Starting phenix.real_space_refine on Sat Sep 12 08:05:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfk_25875/09_2026/7tfk_25875.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 220 atoms to isotropic. 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 59 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 8888 2.51 5 N 2521 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14363 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2862 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 2 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2606 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2694 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "I" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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: 2.94, per 1000 atoms: 0.20 Number of scatterers: 14363 At special positions: 0 Unit cell: (87.768, 119.232, 128.34, 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 68 16.00 P 59 15.00 Mg 4 11.99 O 2823 8.00 N 2521 7.00 C 8888 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 563.1 milliseconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 64.0% alpha, 5.8% beta 15 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 426 through 429 removed outlier: 3.640A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 513 through 528 removed outlier: 3.996A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 removed outlier: 4.432A pdb=" N ASN A 537 " --> pdb=" O HIS A 533 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 565 through 572 removed outlier: 4.079A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.650A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 removed outlier: 3.899A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.540A pdb=" N ALA A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 646 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 655 removed outlier: 3.741A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 655 " --> pdb=" O TYR A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 690 removed outlier: 3.880A pdb=" N ILE A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 85 through 98 removed outlier: 3.645A pdb=" N VAL B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.669A pdb=" N GLN B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.787A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.812A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 302 removed outlier: 4.091A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.707A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.562A pdb=" N TYR C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.620A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.954A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.564A pdb=" N MET C 122 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.952A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.914A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.681A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.140A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.540A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 257 through 271 removed outlier: 3.985A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 292 through 313 removed outlier: 3.818A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.758A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 Proline residue: D 85 - end of helix removed outlier: 4.166A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.844A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 154 through 160 removed outlier: 4.292A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.650A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.687A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.746A pdb=" N GLY D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.599A pdb=" N LYS E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 8' Processing helix chain 'E' and resid 20 through 32 removed outlier: 4.052A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.397A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 149 through 161 removed outlier: 3.830A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 removed outlier: 3.568A pdb=" N LYS E 182 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.963A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 removed outlier: 3.541A pdb=" N LYS E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.074A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 351 removed outlier: 8.715A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP A 424 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.585A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.566A pdb=" N LEU B 76 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.566A pdb=" N LEU B 76 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 46 