Starting phenix.real_space_refine on Wed Jun 18 21:26:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un0_42389/06_2025/8un0_42389_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un0_42389/06_2025/8un0_42389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8un0_42389/06_2025/8un0_42389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un0_42389/06_2025/8un0_42389.map" model { file = "/net/cci-nas-00/data/ceres_data/8un0_42389/06_2025/8un0_42389_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un0_42389/06_2025/8un0_42389_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.06, per 1000 atoms: 0.60 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: 5.22 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 7.79 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: 10.39 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7241 1.36 - 1.51: 5708 1.51 - 1.65: 9152 1.65 - 1.80: 99 1.80 - 1.95: 109 Bond restraints: 22309 Sorted by residual: bond pdb=" CA SER G 42 " pdb=" CB SER G 42 " ideal model delta sigma weight residual 1.529 1.457 0.073 1.63e-02 3.76e+03 1.99e+01 bond pdb=" N ASN B 272 " pdb=" CA ASN B 272 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.79e+00 bond pdb=" N MET G 75 " pdb=" CA MET G 75 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.26e-02 6.30e+03 9.35e+00 bond pdb=" N THR G 185 " pdb=" CA THR G 185 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.15e-02 7.56e+03 7.83e+00 bond pdb=" N ASN B 118 " pdb=" CA ASN B 118 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.37e-02 5.33e+03 7.68e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 29827 2.53 - 5.06: 478 5.06 - 7.59: 72 7.59 - 10.12: 20 10.12 - 12.65: 1 Bond angle restraints: 30398 Sorted by residual: angle pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" CD PRO A 535 " ideal model delta sigma weight residual 112.00 105.26 6.74 1.40e+00 5.10e-01 2.32e+01 angle pdb=" CA GLN E 119 " pdb=" CB GLN E 119 " pdb=" CG GLN E 119 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN A 363 " pdb=" CB GLN A 363 " pdb=" CG GLN A 363 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" C SER G 183 " pdb=" N GLN G 184 " pdb=" CA GLN G 184 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" C PHE A 299 " ideal model delta sigma weight residual 110.97 106.19 4.78 1.09e+00 8.42e-01 1.93e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.73: 12380 26.73 - 53.45: 1106 53.45 - 80.18: 136 80.18 - 106.90: 11 106.90 - 133.62: 2 Dihedral angle restraints: 13635 sinusoidal: 5895 harmonic: 7740 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 166.38 133.62 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" CA SER H 183 " pdb=" C SER H 183 " pdb=" N GLN H 184 " pdb=" CA GLN H 184 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLU G 109 " pdb=" C GLU G 109 " pdb=" N LYS G 110 " pdb=" CA LYS G 110 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3335 0.100 - 0.199: 194 0.199 - 0.299: 6 0.299 - 0.398: 0 0.398 - 0.498: 1 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE A 549 " pdb=" CA ILE A 549 " pdb=" CG1 ILE A 549 " pdb=" CG2 ILE A 549 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" CA LEU E 93 " pdb=" N LEU E 93 " pdb=" C LEU E 93 " pdb=" CB LEU E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE F 241 " pdb=" CA ILE F 241 " pdb=" CG1 ILE F 241 " pdb=" CG2 ILE F 241 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 198 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C GLU H 198 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU H 198 " 0.030 2.00e-02 2.50e+03 pdb=" N MET H 199 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 699 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO E 174 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.053 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 246 2.63 - 3.20: 17537 3.20 - 3.77: 34765 3.77 - 4.33: 46848 4.33 - 4.90: 77869 Nonbonded interactions: 177265 Sorted by model distance: nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.069 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.070 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR A 381 " pdb="MG MG A1201 " model vdw 2.075 2.170 ... (remaining 177260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 56.530 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 22309 Z= 0.224 Angle : 0.803 12.645 30398 Z= 0.452 Chirality : 0.048 0.498 3536 Planarity : 0.007 0.108 3723 Dihedral : 18.780 133.625 8597 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 0.56 % Allowed : 23.90 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (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 TRP 0.062 0.002 TRP F 28 HIS 0.010 0.001 HIS G 246 PHE 0.017 0.002 PHE G 169 TYR 0.016 0.002 TYR B 279 ARG 0.021 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.18909 ( 1071) hydrogen bonds : angle 6.95054 ( 3048) covalent geometry : bond 0.00422 (22309) covalent geometry : angle 0.80271 (30398) *********************** 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 : 3.362 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: 0.5457 (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: 1.3936 time to fit