Starting phenix.real_space_refine on Fri Aug 7 12:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un0_42389/08_2026/8un0_42389_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un0_42389/08_2026/8un0_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_2026/8un0_42389_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2026/8un0_42389_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2026/8un0_42389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un0_42389/08_2026/8un0_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 4.29, per 1000 atoms: 0.20 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: 1.59 Conformation dependent library (CDL) restraints added in 907.5 milliseconds 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: 2.40 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: 3.98 Time building geometry restraints manager: 2.01 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=" O3B AGS A1202 " pdb=" PB AGS A1202 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 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=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.96e+01 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 29726 2.53 - 5.06: 543 5.06 - 7.59: 87 7.59 - 10.12: 38 10.12 - 12.65: 4 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 - 35.41: 12984 35.41 - 70.82: 676 70.82 - 106.23: 35 106.23 - 141.63: 9 141.63 - 177.04: 3 Dihedral angle restraints: 13707 sinusoidal: 5967 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 13704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3318 0.100 - 0.199: 199 0.199 - 0.299: 9 0.299 - 0.398: 1 0.398 - 0.498: 1 Chirality restraints: 3528 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=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.68 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3525 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: 2.760 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 22309 Z= 0.296 Angle : 0.873 12.645 30398 Z= 0.504 Chirality : 0.050 0.498 3528 Planarity : 0.007 0.108 3723 Dihedral : 19.394 177.043 8669 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 are 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/Z covalent geometry : bond 0.00500 / 0.30 (22309) covalent geometry : angle 0.87336 / 0.50 (30398) hydrogen bonds : bond 0.18909 / 12.71 ( 1071) hydrogen bonds : angle 6.95054 / 4.95 ( 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 : 0.867 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: 0.5926 time to fit residues: 224.8617 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 : 0.869 ------------------------------------------------------------------------------- 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: 9.9990 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... A 430 ASN A 493 GLN A 573 GLN A 595 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.174793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129722 restraints weight = 28665.248| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.11 r_work: 0.3360 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22309 Z= 0.243 Angle : 0.687 9.182 30398 Z= 0.353 Chirality : 0.045 0.199 3528 Planarity : 0.006 0.080 3723 Dihedral : 16.574 175.701 3526 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.07 % Allowed : 23.64 % Favored : 72.29 % 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 are not related in a simple way. whole: -0.72 (0.16), residues: 2623 helix: -0.07 (0.14), residues: 1226 sheet: -0.56 (0.23), residues: 504 loop : -0.74 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 52 TYR 0.021 0.002 TYR F 250 PHE 0.017 0.002 PHE E 339 TRP 0.019 0.002 TRP F 28 HIS 0.008 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (22309) covalent geometry : angle 0.68738 / 0.35 (30398) hydrogen bonds : bond 0.04426 / 3.02 ( 1071) hydrogen bonds : angle 4.89011 / 3.52 ( 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 370 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 276 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: D 95 LEU cc_start: 0.8902 (mt) cc_final: 0.8694 (mp) REVERT: E 65 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: E 194 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8248 (t-90) REVERT: E 269 GLN cc_start: 0.8178 (pm20) cc_final: 0.7924 (pm20) REVERT: F 5 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7460 (mmm-85) REVERT: F 42 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8184 (p) REVERT: F 68 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8717 (mmt) REVERT: F 78 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8094 (mp) REVERT: F 239 TYR cc_start: 0.8413 (m-10) cc_final: 0.8180 (m-10) REVERT: G 49 GLN cc_start: 0.8099 (tt0) cc_final: 0.7861 (tm-30) REVERT: G 88 ILE cc_start: 0.7873 (mm) cc_final: 0.7663 (mm) REVERT: G 198 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: H 117 LYS cc_start: 0.5278 (tptp) cc_final: 0.4622 (mmmm) REVERT: H 254 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6423 (mmmt) outliers start: 94 outliers final: 37 residues processed: 339 average time/residue: 0.6054 time to fit residues: 237.3074 Evaluate side-chains 282 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 99 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 213 MET 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 42 SER 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 78 ILE Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 198 GLU 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: 1.9990 