Starting phenix.real_space_refine on Sun Jul 5 04:58:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l7p_62876/07_2026/9l7p_62876_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l7p_62876/07_2026/9l7p_62876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l7p_62876/07_2026/9l7p_62876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l7p_62876/07_2026/9l7p_62876.map" model { file = "/net/cci-nas-00/data/ceres_data/9l7p_62876/07_2026/9l7p_62876_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l7p_62876/07_2026/9l7p_62876_neut.cif" } resolution = 3.03 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 172 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 15192 2.51 5 N 4381 2.21 5 O 5141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 195 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24962 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4206 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain breaks: 1 Chain: "B" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3814 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 15, 'TRANS': 459} Chain breaks: 3 Chain: "C" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3200 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 2 Chain: "D" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3528 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2481 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain: "F" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2481 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain: "H" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1754 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 849 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 14, 'rna3p': 25} Chain: "J" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1501 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 849 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 14, 'rna3p': 25} Chain: "L" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20063 SG CYS H 43 53.683 114.391 145.797 1.00367.12 S ATOM 20086 SG CYS H 46 52.966 114.583 142.432 1.00362.14 S ATOM 20357 SG CYS H 78 53.347 111.188 144.297 1.00355.18 S ATOM 20446 SG CYS H 90 56.087 113.213 142.963 1.00341.89 S Time building chain proxies: 5.71, per 1000 atoms: 0.23 Number of scatterers: 24962 At special positions: 0 Unit cell: (117.75, 158.25, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 172 15.00 Mg 2 11.99 O 5141 8.00 N 4381 7.00 C 15192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 78 " Number of angles added : 6 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 24 sheets defined 51.4% alpha, 13.0% beta 37 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.994A pdb=" N ILE A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 3.791A pdb=" N LYS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.854A pdb=" N LEU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.807A pdb=" N SER A 208 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.783A pdb=" N ALA A 228 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.599A pdb=" N PHE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 removed outlier: 4.051A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.537A pdb=" N VAL A 275 " --> pdb=" O GLN A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 279 through 303 removed outlier: 4.016A pdb=" N ARG A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.742A pdb=" N VAL A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 379 removed outlier: 3.787A pdb=" N PHE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.720A pdb=" N GLY A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.538A pdb=" N GLN A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 407' Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.774A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 433' Processing helix chain 'A' and resid 434 through 435 No H-bonds generated for 'chain 'A' and resid 434 through 435' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 465 through 473 removed outlier: 3.794A pdb=" N ILE A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.595A pdb=" N ASN A 491 " --> pdb=" O HIS A 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 494 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 removed outlier: 3.768A pdb=" N LEU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.580A pdb=" N LEU A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.842A pdb=" N ASN A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.752A pdb=" N ALA B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.624A pdb=" N TYR B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.626A pdb=" N ILE B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.714A pdb=" N LYS B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 190 " --> pdb=" O TRP B 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.517A pdb=" N ALA B 228 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.961A pdb=" N PHE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 245 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.681A pdb=" N LYS