 28 HIS 0.006 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00289 (22309) covalent geometry : angle 0.57425 (30398) hydrogen bonds : bond 0.02925 ( 1071) hydrogen bonds : angle 4.04808 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 250 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7987 (mttt) REVERT: A 500 GLN cc_start: 0.6441 (mp10) cc_final: 0.6188 (mp10) REVERT: A 592 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6582 (tp30) REVERT: C 320 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (mm) REVERT: E 65 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: E 345 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7804 (mppt) REVERT: F 17 GLU cc_start: 0.7743 (pm20) cc_final: 0.7520 (mp0) REVERT: F 128 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.6005 (mt) REVERT: F 199 MET cc_start: 0.5321 (ppp) cc_final: 0.4471 (pp-130) REVERT: G 20 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8118 (tptt) REVERT: G 53 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6520 (mmt-90) REVERT: G 61 ARG cc_start: 0.7768 (ppp80) cc_final: 0.7024 (ppp80) REVERT: G 72 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7106 (tt) REVERT: H 117 LYS cc_start: 0.5047 (tptp) cc_final: 0.4516 (mmmm) outliers start: 73 outliers final: 48 residues processed: 310 average time/residue: 0.4878 time to fit residues: 173.9303 Evaluate side-chains 293 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 155 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 170 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128091 restraints weight = 28472.904| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.10 r_work: 0.3349 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22309 Z= 0.184 Angle : 0.625 14.789 30398 Z= 0.316 Chirality : 0.042 0.192 3536 Planarity : 0.004 0.071 3723 Dihedral : 14.063 142.701 3453 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.25 % Allowed : 27.88 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2623 helix: 1.22 (0.15), residues: 1233 sheet: -0.52 (0.22), residues: 526 loop : -0.20 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 52 TYR 0.014 0.001 TYR E 343 PHE 0.028 0.002 PHE G 2 TRP 0.008 0.001 TRP F 28 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00444 (22309) covalent geometry : angle 0.62473 (30398) hydrogen bonds : bond 0.03391 ( 1071) hydrogen bonds : angle 4.16126 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 247 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: E 65 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: E 345 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7848 (mppt) REVERT: F 128 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5961 (mt) REVERT: F 149 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7526 (mmm-85) REVERT: F 199 MET cc_start: 0.5419 (ppp) cc_final: 0.4499 (pp-130) REVERT: G 20 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8137 (tptt) REVERT: G 25 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6228 (pm20) REVERT: G 53 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6548 (mmt-90) REVERT: G 61 ARG cc_start: 0.7875 (ppp80) cc_final: 0.7152 (ppp80) REVERT: G 72 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7150 (tt) REVERT: H 1 MET cc_start: 0.3354 (pp-130) cc_final: 0.2912 (tmm) REVERT: H 41 ASP cc_start: 0.4522 (OUTLIER) cc_final: 0.4278 (m-30) REVERT: H 68 MET cc_start: 0.2053 (mtt) cc_final: 0.1447 (mtp) REVERT: H 117 LYS cc_start: 0.5115 (tptp) cc_final: 0.4563 (mmmm) REVERT: H 181 LYS cc_start: 0.6916 (mtmm) cc_final: 0.6699 (mppt) outliers start: 75 outliers final: 51 residues processed: 308 average time/residue: 0.5218 time to fit residues: 184.6058 Evaluate side-chains 289 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 140 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN A 728 ASN A 805 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS D 219 ASN E 22 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.175421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130565 restraints weight = 28486.998| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.70 r_work: 0.3385 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22309 Z= 0.127 Angle : 0.595 14.440 30398 Z= 0.301 Chirality : 0.040 0.184 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.977 143.155 3453 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.90 % Allowed : 28.40 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2623 helix: 1.34 (0.15), residues: 1233 sheet: -0.47 (0.22), residues: 527 loop : -0.09 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 52 TYR 0.012 0.001 TYR H 239 PHE 0.019 0.001 PHE G 169 TRP 0.012 0.001 TRP G 28 HIS 0.005 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00301 (22309) covalent geometry : angle 0.59481 (30398) hydrogen bonds : bond 0.02987 ( 1071) hydrogen bonds : angle 4.08055 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 592 GLU cc_start: 0.6528 (tp30) cc_final: 0.6148 (mm-30) REVERT: A 805 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: C 320 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 48 CYS cc_start: 0.8935 (p) cc_final: 0.8463 (t) REVERT: D 221 LYS cc_start: 0.8185 (tppt) cc_final: 0.7982 (pmmt) REVERT: E 65 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: E 345 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7814 (mppt) REVERT: F 40 MET cc_start: 0.8121 (ttt) cc_final: 0.6653 (tpt) REVERT: F 128 ILE cc_start: 0.6188 (OUTLIER) cc_final: 0.5976 (mt) REVERT: F 199 MET cc_start: 0.5289 (ppp) cc_final: 0.4466 (pp-130) REVERT: G 20 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8120 (tptt) REVERT: G 25 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6041 (pm20) REVERT: G 53 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6514 (mmt-90) REVERT: G 61 ARG cc_start: 0.7818 (ppp80) cc_final: 0.7078 (ppp80) REVERT: G 72 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7049 (tt) REVERT: H 1 MET cc_start: 0.3894 (pp-130) cc_final: 0.3036 (tmm) REVERT: H 117 LYS cc_start: 0.5164 (tptp) cc_final: 0.4649 (mmmm) outliers start: 67 outliers final: 44 residues processed: 294 average time/residue: 0.5301 time to fit residues: 178.5984 Evaluate side-chains 288 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 257 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 197 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 178 optimal weight: 0.3980 chunk 203 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN A 805 GLN C 37 HIS E 102 ASN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.175856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131299 restraints weight = 28483.287| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.32 r_work: 0.3385 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22309 Z= 0.121 Angle : 0.588 14.096 30398 Z= 0.298 Chirality : 0.040 0.178 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.943 143.020 3453 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.47 % Allowed : 28.79 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.17), residues: 2623 helix: 1.40 (0.15), residues: 1233 sheet: -0.42 (0.22), residues: 525 loop : -0.05 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 52 TYR 0.017 0.001 TYR E 343 PHE 0.019 0.001 PHE G 169 TRP 0.011 0.001 TRP F 28 HIS 0.005 0.001 HIS G 246 Details of bonding type rmsd covalent geometry : bond 0.00283 (22309) covalent geometry : angle 0.58819 (30398) hydrogen bonds : bond 0.02919 ( 1071) hydrogen bonds : angle 4.05352 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.10 seconds wall clock time: 121 minutes 21.64 seconds (7281.64 seconds total)