chunk 85 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 ASN B 182 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130476 restraints weight = 28781.724| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.17 r_work: 0.3378 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22309 Z= 0.144 Angle : 0.573 8.509 30398 Z= 0.297 Chirality : 0.041 0.271 3528 Planarity : 0.004 0.075 3723 Dihedral : 16.284 174.819 3525 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.77 % Allowed : 24.59 % Favored : 71.65 % 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 are not related in a simple way. whole: -0.11 (0.16), residues: 2623 helix: 0.62 (0.15), residues: 1227 sheet: -0.60 (0.22), residues: 516 loop : -0.50 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 149 TYR 0.012 0.001 TYR C 26 PHE 0.013 0.001 PHE A 632 TRP 0.014 0.001 TRP F 28 HIS 0.009 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (22309) covalent geometry : angle 0.57255 / 0.30 (30398) hydrogen bonds : bond 0.03623 / 2.46 ( 1071) hydrogen bonds : angle 4.52646 / 3.26 ( 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 360 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 273 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 804 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7546 (ptm160) REVERT: C 257 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: E 58 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: E 65 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: E 66 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7737 (mppt) REVERT: E 269 GLN cc_start: 0.8104 (pm20) cc_final: 0.7889 (pm20) REVERT: E 345 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7778 (mppt) REVERT: F 199 MET cc_start: 0.5445 (ppp) cc_final: 0.4401 (pp-130) REVERT: G 49 GLN cc_start: 0.8051 (tt0) cc_final: 0.7837 (tm-30) REVERT: G 88 ILE cc_start: 0.8012 (mm) cc_final: 0.7782 (mm) REVERT: G 175 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6726 (mt) REVERT: H 117 LYS cc_start: 0.5229 (tptp) cc_final: 0.4630 (mmmm) REVERT: H 254 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6335 (mmmt) outliers start: 87 outliers final: 39 residues processed: 337 average time/residue: 0.6120 time to fit residues: 238.8069 Evaluate side-chains 289 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 674 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET 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 231 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 58 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 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 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 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: 7.9990 chunk 136 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 HIS B 118 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 320 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 213 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 = 0.4116 r_free = 0.4116 target = 0.174821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130748 restraints weight = 28695.073| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.20 r_work: 0.3332 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22309 Z= 0.164 Angle : 0.588 8.133 30398 Z= 0.302 Chirality : 0.041 0.196 3528 Planarity : 0.004 0.073 3723 Dihedral : 16.146 175.649 3525 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.42 % Allowed : 24.85 % Favored : 70.74 % 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 are not related in a simple way. whole: 0.10 (0.17), residues: 2623 helix: 0.83 (0.15), residues: 1235 sheet: -0.59 (0.22), residues: 516 loop : -0.42 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 5 TYR 0.013 0.001 TYR H 239 PHE 0.020 0.001 PHE G 2 TRP 0.011 0.001 TRP F 28 HIS 0.009 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (22309) covalent geometry : angle 0.58751 / 0.30 (30398) hydrogen bonds : bond 0.03464 / 2.35 ( 1071) hydrogen bonds : angle 4.38379 / 3.16 ( 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 350 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 248 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7892 (t80) cc_final: 0.6809 (t80) REVERT: A 725 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: A 757 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 804 ARG cc_start: 0.7673 (ptm160) cc_final: 0.7379 (ptm160) REVERT: C 257 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: E 65 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: E 345 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7810 (mppt) REVERT: F 199 MET cc_start: 0.5469 (ppp) cc_final: 0.4429 (pp-130) REVERT: G 88 ILE cc_start: 0.8016 (mm) cc_final: 0.7807 (mm) REVERT: G 116 MET cc_start: 0.7719 (mmm) cc_final: 0.7474 (tpp) REVERT: G 175 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6635 (mt) REVERT: H 117 LYS cc_start: 0.5141 (tptp) cc_final: 0.4616 (mmmm) REVERT: H 254 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6398 (mmmt) outliers start: 102 outliers final: 55 residues processed: 328 average time/residue: 0.5945 time to fit residues: 225.6225 Evaluate side-chains 294 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 725 GLU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE 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 257 GLN 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 310 LEU Chi-restraints excluded: chain E residue 21 GLU 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 95 VAL 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 