B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 379 removed outlier: 3.588A pdb=" N VAL B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.932A pdb=" N GLY B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.106A pdb=" N GLN B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.616A pdb=" N LEU B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 4.023A pdb=" N LEU B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 433' Processing helix chain 'B' and resid 434 through 435 No H-bonds generated for 'chain 'B' and resid 434 through 435' Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 465 through 473 removed outlier: 3.885A pdb=" N GLU B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 487 through 499 removed outlier: 3.661A pdb=" N ASN B 491 " --> pdb=" O HIS B 487 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 519 Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.691A pdb=" N SER B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 13 through 26 removed outlier: 3.999A pdb=" N ALA C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 49 removed outlier: 3.839A pdb=" N MET C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 43 " --> pdb=" O TRP C 39 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 119 removed outlier: 3.829A pdb=" N LEU C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 removed outlier: 3.902A pdb=" N LYS C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 190 " --> pdb=" O TRP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 4.120A pdb=" N SER C 208 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 230 removed outlier: 3.582A pdb=" N TYR C 229 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 254 removed outlier: 3.674A pdb=" N PHE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 243 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 326 removed outlier: 3.667A pdb=" N VAL C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 358 through 379 removed outlier: 3.815A pdb=" N PHE C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 379 " --> pdb=" O MET C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.899A pdb=" N GLY C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.877A pdb=" N GLN C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.859A pdb=" N ASN C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.515A pdb=" N LEU C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR C 434 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 38 through 48 removed outlier: 4.042A pdb=" N TYR D 46 " --> pdb=" O MET D 42 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 119 removed outlier: 3.856A pdb=" N LEU D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 removed outlier: 4.061A pdb=" N ASP D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 190 " --> pdb=" O TRP D 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.584A pdb=" N ARG D 207 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER D 208 " --> pdb=" O VAL D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 204 through 208' Processing helix chain 'D' and resid 224 through 230 removed outlier: 3.567A pdb=" N ALA D 228 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 229 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 255 removed outlier: 3.893A pdb=" N PHE D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 243 " --> pdb=" O PHE D 239 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 277 removed outlier: 3.618A pdb=" N ASN D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 281 removed outlier: 5.917A pdb=" N SER D 281 " --> pdb=" O GLY D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 281' Processing helix chain 'D' and resid 282 through 304 removed outlier: 3.931A pdb=" N ALA D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 326 removed outlier: 3.804A pdb=" N VAL D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 357 Processing helix chain 'D' and resid 358 through 379 removed outlier: 3.865A pdb=" N PHE D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.804A pdb=" N GLY D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 408 through 417 removed outlier: 3.824A pdb=" N ASN D 412 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 435 removed outlier: 4.178A pdb=" N THR D 434 " --> pdb=" O VAL D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 14 through 22 removed outlier: 3.867A pdb=" N ILE E 18 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.502A pdb=" N ILE E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN E 60 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 86 removed outlier: 3.658A pdb=" N ASN E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HIS E 86 " --> pdb=" O ASN E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 removed outlier: 3.861A pdb=" N GLU E 114 " --> pdb=" O TRP E 110 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 116 " --> pdb=" O CYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 155 through 163 removed outlier: 3.750A pdb=" N ILE E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 177 removed outlier: 3.730A pdb=" N ALA