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.515A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.358A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.582A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.963A pdb=" N LEU E 94 " --> pdb=" O CYS E 137 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE E 139 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.628A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 707 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4707 1.36 - 1.51: 3925 1.51 - 1.66: 5953 1.66 - 1.80: 61 1.80 - 1.95: 44 Bond restraints: 14690 Sorted by residual: bond pdb=" C3' DG K 25 " pdb=" C2' DG K 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" N ILE A 547 " pdb=" CA ILE A 547 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC I 19 " pdb=" C2' DC I 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.61e+00 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 ... (remaining 14685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 19416 1.69 - 3.37: 535 3.37 - 5.06: 89 5.06 - 6.74: 24 6.74 - 8.43: 4 Bond angle restraints: 20068 Sorted by residual: angle pdb=" N VAL B 88 " pdb=" CA VAL B 88 " pdb=" C VAL B 88 " ideal model delta sigma weight residual 111.62 106.86 4.76 7.90e-01 1.60e+00 3.63e+01 angle pdb=" CA PRO A 500 " pdb=" N PRO A 500 " pdb=" CD PRO A 500 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.76e+01 angle pdb=" N3 DT K 24 " pdb=" C4 DT K 24 " pdb=" O4 DT K 24 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N GLU C 332 " pdb=" CA GLU C 332 " pdb=" C GLU C 332 " ideal model delta sigma weight residual 112.54 107.29 5.25 1.22e+00 6.72e-01 1.85e+01 angle pdb=" N3 DT K 26 " pdb=" C4 DT K 26 " pdb=" O4 DT K 26 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 20063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 8398 29.06 - 58.12: 444 58.12 - 87.18: 29 87.18 - 116.24: 3 116.24 - 145.30: 1 Dihedral angle restraints: 8875 sinusoidal: 3958 harmonic: 4917 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -169.47 109.47 1 2.00e+01 2.50e-03 3.20e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 77.57 -145.30 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA LEU B 67 " pdb=" C LEU B 67 " pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 8872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1534 0.035 - 0.071: 546 0.071 - 0.106: 186 0.106 - 0.142: 49 0.142 - 0.177: 10 Chirality restraints: 2325 Sorted by residual: chirality pdb=" CA ILE A 547 " pdb=" N ILE A 547 " pdb=" C ILE A 547 " pdb=" CB ILE A 547 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA GLU E 58 " pdb=" N GLU E 58 " pdb=" C GLU E 58 " pdb=" CB GLU E 58 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA GLU C 118 " pdb=" N GLU C 118 " pdb=" C GLU C 118 " pdb=" CB GLU C 118 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 2322 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " -0.099 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO A 500 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 54 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C MET E 54 " 0.034 2.00e-02 2.50e+03 pdb=" O MET E 54 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA E 55 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 605 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 606 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.024 5.00e-02 4.00e+02 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 263 2.65 - 3.22: 13569 3.22 - 3.78: 23990 3.78 - 4.34: 32023 4.34 - 4.90: 51185 Nonbonded interactions: 121030 Sorted by model distance: nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.092 2.170 nonbonded pdb=" OD2 ASP A 424 " pdb="MG MG A 902 " model vdw 2.097 2.170 nonbonded pdb=" O3G AGS A 901 " pdb="MG MG A 902 " model vdw 2.102 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.123 2.170 nonbonded pdb=" O1A AGS B 401 " pdb="MG MG B 402 " model vdw 2.126 2.170 ... (remaining 121025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 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 0.093 14691 Z= 0.245 Angle : 0.671 8.431 20068 Z= 0.423 Chirality : 0.042 0.177 2325 Planarity : 0.005 0.146 2379 Dihedral : 15.769 145.303 5677 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1664 helix: 0.68 (0.17), residues: 974 sheet: -0.31 (0.46), residues: 140 loop : -0.61 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 632 TYR 0.022 0.002 TYR C 71 PHE 0.016 0.001 PHE D 280 TRP 0.028 0.002 TRP E 259 HIS 0.009 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.24 (14690) covalent geometry : angle 0.67104 / 0.42 (20068) hydrogen bonds : bond 0.16448 / 11.17 ( 740) hydrogen bonds : angle 6.13585 / 4.32 ( 2142) Misc. bond : bond 0.00286 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.566 Fit side-chains REVERT: A 423 MET cc_start: 0.6285 (ppp) cc_final: 0.5788 (ppp) REVERT: B 50 MET cc_start: 0.4995 (pmm) cc_final: 