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 85 GLU 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 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 251 LEU 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: 0.9980 chunk 87 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 71 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS H 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129665 restraints weight = 28596.001| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.11 r_work: 0.3363 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22309 Z= 0.152 Angle : 0.568 7.484 30398 Z= 0.295 Chirality : 0.041 0.194 3528 Planarity : 0.004 0.071 3723 Dihedral : 16.043 177.968 3525 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.37 % Allowed : 25.19 % Favored : 70.43 % 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 are not related in a simple way. whole: 0.30 (0.17), residues: 2623 helix: 1.04 (0.15), residues: 1229 sheet: -0.58 (0.22), residues: 522 loop : -0.32 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 52 TYR 0.013 0.001 TYR B 42 PHE 0.022 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/Z covalent geometry : bond 0.00353 / 0.15 (22309) covalent geometry : angle 0.56828 / 0.29 (30398) hydrogen bonds : bond 0.03333 / 2.27 ( 1071) hydrogen bonds : angle 4.27353 / 3.08 ( 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 356 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 255 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8049 (mmm) cc_final: 0.7824 (mmm) REVERT: A 725 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: A 757 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7498 (tp) REVERT: A 804 ARG cc_start: 0.7761 (ptm160) cc_final: 0.7525 (ptm160) REVERT: D 356 MET cc_start: 0.8382 (ttp) cc_final: 0.8038 (ttp) REVERT: E 65 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: E 345 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7792 (mppt) REVERT: F 240 LYS cc_start: 0.8524 (tppt) cc_final: 0.8313 (tppp) REVERT: G 72 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7193 (tt) REVERT: G 88 ILE cc_start: 0.8115 (mm) cc_final: 0.7895 (mm) REVERT: H 117 LYS cc_start: 0.5115 (tptp) cc_final: 0.4542 (mmmm) REVERT: H 254 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6320 (mmmt) outliers start: 101 outliers final: 54 residues processed: 335 average time/residue: 0.6108 time to fit residues: 236.3306 Evaluate side-chains 291 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 725 GLU Chi-restraints excluded: chain A residue 730 MET 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 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 271 VAL 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 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 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 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 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 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 241 ILE 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 G residue 235 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 254 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 0.7980 chunk 254 optimal weight: 20.0000 chunk 239 optimal weight: 30.0000 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 196 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 HIS B 118 ASN ** 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** ** 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 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.173457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128164 restraints weight = 28623.864| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.81 r_work: 0.3348 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22309 Z= 0.175 Angle : 0.589 8.804 30398 Z= 0.303 Chirality : 0.042 0.187 3528 Planarity : 0.004 0.072 3723 Dihedral : 15.996 177.808 3525 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.72 % Allowed : 25.89 % Favored : 69.39 % 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 are not related in a simple way. whole: 0.34 (0.17), residues: 2623 helix: 1.09 (0.15), residues: 1229 sheet: -0.58 (0.22), residues: 522 loop : -0.31 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 52 TYR 0.011 0.001 TYR B 42 PHE 0.025 0.001 PHE G 2 TRP 0.010 0.001 TRP F 28 HIS 0.008 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (22309) covalent geometry : angle 0.58939 / 0.30 (30398) hydrogen bonds : bond 0.03448 / 2.36 ( 1071) hydrogen bonds : angle 4.24935 / 3.07 ( 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 354 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 245 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.6423 (mp10) cc_final: 0.6216 (mp10) REVERT: A 583 ARG cc_start: 0.8252 (ptm160) cc_final: 0.7953 (mpp-170) REVERT: A 725 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: A 757 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7514 (tp) REVERT: A 804 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7543 (ptm160) REVERT: B 208 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8359 (tptt) REVERT: E 65 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: F 199 MET cc_start: 0.5482 (ppp) cc_final: 0.4596 (pp-130) REVERT: F 240 LYS cc_start: 0.8544 (tppt) cc_final: 0.8317 (tppp) REVERT: G 175 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6836 (mt) REVERT: H 117 LYS cc_start: 0.5039 (tptp) cc_final: 0.4503 (mmmm) REVERT: H 254 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6303 (mmmt) outliers start: 109 outliers final: 59 residues processed: 328 average time/residue: 0.6288 time to fit residues: 237.6615 Evaluate side-chains 297 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 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 271 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE 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 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 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 310 LEU 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 64 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 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 79 LEU Chi-restraints excluded: chain F residue 87 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 23 ILE 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 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 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 254 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 221 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 ASN ** 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** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN H 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127411 restraints weight = 28689.067| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.46 r_work: 0.3343 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22309 Z= 0.200 Angle : 0.626 14.273 30398 Z= 0.318 Chirality : 0.043 0.252 3528 Planarity : 0.005 0.073 3723 Dihedral : 15.998 178.477 3525 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.89 % Allowed : 26.06 % Favored : 69.05 % 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 are not related in a simple way. whole: 0.29 (0.17), residues: 2623 helix: 1.04 (0.15), residues: 1232 sheet: -0.62 (0.22), residues: 527 loop : -0.31 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 52 TYR 0.012 0.001 TYR F 250 PHE 0.026 0.002 PHE G 2 TRP 0.009 0.001 TRP F 28 HIS 0.005 0.001 HIS G 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (22309) covalent geometry : angle 0.62575 / 0.32 (30398) hydrogen bonds : bond 0.03596 / 2.45 ( 1071) hydrogen bonds : angle 4.26489 / 3.09 ( 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 358 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 245 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8123 (mmm) cc_final: 0.7894 (mmm) REVERT: A 583 ARG cc_start: 0.8208 (ptm160) cc_final: 0.7959 (mpp-170) REVERT: A 725 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: A 757 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7547 (tp) REVERT: A 804 ARG cc_start: 0.7771 (ptm160) cc_final: 0.7038 (ptm160) REVERT: B 208 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8395 (tptt) REVERT: B 241 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8635 (p) REVERT: C 320 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8268 (mm) REVERT: E 65 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: F 88 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8377 (mp) REVERT: F 199 MET cc_start: 0.5460 (ppp) cc_final: 0.4519 (pp-130) REVERT: G 25 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: G 61 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7862 (ppp80) REVERT: G 175 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6905 (mt) REVERT: H 117 LYS cc_start: 0.5017 (tptp) cc_final: 0.4452 (mmmm) outliers start: 113 outliers final: 60 residues processed: 331 average time/residue: 0.6492 time to fit residues: 246.4841 Evaluate side-chains 300 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 442 VAL 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 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 271 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 149 THR 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 272 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU 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 64 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 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 79 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 88 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 25 GLU Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 161 SER 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 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: 5.9990 chunk 85 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 158 optimal weight: 0.1980 chunk 213 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 HIS B 118 ASN B 269 HIS ** 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** ** 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 = 0.4088 r_free = 0.4088 target = 0.172282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127567 restraints weight = 28454.198| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.36 r_work: 0.3327 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22309 Z= 0.181 Angle : 0.624 17.534 30398 Z= 0.316 Chirality : 0.042 0.180 3528 Planarity : 0.004 0.072 3723 Dihedral : 15.983 179.650 3525 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.20 % Allowed : 26.62 % Favored : 69.18 % 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 are not related in a simple way. whole: 0.31 (0.17), residues: 2623 helix: 1.07 (0.15), residues: 1232 sheet: -0.67 (0.22), residues: 534 loop : -0.29 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 5 TYR 0.012 0.001 TYR C 310 PHE 0.022 0.001 PHE G 2 TRP 0.010 0.001 TRP F 28 HIS 0.006 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (22309) covalent