residues: 529.2862 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 : 2.303 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 493 GLN A 573 GLN A 595 GLN C 37 HIS C 241 HIS C 317 ASN D 308 ASN F 71 ASN G 246 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131968 restraints weight = 28607.503| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.12 r_work: 0.3391 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22309 Z= 0.179 Angle : 0.605 7.914 30398 Z= 0.312 Chirality : 0.042 0.192 3536 Planarity : 0.005 0.082 3723 Dihedral : 14.319 138.170 3454 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.72 % Allowed : 23.55 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2623 helix: 0.07 (0.14), residues: 1222 sheet: -0.56 (0.23), residues: 511 loop : -0.63 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 28 HIS 0.007 0.001 HIS G 246 PHE 0.016 0.001 PHE A 632 TYR 0.018 0.001 TYR F 250 ARG 0.010 0.001 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1071) hydrogen bonds : angle 4.71315 ( 3048) covalent geometry : bond 0.00418 (22309) covalent geometry : angle 0.60488 (30398) *********************** 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 371 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 2.302 Fit side-chains revert: symmetry clash REVERT: A 725 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: E 65 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: E 269 GLN cc_start: 0.8135 (pm20) cc_final: 0.7895 (pm20) REVERT: F 68 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: F 78 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8136 (mp) REVERT: F 239 TYR cc_start: 0.8358 (m-10) cc_final: 0.8110 (m-10) REVERT: G 49 GLN cc_start: 0.8111 (tt0) cc_final: 0.7859 (tm-30) REVERT: G 198 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: H 117 LYS cc_start: 0.5354 (tptp) cc_final: 0.4705 (mmmm) REVERT: H 180 ILE cc_start: 0.5772 (mt) cc_final: 0.5538 (tp) REVERT: H 254 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6329 (mmmt) outliers start: 86 outliers final: 36 residues processed: 342 average time/residue: 1.2348 time to fit residues: 488.1903 Evaluate side-chains 290 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS 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 B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 133 ASP 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 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 206 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 241 ILE 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 68 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN E 302 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS 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 = 0.175928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131078 restraints weight = 28512.916| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.51 r_work: 0.3386 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22309 Z= 0.151 Angle : 0.561 8.439 30398 Z= 0.289 Chirality : 0.041 0.169 3536 Planarity : 0.004 0.074 3723 Dihedral : 14.177 138.483 3453 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.94 % Allowed : 24.03 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2623 helix: 0.66 (0.15), residues: 1234 sheet: -0.52 (0.22), residues: 511 loop : -0.44 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 28 HIS 0.008 0.001 HIS G 246 PHE 0.014 0.001 PHE A 558 TYR 0.017 0.001 TYR H 239 ARG 0.012 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1071) hydrogen bonds : angle 4.41318 ( 3048) covalent geometry : bond 0.00353 (22309) covalent geometry : angle 0.56088 (30398) *********************** 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 353 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 262 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7900 (t80) cc_final: 0.6819 (t80) REVERT: A 725 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: A 804 ARG cc_start: 0.7794 (ptm160) cc_final: 0.7539 (ptm160) REVERT: C 257 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: E 65 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: E 66 LYS cc_start: 0.7980 (mmmm) cc_final: 0.7724 (mppt) REVERT: E 269 GLN cc_start: 0.8133 (pm20) cc_final: 0.7928 (pm20) REVERT: E 345 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7771 (mppt) REVERT: F 199 MET cc_start: 0.5467 (ppp) cc_final: 0.4449 (pp-130) REVERT: F 239 TYR cc_start: 0.8390 (m-10) cc_final: 0.8167 (m-10) REVERT: G 72 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7097 (tt) REVERT: G 88 ILE cc_start: 0.7961 (mm) cc_final: 0.7724 (mm) REVERT: G 175 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6706 (mt) REVERT: H 25 GLU cc_start: 0.1405 (OUTLIER) cc_final: 0.1116 (tp30) REVERT: H 117 LYS cc_start: 0.5116 (tptp) cc_final: 0.4535 (mmmm) REVERT: H 180 ILE cc_start: 0.5819 (mt) cc_final: 0.5548 (tp) REVERT: H 212 LEU cc_start: 0.8664 (mt) cc_final: 0.8330 (tm) REVERT: H 254 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6365 (mmmt) outliers start: 91 outliers final: 45 residues processed: 328 average time/residue: 1.1914 time to fit residues: 451.4223 Evaluate side-chains 286 