E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 201 through 215 removed outlier: 4.044A pdb=" N THR E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 4.085A pdb=" N THR E 225 " --> pdb=" O HIS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 266 removed outlier: 3.631A pdb=" N LEU E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 266 " --> pdb=" O ASN E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 288 removed outlier: 4.346A pdb=" N HIS E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 299 removed outlier: 4.162A pdb=" N THR E 293 " --> pdb=" O PRO E 289 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 294 " --> pdb=" O SER E 290 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 308 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 14 through 22 Processing helix chain 'F' and resid 24 through 27 Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.514A pdb=" N ASP F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 59 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR F 62 " --> pdb=" O PHE F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 85 removed outlier: 3.629A pdb=" N ASN F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 104 removed outlier: 3.528A pdb=" N SER F 103 " --> pdb=" O PHE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 115 Processing helix chain 'F' and resid 124 through 136 removed outlier: 3.808A pdb=" N LYS F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE F 130 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 3.608A pdb=" N ASN F 161 " --> pdb=" O PRO F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 177 removed outlier: 4.206A pdb=" N LYS F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.873A pdb=" N THR F 205 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 207 " --> pdb=" O PRO F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 225 removed outlier: 3.909A pdb=" N THR F 225 " --> pdb=" O HIS F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 266 removed outlier: 3.759A pdb=" N HIS F 259 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F 260 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR F 266 " --> pdb=" O ASN F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 288 removed outlier: 3.762A pdb=" N ALA F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 299 removed outlier: 3.853A pdb=" N THR F 293 " --> pdb=" O PRO F 289 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN F 296 " --> pdb=" O ILE F 292 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 298 " --> pdb=" O ARG F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 308 removed outlier: 3.638A pdb=" N ARG F 308 " --> pdb=" O MET F 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 22 through 26 Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 31 through 40 removed outlier: 3.586A pdb=" N GLU H 37 " --> pdb=" O PRO H 33 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 90 through 97 removed outlier: 3.733A pdb=" N ASP H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 106 removed outlier: 3.906A pdb=" N LEU H 106 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 Processing helix chain 'H' and resid 133 through 147 removed outlier: 3.701A pdb=" N LYS H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 165 Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.574A pdb=" N LEU H 189 " --> pdb=" O TRP H 185 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU H 192 " --> pdb=" O MET H 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU H 197 " --> pdb=" O LEU H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 210 removed outlier: 3.827A pdb=" N LEU H 205 " --> pdb=" O TYR H 201 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP H 209 " --> pdb=" O LEU H 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 83 removed outlier: 3.551A pdb=" N LEU A 69 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 147 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 69 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER A 145 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU A 71 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP A 143 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 3.865A pdb=" N THR A 425 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 396 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 89 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 336 removed outlier: 4.261A pdb=" N ASN A 331 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 83 removed outlier: 3.578A pdb=" N PHE B 74 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 79 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS B 72 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU B 81 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR B 70 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS B 83 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG B 68 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 65 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 147 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 69 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER B 145 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU B 71 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP B 143 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP B 73 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR B 141 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 159 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 203 removed outlier: 3.709A pdb=" N THR B 425 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B 89 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR B 426 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 91 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 90 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 335 removed outlier: 4.044A pdb=" N ASN B 331 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 83 removed outlier: 6.783A pdb=" N LEU C 79 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 72 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU C 81 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR C 70 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS C 83 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG C 68 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR C 147 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU C 69 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER C 145 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU C 71 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP C 143 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP C 73 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR C 141 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 159 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 203 removed outlier: 3.507A pdb=" N ALA C 201 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 425 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 89 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR C 426 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 91 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 90 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 335 removed outlier: 4.096A pdb=" N ASN C 331 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.718A pdb=" N LEU D 79 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS D 72 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU D 81 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR D 70 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS D 83 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ARG D 68 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR D 147 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU D 69 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER D 145 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU D 71 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP D 143 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP D 73 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR D 141 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 199 through 203 removed outlier: 3.589A pdb=" N THR D 425 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR D 89 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR D 426 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 91 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 90 " --> pdb=" O ARG D 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 329 through 337 removed outlier: 3.944A pdb=" N ASN D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 29 through 35 Processing sheet with id=AB9, first strand: chain 'E' and resid 181 through 184 removed outlier: 3.565A pdb=" N THR E 183 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 189 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER E 193 " --> pdb=" O TYR E 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC2, first strand: chain 'F' and resid 29 through 35 Processing sheet with id=AC3, first strand: chain 'F' and resid 181 through 185 removed outlier: 3.604A pdb=" N THR F 183 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 235 through 236 Processing sheet with id=AC5, first strand: chain 'H' and resid 53 through 57 Processing sheet with id=AC6, first strand: chain 'H' and resid 118 through 120 832 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4316 1.31 - 1.44: 7222 1.44 - 1.57: 13789 1.57 - 1.70: 327 1.70 - 1.83: 122 Bond restraints: 25776 Sorted by residual: bond pdb=" C SER B 478 " pdb=" N THR B 479 " ideal model delta sigma weight residual 1.328 1.231 0.097 1.14e-02 7.69e+03 7.21e+01 bond pdb=" C ASP A 498 " pdb=" N ASN A 499 " ideal model delta sigma weight residual 1.335 1.443 -0.108 1.39e-02 5.18e+03 6.03e+01 bond pdb=" C ASP B 139 " pdb=" N ARG B 140 " ideal model delta sigma weight residual 1.333 1.437 -0.104 1.45e-02 4.76e+03 5.19e+01 bond pdb=" C ARG E 37 " pdb=" N THR E 38 " ideal model delta sigma weight residual 1.333 1.250 0.083 1.16e-02 7.43e+03 5.07e+01 bond pdb=" C THR E 38 " pdb=" N THR E 39 " ideal model delta sigma weight residual 1.332 1.417 -0.086 1.25e-02 6.40e+03 4.68e+01 ... (remaining 25771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 34520 3.83 - 7.65: 