geometry : angle 0.62417 / 0.32 (30398) hydrogen bonds : bond 0.03475 / 2.36 ( 1071) hydrogen bonds : angle 4.24809 / 3.08 ( 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 336 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 239 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 483 MET cc_start: 0.8131 (mmm) cc_final: 0.7884 (mmm) REVERT: A 500 GLN cc_start: 0.6548 (mp10) cc_final: 0.6307 (mp10) REVERT: A 583 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7971 (mpp-170) REVERT: A 725 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: A 757 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7570 (tp) REVERT: B 208 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8434 (tptt) REVERT: B 241 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8581 (p) REVERT: C 320 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8251 (mm) REVERT: E 65 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: E 194 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (t-90) REVERT: E 345 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7855 (mppt) REVERT: F 88 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8381 (mp) REVERT: F 128 ILE cc_start: 0.6287 (OUTLIER) cc_final: 0.6066 (mt) REVERT: F 149 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7547 (mmm-85) REVERT: F 199 MET cc_start: 0.5439 (ppp) cc_final: 0.4533 (pp-130) REVERT: F 240 LYS cc_start: 0.8545 (tppt) cc_final: 0.8250 (tppp) REVERT: G 25 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6328 (pm20) REVERT: G 61 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7862 (ppp80) REVERT: G 72 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7189 (tt) REVERT: G 175 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6907 (mt) REVERT: H 117 LYS cc_start: 0.5016 (tptp) cc_final: 0.4448 (mmmm) outliers start: 97 outliers final: 57 residues processed: 318 average time/residue: 0.6166 time to fit residues: 225.8821 Evaluate side-chains 298 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 271 VAL Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 69 THR 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 272 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU 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 64 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 E residue 194 HIS Chi-restraints excluded: chain E residue 253 VAL 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 88 ILE 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 F residue 237 VAL Chi-restraints excluded: chain G residue 25 GLU 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 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 175 LEU 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 Chi-restraints excluded: chain H residue 251 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 ASN A 805 GLN B 118 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 265 GLN F 36 ASN G 71 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.173189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127924 restraints weight = 28563.072| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.38 r_work: 0.3358 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2725 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= 0.148 Angle : 0.608 15.890 30398 Z= 0.309 Chirality : 0.041 0.196 3528 Planarity : 0.004 0.071 3723 Dihedral : 15.941 178.909 3525 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.51 % Allowed : 27.49 % Favored : 69.00 % 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 are not related in a simple way. whole: 0.37 (0.17), residues: 2623 helix: 1.14 (0.15), residues: 1231 sheet: -0.69 (0.22), residues: 533 loop : -0.24 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 5 TYR 0.021 0.001 TYR B 279 PHE 0.021 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/Z covalent geometry : bond 0.00347 / 0.15 (22309) covalent geometry : angle 0.60787 / 0.31 (30398) hydrogen bonds : bond 0.03303 / 2.24 ( 1071) hydrogen bonds : angle 4.22190 / 3.06 ( 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 324 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 243 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8108 (mmm) cc_final: 0.7857 (mmm) REVERT: A 500 GLN cc_start: 0.6618 (mp10) cc_final: 0.6408 (mp10) REVERT: A 583 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7982 (mpp-170) REVERT: A 725 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: A 757 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7576 (tp) REVERT: B 208 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8407 (tptt) REVERT: C 320 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (mm) REVERT: E 65 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: E 345 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7854 (mppt) REVERT: F 87 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7950 (mt) REVERT: F 128 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.6037 (mt) REVERT: F 199 MET cc_start: 0.5465 (ppp) cc_final: 0.4587 (pp-130) REVERT: F 240 LYS cc_start: 0.8557 (tppt) cc_final: 0.8277 (tppp) REVERT: G 5 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.6277 (tpp80) REVERT: G 25 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6248 (pm20) REVERT: G 61 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7877 (ppp80) REVERT: G 175 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6771 (mt) REVERT: H 117 LYS cc_start: 0.5014 (tptp) cc_final: 0.4432 (mmmm) outliers start: 81 outliers final: 52 residues processed: 306 average