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 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 778 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE 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 149 THR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 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 D residue 333 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 74 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 LEU 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 25 GLU 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 77 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 236 optimal weight: 30.0000 chunk 234 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS D 219 ASN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130278 restraints weight = 28772.856| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.13 r_work: 0.3370 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2026 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= 0.161 Angle : 0.564 7.662 30398 Z= 0.289 Chirality : 0.041 0.154 3536 Planarity : 0.004 0.072 3723 Dihedral : 14.111 139.995 3453 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.59 % Allowed : 24.29 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2623 helix: 0.89 (0.15), residues: 1235 sheet: -0.52 (0.22), residues: 516 loop : -0.36 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 28 HIS 0.008 0.001 HIS G 246 PHE 0.021 0.001 PHE G 2 TYR 0.015 0.001 TYR H 239 ARG 0.012 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 1071) hydrogen bonds : angle 4.28087 ( 3048) covalent geometry : bond 0.00379 (22309) covalent geometry : angle 0.56388 (30398) *********************** 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 360 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 254 time to evaluate : 2.279 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7919 (mttt) REVERT: A 483 MET cc_start: 0.8099 (mmm) cc_final: 0.7846 (mmm) REVERT: A 725 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: A 757 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7358 (tp) REVERT: A 804 ARG cc_start: 0.7748 (ptm160) cc_final: 0.7482 (ptm160) REVERT: B 208 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8163 (tptp) REVERT: D 356 MET cc_start: 0.8397 (ttp) cc_final: 0.8043 (ttp) REVERT: E 65 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: E 66 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7709 (mppt) REVERT: E 269 GLN cc_start: 0.8161 (pm20) cc_final: 0.7947 (pm20) REVERT: E 345 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7731 (mppt) REVERT: F 199 MET cc_start: 0.5525 (ppp) cc_final: 0.4462 (pp-130) REVERT: F 239 TYR cc_start: 0.8427 (m-10) cc_final: 0.8222 (m-10) REVERT: G 20 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8100 (tptt) REVERT: G 72 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7134 (tt) REVERT: G 88 ILE cc_start: 0.8048 (mm) cc_final: 0.7814 (mm) REVERT: G 175 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6784 (mt) REVERT: G 197 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8190 (tp) REVERT: H 117 LYS cc_start: 0.5064 (tptp) cc_final: 0.4563 (mmmm) REVERT: H 180 ILE cc_start: 0.5804 (mt) cc_final: 0.5510 (tp) REVERT: H 212 LEU cc_start: 0.8692 (mt) cc_final: 0.8350 (tm) REVERT: H 254 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6360 (mmmt) outliers start: 106 outliers final: 60 residues processed: 338 average time/residue: 1.2726 time to fit residues: 495.0827 Evaluate side-chains 299 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 306 LYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 646 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 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 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 272 GLU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 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 206 ASN Chi-restraints excluded: chain F residue 8 GLN 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 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 23 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 161 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 197 ILE 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 224 THR 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 100 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 250 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 71 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 49 GLN ** 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 = 0.4108 r_free = 0.4108 target = 0.173862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128489 restraints weight = 28817.383| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.41 r_work: 0.3358 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2286 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= 0.165 Angle : 0.574 8.767 30398 Z= 0.294 Chirality : 0.041 0.187 3536 Planarity : 0.004 0.072 3723 Dihedral : 14.088 141.664 3453 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.11 % Allowed : 24.50 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2623 helix: 1.03 (0.15), residues: 1229 