1017 7.65 - 11.48: 28 11.48 - 15.30: 3 15.30 - 19.13: 3 Bond angle restraints: 35571 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.74 19.13 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.88 18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 124.04 12.79 1.00e+00 1.00e+00 1.64e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 125.25 11.58 1.00e+00 1.00e+00 1.34e+02 ... (remaining 35566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 14883 35.84 - 71.67: 596 71.67 - 107.51: 37 107.51 - 143.34: 1 143.34 - 179.18: 4 Dihedral angle restraints: 15521 sinusoidal: 7744 harmonic: 7777 Sorted by residual: dihedral pdb=" O4' U I 57 " pdb=" C1' U I 57 " pdb=" N1 U I 57 " pdb=" C2 U I 57 " ideal model delta sinusoidal sigma weight residual -128.00 51.18 -179.18 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U K 58 " pdb=" C1' U K 58 " pdb=" N1 U K 58 " pdb=" C2 U K 58 " ideal model delta sinusoidal sigma weight residual 232.00 53.42 178.58 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 58 " pdb=" C1' U I 58 " pdb=" N1 U I 58 " pdb=" C2 U I 58 " ideal model delta sinusoidal sigma weight residual 232.00 55.64 176.36 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3628 0.147 - 0.294: 382 0.294 - 0.442: 15 0.442 - 0.589: 0 0.589 - 0.736: 1 Chirality restraints: 4026 Sorted by residual: chirality pdb=" CA LYS D 216 " pdb=" N LYS D 216 " pdb=" C LYS D 216 " pdb=" CB LYS D 216 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA TRP A 488 " pdb=" N TRP A 488 " pdb=" C TRP A 488 " pdb=" CB TRP A 488 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA PRO B 327 " pdb=" N PRO B 327 " pdb=" C PRO B 327 " pdb=" CB PRO B 327 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4023 not shown) Planarity restraints: 3987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP C 601 " -0.194 2.00e-02 2.50e+03 7.87e-02 1.70e+02 pdb=" C2 ATP C 601 " 0.032 2.00e-02 2.50e+03 pdb=" C4 ATP C 601 " 0.057 2.00e-02 2.50e+03 pdb=" C5 ATP C 601 " 0.027 2.00e-02 2.50e+03 pdb=" C6 ATP C 601 " -0.022 2.00e-02 2.50e+03 pdb=" C8 ATP C 601 " 0.065 2.00e-02 2.50e+03 pdb=" N1 ATP C 601 " -0.019 2.00e-02 2.50e+03 pdb=" N3 ATP C 601 " 0.057 2.00e-02 2.50e+03 pdb=" N6 ATP C 601 " -0.107 2.00e-02 2.50e+03 pdb=" N7 ATP C 601 " 0.036 2.00e-02 2.50e+03 pdb=" N9 ATP C 601 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 601 " 0.140 2.00e-02 2.50e+03 5.80e-02 9.24e+01 pdb=" C2 ATP B 601 " -0.026 2.00e-02 2.50e+03 pdb=" C4 ATP B 601 " -0.040 2.00e-02 2.50e+03 pdb=" C5 ATP B 601 " -0.021 2.00e-02 2.50e+03 pdb=" C6 ATP B 601 " 0.018 2.00e-02 2.50e+03 pdb=" C8 ATP B 601 " -0.054 2.00e-02 2.50e+03 pdb=" N1 ATP B 601 " 0.013 2.00e-02 2.50e+03 pdb=" N3 ATP B 601 " -0.044 2.00e-02 2.50e+03 pdb=" N6 ATP B 601 " 0.083 2.00e-02 2.50e+03 pdb=" N7 ATP B 601 " -0.031 2.00e-02 2.50e+03 pdb=" N9 ATP B 601 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 5 " 0.108 2.00e-02 2.50e+03 6.45e-02 8.33e+01 pdb=" CG TYR C 5 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 5 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR C 5 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR C 5 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR C 5 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR C 5 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR C 5 " 0.114 2.00e-02 2.50e+03 ... (remaining 3984 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2569 2.78 - 3.31: 22839 3.31 - 3.84: 34464 3.84 - 4.37: 44361 4.37 - 4.90: 73042 Nonbonded interactions: 177275 Sorted by model distance: nonbonded pdb=" OP2 U I 58 " pdb="MG MG I 201 " model vdw 2.255 2.170 nonbonded pdb=" OH TYR H 174 " pdb=" O TRP H 209 " model vdw 2.357 3.040 nonbonded pdb=" N LEU H 173 " pdb=" O LEU H 173 " model vdw 2.404 2.496 nonbonded pdb=" O LEU A 20 " pdb=" O ARG A 23 " model vdw 2.442 3.040 nonbonded pdb=" OP2 U K 58 " pdb="MG MG K 201 " model vdw 2.451 2.170 ... (remaining 177270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 210 or resid 222 through 256 or resid 306 throu \ gh 545)) selection = (chain 'B' and (resid 12 through 25 or resid 36 through 545)) } ncs_group { reference = (chain 'C' and (resid 6 through 25 or resid 37 through 215 or (resid 216 and (na \ me N or name CA or name C or name O or name CB )) or resid 217 through 601)) selection = (chain 'D' and (resid 6 through 256 or resid 306 through 601)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 8.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.090 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 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 : 0.012 0.196 25780 Z= 0.791 Angle : 1.711 19.131 35577 Z= 1.178 Chirality : 0.089 0.736 4026 Planarity : 0.011 0.113 3987 Dihedral : 17.086 179.180 10475 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.21 % Favored : 96.60 % Rotamer: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.28 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 2645 helix: -1.22 (0.13), residues: 1001 sheet: 0.35 (0.39), residues: 161 loop : -0.94 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 160 TYR 0.114 0.013 TYR C 5 PHE 0.045 0.007 PHE E 162 TRP 0.095 0.018 TRP B 405 HIS 0.012 0.003 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.01231 / 0.79 (25776) covalent geometry : angle 1.70769 / 1.18 (35571) hydrogen bonds : bond 0.29256 / 19.27 ( 921) hydrogen bonds : angle 7.15086 / 5.03 ( 2442) metal coordination : bond 0.11271 / 6.61 ( 4) metal coordination : angle 8.32740 / 4.