time/residue: 0.6446 time to fit residues: 226.1072 Evaluate side-chains 291 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 145 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 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 272 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 334 VAL 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 24 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 79 LEU Chi-restraints excluded: chain F residue 87 ILE 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 F residue 237 VAL Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 175 LEU 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 Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 0.0050 chunk 140 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 HIS A 805 GLN B 118 ASN C 37 HIS D 219 ASN ** G 107 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 = 0.4100 r_free = 0.4100 target = 0.173245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128590 restraints weight = 28518.396| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.30 r_work: 0.3344 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2749 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= 0.145 Angle : 0.611 15.136 30398 Z= 0.311 Chirality : 0.041 0.201 3528 Planarity : 0.004 0.071 3723 Dihedral : 15.918 177.808 3525 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 28.10 % Favored : 68.83 % 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 are not related in a simple way. whole: 0.42 (0.17), residues: 2623 helix: 1.18 (0.15), residues: 1232 sheet: -0.66 (0.22), residues: 523 loop : -0.23 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 5 TYR 0.019 0.001 TYR B 279 PHE 0.020 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/Z covalent geometry : bond 0.00339 / 0.14 (22309) covalent geometry : angle 0.61148 / 0.31 (30398) hydrogen bonds : bond 0.03252 / 2.20 ( 1071) hydrogen bonds : angle 4.20990 / 3.06 ( 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 313 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 242 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 483 MET cc_start: 0.8024 (mmm) cc_final: 0.7782 (mmm) REVERT: A 725 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: A 757 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7496 (tp) REVERT: A 805 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: C 320 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8166 (mm) REVERT: E 65 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: E 298 GLU cc_start: 0.8207 (tp30) cc_final: 0.7832 (tp30) REVERT: E 345 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7908 (mppt) REVERT: F 87 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7902 (mt) REVERT: F 128 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5915 (mt) REVERT: F 199 MET cc_start: 0.5389 (ppp) cc_final: 0.4541 (pp-130) REVERT: F 240 LYS cc_start: 0.8472 (tppt) cc_final: 0.8196 (tppp) REVERT: G 25 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: G 61 ARG cc_start: 0.8088 (ppp80) cc_final: 0.7842 (ppp80) REVERT: G 175 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6649 (mt) REVERT: H 117 LYS cc_start: 0.5013 (tptp) cc_final: 0.4457 (mmmm) outliers start: 71 outliers final: 51 residues processed: 302 average time/residue: 0.5461 time to fit residues: 189.6781 Evaluate side-chains 285 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 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 145 SER Chi-restraints excluded: chain B residue 157 THR 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 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 233 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 334 VAL 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 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 79 LEU Chi-restraints excluded: chain F residue 87 ILE 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 F residue 237 VAL Chi-restraints excluded: chain G residue 25 GLU 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 139 MET Chi-restraints excluded: chain G residue 175 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 257 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 HIS ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN C 37 HIS G 36 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 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 = 0.173251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127798 restraints weight = 28513.457| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.55 r_work: 0.3363 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 22309 Z= 0.201 Angle : 0.782 59.181 30398 Z= 0.423 Chirality : 0.043 0.798 3528 Planarity : 0.004 0.071 3723 Dihedral : 15.922 177.816 3525 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.07 % Allowed : 28.44 % Favored : 68.48 % Cbeta Deviations : 0.04 % 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 are not related in a simple way. whole: 0.42 (0.17), residues: 2623 helix: 1.18 (0.15), residues: 1232 sheet: -0.67 (0.22), residues: 523 loop : -0.22 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 5 TYR 0.017 0.001 TYR B 279 PHE 0.016 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/Z covalent geometry : bond 0.00429 / 0.20 (22309) covalent geometry : angle 0.78240 / 0.42 (30398) hydrogen bonds : bond 0.03273 / 2.22 ( 1071) hydrogen bonds : angle 4.20984 / 3.06 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8095.37 seconds wall clock time: 138 minutes 53.63 seconds (8333.63 seconds total)