sheet: -0.51 (0.22), residues: 522 loop : -0.31 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 28 HIS 0.008 0.001 HIS G 246 PHE 0.024 0.001 PHE G 2 TYR 0.015 0.001 TYR H 239 ARG 0.014 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1071) hydrogen bonds : angle 4.20258 ( 3048) covalent geometry : bond 0.00393 (22309) covalent geometry : angle 0.57425 (30398) *********************** 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 379 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 261 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7981 (mttt) REVERT: A 583 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7790 (ptm160) REVERT: A 725 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: A 757 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7475 (tp) REVERT: A 804 ARG cc_start: 0.7755 (ptm160) cc_final: 0.7534 (ptm160) REVERT: C 257 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: E 65 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: E 66 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7904 (mppt) REVERT: E 112 LEU cc_start: 0.8367 (mm) cc_final: 0.8053 (mt) REVERT: E 269 GLN cc_start: 0.8186 (pm20) cc_final: 0.7979 (pm20) REVERT: E 345 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7781 (mppt) REVERT: G 20 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8142 (tptt) REVERT: G 53 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6563 (mmt-90) REVERT: G 68 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5680 (tpt) REVERT: G 72 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7161 (tt) REVERT: G 175 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6795 (mt) REVERT: H 19 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4538 (tm) REVERT: H 117 LYS cc_start: 0.4989 (tptp) cc_final: 0.4476 (mmmm) REVERT: H 180 ILE cc_start: 0.5759 (mt) cc_final: 0.5435 (tp) REVERT: H 212 LEU cc_start: 0.8672 (mt) cc_final: 0.8307 (tm) outliers start: 118 outliers final: 59 residues processed: 350 average time/residue: 1.2781 time to fit residues: 512.4167 Evaluate side-chains 309 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 442 VAL 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 762 LEU 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 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 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 333 GLU 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 8 GLN 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 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 68 MET 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 161 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 19 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 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 95 optimal weight: 0.0970 chunk 232 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS D 219 ASN E 302 ASN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN G 49 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131152 restraints weight = 28546.497| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.17 r_work: 0.3389 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22309 Z= 0.114 Angle : 0.537 8.551 30398 Z= 0.275 Chirality : 0.039 0.196 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.982 141.145 3453 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.55 % Allowed : 26.67 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2623 helix: 1.19 (0.15), residues: 1241 sheet: -0.44 (0.22), residues: 514 loop : -0.24 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 28 HIS 0.008 0.001 HIS G 246 PHE 0.025 0.001 PHE G 2 TYR 0.013 0.001 TYR H 239 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 1071) hydrogen bonds : angle 4.06015 ( 3048) covalent geometry : bond 0.00260 (22309) covalent geometry : angle 0.53745 (30398) *********************** 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: 82 poor density : 272 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.7972 (mmm) cc_final: 0.7766 (mmm) REVERT: A 500 GLN cc_start: 0.6482 (mp10) cc_final: 0.6275 (mp10) REVERT: A 583 ARG cc_start: 0.7994 (ttt180) cc_final: 0.7788 (ptm160) REVERT: A 725 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: C 320 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8181 (mm) REVERT: E 66 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7917 (mppt) REVERT: E 345 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7815 (mppt) REVERT: F 42 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8214 (p) REVERT: F 149 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7544 (mmm-85) REVERT: F 199 MET cc_start: 0.5449 (ppp) cc_final: 0.4621 (pp-130) REVERT: F 240 LYS cc_start: 0.8590 (tppt) cc_final: 0.8367 (tppp) REVERT: G 20 LYS cc_start: 0.8387 (ttpt) cc_final: 0.8105 (tptt) REVERT: G 61 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7847 (ppp80) REVERT: G 175 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6708 (mt) REVERT: H 117 LYS cc_start: 0.5036 (tptp) cc_final: 0.4506 (mmmm) REVERT: H 180 ILE cc_start: 0.5869 (mt) cc_final: 0.5587 (tp) REVERT: H 212 LEU cc_start: 0.8663 (mt) cc_final: 0.8263 (tm) outliers start: 82 outliers