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: E 119 GLN cc_start: 0.8443 (mm110) cc_final: 0.7615 (pp30) REVERT: E 122 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8205 (mp-120) REVERT: F 119 GLN cc_start: 0.8401 (mm110) cc_final: 0.8065 (tp-100) REVERT: H 215 PHE cc_start: 0.8966 (p90) cc_final: 0.8754 (t80) outliers start: 14 outliers final: 5 residues processed: 139 average time/residue: 0.2116 time to fit residues: 44.5322 Evaluate side-chains 81 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 272 GLN B 190 ASN B 196 ASN B 491 ASN B 542 ASN C 135 ASN C 407 GLN D 190 ASN D 196 ASN D 356 GLN D 427 HIS F 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045449 restraints weight = 95857.265| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.80 r_work: 0.2741 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25780 Z= 0.190 Angle : 0.704 9.484 35577 Z= 0.406 Chirality : 0.046 0.180 4026 Planarity : 0.005 0.045 3987 Dihedral : 18.720 179.332 5160 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 0.63 % Allowed : 4.27 % Favored : 95.10 % 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: -0.93 (0.15), residues: 2645 helix: 0.10 (0.15), residues: 1064 sheet: -0.76 (0.26), residues: 367 loop : -1.14 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 362 TYR 0.022 0.002 TYR C 104 PHE 0.019 0.002 PHE A 239 TRP 0.026 0.002 TRP A 245 HIS 0.007 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (25776) covalent geometry : angle 0.70114 / 0.41 (35571) hydrogen bonds : bond 0.07804 / 5.00 ( 921) hydrogen bonds : angle 4.94033 / 3.52 ( 2442) metal coordination : bond 0.00560 / 0.29 ( 4) metal coordination : angle 5.12574 / 2.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8125 (ttm110) REVERT: D 279 MET cc_start: 0.3455 (mmm) cc_final: 0.3008 (pmm) REVERT: E 119 GLN cc_start: 0.8448 (mm110) cc_final: 0.7654 (pp30) REVERT: E 304 MET cc_start: 0.9049 (tpp) cc_final: 0.8846 (tpp) REVERT: F 119 GLN cc_start: 0.9007 (mm110) cc_final: 0.8541 (tp-100) REVERT: H 96 ASN cc_start: 0.7937 (m-40) cc_final: 0.7596 (p0) REVERT: H 215 PHE cc_start: 0.8741 (p90) cc_final: 0.8537 (t80) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.1546 time to fit residues: 25.3087 Evaluate side-chains 80 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 182 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 236 optimal weight: 0.0570 chunk 181 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046819 restraints weight = 96108.192| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.78 r_work: 0.2786 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25780 Z= 0.134 Angle : 0.539 9.199 35577 Z= 0.315 Chirality : 0.042 0.166 4026 Planarity : 0.004 0.046 3987 Dihedral : 18.521 179.361 5154 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 0.63 % Allowed : 5.19 % Favored : 94.17 % 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: -0.56 (0.15), residues: 2645 helix: 0.72 (0.15), residues: 1067 sheet: -0.91 (0.24), residues: 402 loop : -1.13 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 27 TYR 0.016 0.001 TYR C 104 PHE 0.052 0.001 PHE D 291 TRP 0.015 0.001 TRP D 245 HIS 0.006 0.001 HIS H 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (25776) covalent geometry : angle 0.53717 / 0.31 (35571) hydrogen bonds : bond 0.05734 / 3.71 ( 921) hydrogen bonds : angle 4.24222 / 3.03 ( 2442) metal coordination : bond 0.00220 / 0.13 ( 4) metal coordination : angle 3.59248 / 2.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 537 MET cc_start: 0.8401 (mpp) cc_final: 0.8141 (mpp) REVERT: D 279 MET cc_start: 0.3310 (mmm) cc_final: 0.2941 (pmm) REVERT: E 119 GLN cc_start: 0.8496 (mm110) cc_final: 0.7709 (pp30) REVERT: F 119 GLN cc_start: 0.9108 (mm110) cc_final: 0.8602 (tp40) REVERT: H 20 GLN cc_start: 0.8557 (mp10) cc_final: 0.8293 (mp10) REVERT: H 96 ASN cc_start: 0.7917 (m-40) cc_final: 0.7638 (p0) REVERT: H 188 MET cc_start: 0.7830 (mmm) cc_final: 0.7619 (mtp) outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 0.1470 time to fit residues: 24.8198 Evaluate side-chains 82 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 224 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 278 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 266 GLN E 13 GLN F 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.044913 restraints weight = 94848.342| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.80 r_work: 0.2727 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25780 Z= 0.153 Angle : 0.549 9.082 35577 Z= 0.317 Chirality : 0.043 0.180 4026 Planarity : 0.005 0.060 3987 Dihedral : 18.459 179.757 5154 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 0.97 % Allowed : 6.04 % Favored : 92.99 % 