0.4573 (pmm) REVERT: B 177 GLN cc_start: 0.6174 (mt0) cc_final: 0.5296 (mm-40) REVERT: C 135 GLU cc_start: 0.5772 (mm-30) cc_final: 0.5348 (mm-30) REVERT: C 200 LEU cc_start: 0.5980 (tt) cc_final: 0.5089 (pp) outliers start: 2 outliers final: 1 residues processed: 241 average time/residue: 0.1074 time to fit residues: 40.3665 Evaluate side-chains 191 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 546 ASN A 610 HIS B 79 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 333 ASN D 128 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.193117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.166185 restraints weight = 20642.327| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 2.40 r_work: 0.4168 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14691 Z= 0.153 Angle : 0.610 8.381 20068 Z= 0.329 Chirality : 0.042 0.160 2325 Planarity : 0.005 0.085 2379 Dihedral : 15.758 149.229 2349 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.41 % Allowed : 7.27 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1664 helix: 0.99 (0.17), residues: 974 sheet: -0.50 (0.44), residues: 146 loop : -0.51 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 88 TYR 0.020 0.002 TYR B 186 PHE 0.020 0.002 PHE A 443 TRP 0.015 0.002 TRP A 323 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (14690) covalent geometry : angle 0.60957 / 0.33 (20068) hydrogen bonds : bond 0.04951 / 3.31 ( 740) hydrogen bonds : angle 4.68241 / 3.34 ( 2142) Misc. bond : bond 0.00149 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 423 MET cc_start: 0.6659 (ppp) cc_final: 0.6347 (ppp) REVERT: A 538 GLU cc_start: 0.7282 (mp0) cc_final: 0.7073 (mp0) REVERT: B 50 MET cc_start: 0.5146 (pmm) cc_final: 0.4483 (pmm) REVERT: B 177 GLN cc_start: 0.6156 (mt0) cc_final: 0.5327 (mm-40) REVERT: C 135 GLU cc_start: 0.6273 (mm-30) cc_final: 0.5931 (mm-30) REVERT: C 148 ASN cc_start: 0.6844 (m-40) cc_final: 0.6498 (m-40) REVERT: C 200 LEU cc_start: 0.5917 (tt) cc_final: 0.5087 (pp) outliers start: 21 outliers final: 15 residues processed: 211 average time/residue: 0.1047 time to fit residues: 34.0042 Evaluate side-chains 198 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 204 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 319 GLN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.189386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.161848 restraints weight = 20874.955| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.33 r_work: 0.4120 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14691 Z= 0.166 Angle : 0.612 9.881 20068 Z= 0.325 Chirality : 0.041 0.166 2325 Planarity : 0.004 0.064 2379 Dihedral : 15.965 155.130 2347 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.55 % Allowed : 10.71 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1664 helix: 0.97 (0.17), residues: 976 sheet: -0.43 (0.45), residues: 142 loop : -0.65 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 183 TYR 0.020 0.002 TYR B 186 PHE 0.016 0.002 PHE A 496 TRP 0.022 0.002 TRP A 669 HIS 0.007 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (14690) covalent geometry : angle 0.61212 / 0.33 (20068) hydrogen bonds : bond 0.04498 / 3.00 ( 740) hydrogen bonds : angle 4.45108 / 3.18 ( 2142) Misc. bond : bond 0.00224 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 TRP cc_start: 0.6541 (t60) cc_final: 0.6299 (t60) REVERT: A 423 MET cc_start: 0.6790 (ppp) cc_final: 0.6562 (ppp) REVERT: A 504 ASP cc_start: 0.7081 (m-30) cc_final: 0.6765 (p0) REVERT: B 177 GLN cc_start: 0.6126 (mt0) cc_final: 0.5264 (mm-40) REVERT: C 134 ILE cc_start: 0.8403 (mt) cc_final: 0.8179 (mt) REVERT: C 135 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6027 (mm-30) REVERT: C 200 LEU cc_start: 0.5866 (tt) cc_final: 0.5051 (pp) REVERT: E 1 MET cc_start: 0.2966 (tpp) cc_final: 0.2343 (tpp) REVERT: E 66 TYR cc_start: 0.5070 (m-80) cc_final: 0.4540 (m-80) REVERT: E 156 ARG cc_start: 0.8038 (tpt170) cc_final: 0.7810 (tpt170) outliers start: 23 outliers final: 18 residues processed: 214 average time/residue: 0.1020 time to fit residues: 34.3026 Evaluate side-chains 207 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 70 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 208 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.189652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.162741 restraints weight = 20680.220| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.30 r_work: 0.4123 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14691 Z= 0.140 Angle : 0.579 9.808 20068 Z= 0.309 Chirality : 0.040 0.202 2325 Planarity : 0.004 0.057 2379 Dihedral : 15.924 154.178 2347 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.95 % Allowed : 11.58 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1664 helix: 1.07 (0.17), residues: 976 sheet: -0.39 (0.44), residues: 147 loop : -0.63 