final: 36 residues processed: 335 average time/residue: 1.2666 time to fit residues: 488.1401 Evaluate side-chains 294 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 762 LEU Chi-restraints excluded: chain A residue 776 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 153 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain 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 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 74 SER 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 61 ARG 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 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 224 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 202 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 chunk 121 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 127 optimal weight: 0.0770 chunk 2 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN E 71 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 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 = 0.4103 r_free = 0.4103 target = 0.173544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128529 restraints weight = 28549.154| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.13 r_work: 0.3360 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2527 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= 0.167 Angle : 0.591 16.695 30398 Z= 0.300 Chirality : 0.041 0.192 3536 Planarity : 0.004 0.075 3723 Dihedral : 14.034 141.978 3453 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.20 % Allowed : 26.19 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2623 helix: 1.22 (0.15), residues: 1232 sheet: -0.51 (0.22), residues: 527 loop : -0.24 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 28 HIS 0.006 0.001 HIS G 246 PHE 0.028 0.001 PHE G 2 TYR 0.016 0.001 TYR E 343 ARG 0.019 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 1071) hydrogen bonds : angle 4.10266 ( 3048) covalent geometry : bond 0.00400 (22309) covalent geometry : angle 0.59104 (30398) *********************** 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 352 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 255 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8094 (mmm) cc_final: 0.7851 (mmm) REVERT: A 583 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7753 (ptm160) REVERT: A 725 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: A 757 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7483 (tp) REVERT: B 208 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8146 (tptp) REVERT: C 320 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8265 (mm) REVERT: D 218 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7453 (mm-30) REVERT: E 65 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: E 345 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7830 (mppt) REVERT: F 128 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5995 (mt) REVERT: F 149 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7554 (mmm-85) REVERT: F 199 MET cc_start: 0.5452 (ppp) cc_final: 0.4517 (pp-130) REVERT: F 240 LYS cc_start: 0.8579 (tppt) cc_final: 0.8337 (tppp) REVERT: G 20 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8157 (tptt) REVERT: G 53 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6522 (mmt-90) REVERT: G 61 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7899 (ppp80) REVERT: G 72 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7200 (tt) REVERT: G 175 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6751 (mt) REVERT: H 68 MET cc_start: 0.2029 (mtt) cc_final: 0.1424 (mtp) REVERT: H 117 LYS cc_start: 0.5060 (tptp) cc_final: 0.4498 (mmmm) REVERT: H 139 MET cc_start: 0.4144 (OUTLIER) cc_final: 0.3442 (ppp) outliers start: 97 outliers final: 56 residues processed: 329 average time/residue: 1.3326 time to fit residues: 505.7841 Evaluate side-chains 301 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 235 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU 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 333 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 24 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 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 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 139 MET 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 256 optimal weight: 30.0000 chunk 178 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 193 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 805 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130456 restraints weight = 28573.917| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.63 r_work: 0.3390 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22309 Z= 0.123 Angle : 0.571 14.451 30398 Z= 0.290 Chirality : 0.040 0.188 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.981 142.296 3453 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.38 % Allowed : 27.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2623 helix: 1.30 (0.15), residues: 1232 sheet: -0.45 (0.22), residues: 520 loop : -0.14 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 675 HIS 0.007 0.001 HIS G 246 PHE 0.025 0.001 PHE G 2 TYR 0.012 0.001 TYR H 239 ARG 0.007 0.000 ARG A 532 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 1071) hydrogen bonds : angle 4.05226 ( 3048) covalent geometry : bond 0.00289 (22309) covalent geometry : angle 0.57065 (30398) *********************** 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 337 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 259 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8088 (mmm) cc_final: 0.7848 (mmm) REVERT: A 583 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7839 (ptm160) REVERT: A 725 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: A 805 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6696 (mp10) REVERT: B 208 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8088 (tptp) REVERT: C 320 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8190 (mm) REVERT: D 218 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7439 (mm-30) REVERT: E 345 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7787 (mppt) REVERT: F 128 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5985 (mt) REVERT: F 199 MET cc_start: 0.5374 (ppp) cc_final: 0.4548 (pp-130) REVERT: F 240 LYS cc_start: 0.8581 (tppt) cc_final: 0.8343 (tppp) REVERT: G 20 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8113 (tptt) REVERT: G 25 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: G 61 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7901 (ppp80) REVERT: G 72 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7120 (tt) REVERT: G 175 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6720 (mt) REVERT: H 1 MET cc_start: 0.3955 (pp-130) cc_final: 0.3430 (tmm) REVERT: H 25 GLU cc_start: 0.1794 (OUTLIER) cc_final: 0.0464 (tp30) REVERT: H 41 ASP cc_start: 0.4341 (OUTLIER) cc_final: 0.4115 (m-30) REVERT: H 68 MET cc_start: 0.1973 (mtt) cc_final: 0.1399 (mtp) REVERT: H 117 LYS cc_start: 0.5041 (tptp) cc_final: 0.4525 (mmmm) REVERT: H 181 LYS cc_start: 0.7446 (mtmm) cc_final: 0.7234 (mppt) outliers start: 78 outliers final: 46 residues processed: 323 average time/residue: 1.2470 time to fit residues: 465.8206 Evaluate side-chains 302 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 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 E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE 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 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 0.0670 chunk 255 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 805 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN E 102 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 = 0.4121 r_free = 0.4121 target = 0.175182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130627 restraints weight = 28382.452| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.38 r_work: 0.3377 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22309 Z= 0.130 Angle : 0.580 14.306 30398 Z= 0.295 Chirality : 0.040 0.185 3536 Planarity : 0.004 0.071 3723 Dihedral : 13.967 142.121 3453 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.16 % Allowed : 27.62 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2623 helix: 1.32 (0.15), residues: 1234 sheet: -0.44 (0.22), residues: 519 loop : -0.12 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.006 0.001 HIS G 246 PHE 0.025 0.001 PHE G 2 TYR 0.017 0.001 TYR E 343 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 1071) hydrogen bonds : angle 4.05467 ( 3048) covalent geometry : bond 0.00308 (22309) covalent geometry : angle 0.57961 (30398) *********************** 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 319 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8046 (mmm) cc_final: 0.7832 (mmm) REVERT: A 583 ARG cc_start: 0.8064 (ttt180) cc_final: 0.7840 (ptm160) REVERT: A 725 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: A 757 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7482 (tp) REVERT: B 208 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8082 (tptp) REVERT: C 320 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8216 (mm) REVERT: D 218 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7544 (mm-30) REVERT: E 345 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7804 (mppt) REVERT: F 128 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5961 (mt) REVERT: F 199 MET cc_start: 0.5394 (ppp) cc_final: 0.4503 (pp-130) REVERT: F 240 LYS cc_start: 0.8612 (tppt) cc_final: 0.8386 (tppp) REVERT: G 20 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8122 (tptt) REVERT: G 25 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: G 53 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6473 (mmt-90) REVERT: G 72 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7119 (tt) REVERT: G 175 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6727 (mt) REVERT: H 1 MET cc_start: 0.4117 (pp-130) cc_final: 0.3377 (tmm) REVERT: H 68 MET cc_start: 0.1998 (mtt) cc_final: 0.1496 (mtp) REVERT: H 117 LYS cc_start: 0.5119 (tptp) cc_final: 0.4578 (mmmm) REVERT: H 139 MET cc_start: 0.3994 (OUTLIER) cc_final: 0.3308 (ppp) REVERT: H 181 LYS cc_start: 0.7467 (mtmm) cc_final: 0.7241 (mppt) REVERT: H 256 GLU cc_start: 0.5170 (pm20) cc_final: 0.3370 (pm20) REVERT: H 257 ASP cc_start: 0.7180 (p0) cc_final: 