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.019 0.002 TYR B 186 PHE 0.013 0.002 PHE E 345 TRP 0.024 0.001 TRP A 669 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14690) covalent geometry : angle 0.57893 / 0.31 (20068) hydrogen bonds : bond 0.04038 / 2.70 ( 740) hydrogen bonds : angle 4.36181 / 3.12 ( 2142) Misc. bond : bond 0.00124 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 423 MET cc_start: 0.6900 (ppp) cc_final: 0.6610 (ppp) REVERT: A 504 ASP cc_start: 0.7027 (m-30) cc_final: 0.6750 (p0) REVERT: A 538 GLU cc_start: 0.7228 (mp0) cc_final: 0.6944 (mp0) REVERT: B 177 GLN cc_start: 0.6109 (mt0) cc_final: 0.5241 (mm-40) REVERT: C 134 ILE cc_start: 0.8418 (mt) cc_final: 0.8205 (mt) REVERT: C 135 GLU cc_start: 0.6403 (mm-30) cc_final: 0.6023 (mm-30) REVERT: C 199 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: C 334 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: E 1 MET cc_start: 0.2969 (tpp) cc_final: 0.2485 (tpp) REVERT: E 7 LYS cc_start: 0.8092 (pttt) cc_final: 0.7232 (ptpp) REVERT: E 156 ARG cc_start: 0.7976 (tpt170) cc_final: 0.7765 (tpt170) outliers start: 29 outliers final: 20 residues processed: 214 average time/residue: 0.1059 time to fit residues: 35.2375 Evaluate side-chains 202 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 319 GLN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.185997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.158042 restraints weight = 20926.515| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.25 r_work: 0.4085 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14691 Z= 0.181 Angle : 0.625 9.786 20068 Z= 0.331 Chirality : 0.042 0.193 2325 Planarity : 0.004 0.052 2379 Dihedral : 16.037 160.223 2347 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.29 % Allowed : 13.20 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1664 helix: 0.89 (0.17), residues: 990 sheet: -0.51 (0.44), residues: 147 loop : -0.74 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 206 TYR 0.029 0.002 TYR C 71 PHE 0.018 0.002 PHE A 443 TRP 0.030 0.002 TRP A 669 HIS 0.004 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (14690) covalent geometry : angle 0.62516 / 0.33 (20068) hydrogen bonds : bond 0.04309 / 2.88 ( 740) hydrogen bonds : angle 4.39788 / 3.16 ( 2142) Misc. bond : bond 0.00155 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.6855 (ppp) cc_final: 0.6583 (ppp) REVERT: A 504 ASP cc_start: 0.7244 (m-30) cc_final: 0.6806 (p0) REVERT: B 177 GLN cc_start: 0.6190 (mt0) cc_final: 0.5200 (mm-40) REVERT: C 134 ILE cc_start: 0.8412 (mt) cc_final: 0.8202 (mt) REVERT: C 135 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6121 (mm-30) REVERT: C 199 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: C 200 LEU cc_start: 0.6102 (tt) cc_final: 0.5083 (pp) REVERT: C 334 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6972 (pt0) REVERT: E 1 MET cc_start: 0.2894 (tpp) cc_final: 0.2387 (tpp) REVERT: E 7 LYS cc_start: 0.8111 (pttt) cc_final: 0.7344 (ptpp) REVERT: E 174 MET cc_start: 0.3995 (mtm) cc_final: 0.3770 (mtm) outliers start: 34 outliers final: 25 residues processed: 218 average time/residue: 0.1114 time to fit residues: 37.5190 Evaluate side-chains 212 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.188003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.160108 restraints weight = 20797.051| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.28 r_work: 0.4108 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14691 Z= 0.138 Angle : 0.594 9.945 20068 Z= 0.317 Chirality : 0.040 0.177 2325 Planarity : 0.004 0.050 2379 Dihedral : 15.990 156.585 2347 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.82 % Allowed : 14.88 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1664 helix: 1.05 (0.17), residues: 978 sheet: -0.54 (0.44), residues: 153 loop : -0.61 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 221 TYR 0.020 0.002 TYR B 186 PHE 0.016 0.002 PHE E 345 TRP 0.029 0.002 TRP A 669 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14690) covalent geometry : angle 0.59449 / 0.32 (20068) hydrogen bonds : bond 0.03939 / 2.65 ( 740) hydrogen bonds : angle 4.30405 / 3.08 ( 2142) Misc. bond : bond 0.00109 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.6793 (ppp) cc_final: 0.6491 (ppp) REVERT: B 177 GLN cc_start: 0.6146 (mt0) cc_final: 0.5416 (mm110) REVERT: C 134 ILE cc_start: 0.8431 (mt) cc_final: 0.8188 (mt) REVERT: C 135 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6184 (mm-30) REVERT: C 199 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: C 200 LEU cc_start: 0.6053 (tt) cc_final: 0.5115 (pp) REVERT: C 334 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7020 (pt0) REVERT: E 1 MET cc_start: 0.2971 (tpp) cc_final: 0.2471 (tpp) REVERT: E 7 LYS cc_start: 0.8145 (pttt) cc_final: 0.7377 (ptpp) REVERT: E 174 MET cc_start: 0.4456 (mtm) cc_final: 0.4094 (mtm) outliers start: 