0.6909 (p0) outliers start: 73 outliers final: 49 residues processed: 305 average time/residue: 1.6209 time to fit residues: 570.4221 Evaluate side-chains 296 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 3.550 ------------------------------------------------------------------------------- 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 419 MET 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 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 139 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 138 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN E 102 ASN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132366 restraints weight = 28583.124| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.94 r_work: 0.3386 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22309 Z= 0.125 Angle : 0.581 13.450 30398 Z= 0.294 Chirality : 0.040 0.184 3536 Planarity : 0.004 0.071 3723 Dihedral : 13.952 142.690 3453 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.07 % Allowed : 27.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2623 helix: 1.33 (0.15), residues: 1240 sheet: -0.40 (0.22), residues: 517 loop : -0.08 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.006 0.001 HIS G 246 PHE 0.023 0.001 PHE G 169 TYR 0.012 0.001 TYR H 239 ARG 0.015 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 1071) hydrogen bonds : angle 4.04321 ( 3048) covalent geometry : bond 0.00293 (22309) covalent geometry : angle 0.58078 (30398) ********************** 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 315 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8037 (mmm) cc_final: 0.7822 (mmm) REVERT: A 583 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7838 (ptm160) REVERT: A 725 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: A 757 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 208 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8063 (tptp) REVERT: C 320 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8180 (mm) REVERT: D 218 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7546 (mm-30) REVERT: E 345 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7831 (mppt) REVERT: F 128 ILE cc_start: 0.6142 (OUTLIER) cc_final: 0.5930 (mt) REVERT: F 199 MET cc_start: 0.5348 (ppp) cc_final: 0.4479 (pp-130) REVERT: F 240 LYS cc_start: 0.8601 (tppt) cc_final: 0.8343 (tppp) REVERT: G 20 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8117 (tptt) REVERT: G 25 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6093 (pm20) REVERT: G 61 ARG cc_start: 0.7845 (ppp80) cc_final: 0.7343 (ppp80) REVERT: G 72 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7100 (tt) REVERT: G 175 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6736 (mt) REVERT: H 1 MET cc_start: 0.4145 (pp-130) cc_final: 0.3277 (tmm) REVERT: H 25 GLU cc_start: 0.1737 (OUTLIER) cc_final: 0.0373 (tp30) REVERT: H 68 MET cc_start: 0.2005 (mtt) cc_final: 0.1438 (mtp) REVERT: H 117 LYS cc_start: 0.5115 (tptp) cc_final: 0.4572 (mmmm) REVERT: H 139 MET cc_start: 0.4004 (OUTLIER) cc_final: 0.3362 (ppp) REVERT: H 181 LYS cc_start: 0.7510 (mtmm) cc_final: 0.7291 (mppt) outliers start: 71 outliers final: 47 residues processed: 302 average time/residue: 1.3850 time to fit residues: 486.8579 Evaluate side-chains 295 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 2.269 ------------------------------------------------------------------------------- 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 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 8 GLN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 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 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 25 GLU 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 139 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 0 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 213 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 187 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 582 GLN A 805 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN E 102 ASN G 71 ASN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.176665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132873 restraints weight = 28478.306| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.41 r_work: 0.3408 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22309 Z= 0.111 Angle : 0.577 12.908 30398 Z= 0.291 Chirality : 0.040 0.328 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.883 144.070 3453 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.47 % Allowed : 28.27 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2623 helix: 1.40 (0.15), residues: 1240 sheet: -0.34 (0.22), residues: 512 loop : -0.02 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 28 HIS 0.006 0.000 HIS G 246 PHE 0.021 0.001 PHE G 169 TYR 0.015 0.001 TYR E 343 ARG 0.015 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 1071) hydrogen bonds : angle 4.00756 ( 3048) covalent geometry : bond 0.00257 (22309) covalent geometry : angle 0.57674 (30398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17981.85 seconds wall clock time: 314 minutes 31.28 seconds (18871.28 seconds total)