27 outliers final: 20 residues processed: 216 average time/residue: 0.1092 time to fit residues: 36.5033 Evaluate side-chains 207 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.188222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.160492 restraints weight = 20587.927| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.25 r_work: 0.4110 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14691 Z= 0.133 Angle : 0.583 10.159 20068 Z= 0.309 Chirality : 0.040 0.211 2325 Planarity : 0.004 0.048 2379 Dihedral : 15.971 156.817 2347 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.36 % Allowed : 15.22 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1664 helix: 1.08 (0.17), residues: 976 sheet: -0.54 (0.44), residues: 153 loop : -0.58 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.020 0.001 TYR B 186 PHE 0.014 0.002 PHE E 345 TRP 0.034 0.002 TRP A 669 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (14690) covalent geometry : angle 0.58307 / 0.31 (20068) hydrogen bonds : bond 0.03786 / 2.53 ( 740) hydrogen bonds : angle 4.25462 / 3.04 ( 2142) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.6817 (ppp) cc_final: 0.6509 (ppp) REVERT: A 538 GLU cc_start: 0.7154 (mp0) cc_final: 0.6900 (mp0) REVERT: B 177 GLN cc_start: 0.6167 (mt0) cc_final: 0.5257 (mm-40) REVERT: C 134 ILE cc_start: 0.8440 (mt) cc_final: 0.8203 (mt) REVERT: C 135 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6102 (mm-30) REVERT: C 199 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 200 LEU cc_start: 0.6055 (tt) cc_final: 0.5158 (pp) REVERT: C 334 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: D 25 GLN cc_start: 0.5806 (pp30) cc_final: 0.5604 (pp30) REVERT: E 1 MET cc_start: 0.2933 (tpp) cc_final: 0.2409 (tpp) REVERT: E 7 LYS cc_start: 0.8167 (pttt) cc_final: 0.7373 (ptpp) REVERT: E 58 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6863 (mm-30) REVERT: E 174 MET cc_start: 0.4499 (mtm) cc_final: 0.4179 (mtm) outliers start: 35 outliers final: 28 residues processed: 213 average time/residue: 0.1094 time to fit residues: 36.0293 Evaluate side-chains 214 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 319 GLN E 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.187177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.159325 restraints weight = 20662.962| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.23 r_work: 0.4100 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14691 Z= 0.146 Angle : 0.602 10.211 20068 Z= 0.318 Chirality : 0.040 0.179 2325 Planarity : 0.004 0.047 2379 Dihedral : 15.996 158.177 2347 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.49 % Allowed : 15.76 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1664 helix: 1.10 (0.17), residues: 970 sheet: -0.57 (0.44), residues: 153 loop : -0.64 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.019 0.002 TYR B 186 PHE 0.017 0.002 PHE A 443 TRP 0.036 0.002 TRP A 669 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (14690) covalent geometry : angle 0.60164 / 0.32 (20068) hydrogen bonds : bond 0.03830 / 2.55 ( 740) hydrogen bonds : angle 4.28361 / 3.05 ( 2142) Misc. bond : bond 0.00104 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.6836 (ppp) cc_final: 0.6495 (ppp) REVERT: B 103 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7464 (mm) REVERT: B 177 GLN cc_start: 0.6171 (mt0) cc_final: 0.5262 (mm-40) REVERT: C 134 ILE cc_start: 0.8440 (mt) cc_final: 0.8209 (mt) REVERT: C 135 GLU cc_start: 0.6357 (mm-30) cc_final: 0.6113 (mm-30) REVERT: C 199 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: C 200 LEU cc_start: 0.6004 (tt) cc_final: 0.5124 (pp) REVERT: C 334 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: D 25 GLN cc_start: 0.5807 (pp30) cc_final: 0.5578 (pp30) REVERT: E 1 MET cc_start: 0.2957 (tpp) cc_final: 0.2422 (tpp) REVERT: E 7 LYS cc_start: 0.8173 (pttt) cc_final: 0.7360 (ptpp) REVERT: E 58 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6949 (mm-30) outliers start: 37 outliers final: 27 residues processed: 211 average time/residue: 0.1002 time to fit residues: 32.9395 Evaluate side-chains 212 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 0.0770 chunk 115 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 319 GLN E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.187921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.160127 restraints weight = 20861.450| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.24 r_work: 0.4110 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14691 Z= 0.137 Angle : 0.601 11.413 20068 Z= 0.318 Chirality : 0.040 0.185 2325 Planarity : 0.004 0.047 2379 Dihedral : 15.988 157.592 2347 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.15 % Allowed : 16.36 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1664 helix: 1.10 (0.17), residues: 976 sheet: -0.57 (0.44), residues: 153 loop : -0.60 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.019 0.001 TYR B 186 PHE 0.019 0.002 PHE D 290 TRP 0.040 0.002 TRP A 669 HIS 0.003 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14690) covalent geometry : angle 0.60127 / 0.32 (20068) hydrogen bonds : bond 0.03741 / 2.51 ( 740) hydrogen bonds : angle 4.28922 / 3.06 ( 2142) Misc. bond : bond 0.00086 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.6833 (ppp) cc_final: 0.6487 (ppp) REVERT: A 538 GLU cc_start: 0.7137 (mp0) cc_final: 0.6926 (mp0) REVERT: B 103 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7462 (mm) REVERT: B 177 GLN cc_start: 0.6156 (mt0) cc_final: 0.5263 (mm-40) REVERT: C 134 ILE cc_start: 0.8435 (mt) cc_final: 0.8202 (mt) REVERT: C 135 GLU cc_start: 0.6348 (mm-30) cc_final: 0.6120 (mm-30) REVERT: C 199 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: C 200 LEU cc_start: 0.5941 (tt) cc_final: 0.5096 (pp) REVERT: C 334 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: D 25 GLN cc_start: 0.5829 (pp30) cc_final: 0.5593 (pp30) REVERT: E 1 MET cc_start: 0.2992 (tpp) cc_final: 0.2452 (tpp) REVERT: E 7 LYS cc_start: 0.8168 (pttt) cc_final: 0.7347 (ptpp) REVERT: E 58 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6896 (mm-30) outliers start: 32 outliers final: 28 residues processed: 213 average time/residue: 0.1061 time to fit residues: 35.2220 Evaluate side-chains 216 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 0.0050 chunk 153 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 319 GLN E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.186321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.158590 restraints weight = 20745.932| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.21 r_work: 0.4090 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14691 Z= 0.160 Angle : 0.621 11.255 20068 Z= 0.328 Chirality : 0.041 0.176 2325 Planarity : 0.004 0.046 2379 Dihedral : 16.027 159.963 2347 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.49 % Allowed : 16.23 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1664 helix: 1.01 (0.16), residues: 978 sheet: -0.66 (0.44), residues: 155 loop : -0.65 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 90 TYR 0.019 0.002 TYR B 186 PHE 0.018 0.002 PHE D 290 TRP 0.036 0.002 TRP A 669 HIS 0.005 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14690) covalent geometry : angle 0.62117 / 0.33 (20068) hydrogen bonds : bond 0.03916 / 2.62 ( 740) hydrogen bonds : angle 4.30799 / 3.07 ( 2142) Misc. bond : bond 0.00101 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.6854 (ppp) cc_final: 0.6465 (ppp) REVERT: A 538 GLU cc_start: 0.7134 (mp0) cc_final: 0.6914 (mp0) REVERT: B 90 ARG cc_start: 0.6037 (OUTLIER) cc_final: 0.5831 (ptt90) REVERT: B 103 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7536 (mm) REVERT: B 177 GLN cc_start: 0.6170 (mt0) cc_final: 0.5267 (mm-40) REVERT: B 192 GLU cc_start: 0.7904 (pp20) cc_final: 0.7677 (pp20) REVERT: C 134 ILE cc_start: 0.8444 (mt) cc_final: 0.8211 (mt) REVERT: C 135 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6167 (mm-30) REVERT: C 199 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 200 LEU cc_start: 0.5973 (tt) cc_final: 0.5126 (pp) REVERT: C 334 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: D 25 GLN cc_start: 0.5874 (pp30) cc_final: 0.5624 (pp30) REVERT: E 1 MET cc_start: 0.3005 (tpp) cc_final: 0.2429 (tpp) REVERT: E 7 LYS cc_start: 0.8172 (pttt) cc_final: 0.7359 (ptpp) REVERT: E 58 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6941 (mm-30) outliers start: 37 outliers final: 29 residues processed: 211 average time/residue: 0.1060 time to fit residues: 34.9675 Evaluate side-chains 217 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 319 GLN E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.186236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.158299 restraints weight = 20793.918| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.22 r_work: 0.4087 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14691 Z= 0.158 Angle : 0.627 11.739 20068 Z= 0.331 Chirality : 0.041 0.284 2325 Planarity : 0.004 0.046 2379 Dihedral : 16.032 160.423 2347 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.22 % Allowed : 16.43 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1664 helix: 1.01 (0.17), residues: 976 sheet: -0.71 (0.44), residues: 153 loop : -0.65 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.019 0.002 TYR B 186 PHE 0.018 0.002 PHE D 290 TRP 0.034 0.002 TRP A 669 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (14690) covalent geometry : angle 0.62743 / 0.33 (20068) hydrogen bonds : bond 0.03918 / 2.62 ( 740) hydrogen bonds : angle 4.32003 / 3.08 ( 2142) Misc. bond : bond 0.00090 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3449.86 seconds wall clock time: 60 minutes 13.90 seconds (3613.90 seconds total)