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 (0.15), residues: 2645 helix: 0.93 (0.16), residues: 1065 sheet: -0.90 (0.25), residues: 409 loop : -1.32 (0.16), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 59 TYR 0.019 0.001 TYR C 104 PHE 0.020 0.001 PHE H 64 TRP 0.016 0.001 TRP A 245 HIS 0.006 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (25776) covalent geometry : angle 0.54782 / 0.32 (35571) hydrogen bonds : bond 0.06000 / 3.89 ( 921) hydrogen bonds : angle 4.19162 / 2.99 ( 2442) metal coordination : bond 0.00209 / 0.13 ( 4) metal coordination : angle 3.33371 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 537 MET cc_start: 0.8463 (mpp) cc_final: 0.8156 (mpp) REVERT: E 119 GLN cc_start: 0.8535 (mm110) cc_final: 0.7715 (pp30) REVERT: F 119 GLN cc_start: 0.9225 (mm110) cc_final: 0.8700 (tp40) REVERT: H 20 GLN cc_start: 0.8544 (mp10) cc_final: 0.8261 (mp10) REVERT: H 96 ASN cc_start: 0.7944 (m-40) cc_final: 0.7657 (p0) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.1388 time to fit residues: 22.7455 Evaluate side-chains 86 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 88 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 272 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 269 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 347 ASN E 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.042611 restraints weight = 93819.605| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.81 r_work: 0.2654 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25780 Z= 0.211 Angle : 0.612 9.964 35577 Z= 0.352 Chirality : 0.046 0.209 4026 Planarity : 0.005 0.055 3987 Dihedral : 18.542 178.793 5154 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 1.22 % Allowed : 6.88 % Favored : 91.89 % 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: -0.74 (0.15), residues: 2645 helix: 0.89 (0.16), residues: 1063 sheet: -0.95 (0.26), residues: 378 loop : -1.61 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 160 TYR 0.022 0.002 TYR C 104 PHE 0.030 0.002 PHE D 453 TRP 0.019 0.001 TRP A 245 HIS 0.009 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (25776) covalent geometry : angle 0.60999 / 0.35 (35571) hydrogen bonds : bond 0.07489 / 4.87 ( 921) hydrogen bonds : angle 4.36298 / 3.11 ( 2442) metal coordination : bond 0.00256 / 0.15 ( 4) metal coordination : angle 3.39310 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.856 Fit side-chains REVERT: A 537 MET cc_start: 0.8517 (mpp) cc_final: 0.8222 (mpp) REVERT: D 279 MET cc_start: 0.2836 (mmm) cc_final: 0.2551 (pmm) REVERT: F 119 GLN cc_start: 0.9321 (mm110) cc_final: 0.8751 (tp40) REVERT: F 122 GLN cc_start: 0.8594 (mm110) cc_final: 0.8330 (mm110) REVERT: H 20 GLN cc_start: 0.8540 (mp10) cc_final: 0.8219 (mp10) REVERT: H 96 ASN cc_start: 0.7960 (m-40) cc_final: 0.7730 (p0) outliers start: 29 outliers final: 17 residues processed: 98 average time/residue: 0.1426 time to fit residues: 24.2047 Evaluate side-chains 92 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 131 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.063871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.044020 restraints weight = 94340.278| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.80 r_work: 0.2701 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25780 Z= 0.133 Angle : 0.520 7.633 35577 Z= 0.301 Chirality : 0.041 0.181 4026 Planarity : 0.004 0.052 3987 Dihedral : 18.487 179.470 5154 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.01 % Allowed : 7.52 % Favored : 91.47 % 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: -0.56 (0.16), residues: 2645 helix: 1.11 (0.16), residues: 1059 sheet: -0.89 (0.26), residues: 398 loop : -1.57 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.017 0.001 TYR C 104 PHE 0.020 0.001 PHE D 291 TRP 0.014 0.001 TRP A 245 HIS 0.005 0.001 HIS D 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (25776) covalent geometry : angle 0.51872 / 0.30 (35571) hydrogen bonds : bond 0.05623 / 3.64 ( 921) hydrogen bonds : angle 4.09834 / 2.92 ( 2442) metal coordination : bond 0.00228 / 0.15 ( 4) metal coordination : angle 3.32599 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.909 Fit side-chains REVERT: A 537 MET cc_start: 0.8544 (mpp) cc_final: 0.8300 (mpp) REVERT: C 81 GLU cc_start: 0.8543 (mp0) cc_final: 0.8003 (mp0) REVERT: D 279 MET cc_start: 0.2759 (mmm) cc_final: 0.2398 (pmm) REVERT: E 119 GLN cc_start: 0.8615 (mm110) cc_final: 0.7642 (pp30) REVERT: F 119 GLN cc_start: 0.9353 (mm110) cc_final: 0.8786 (tp40) REVERT: F 122 GLN cc_start: 0.8564 (mm110) cc_final: 0.8279 (mm110) outliers start: 24 outliers final: 18 residues processed: 95 average time/residue: 0.1279 time to fit residues: 20.7727 Evaluate side-chains 93 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 104 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 277 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.042941 restraints weight = 94230.358| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.87 r_work: 0.2666 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25780 Z= 0.188 Angle : 0.565 8.447 35577 Z= 0.324 Chirality : 0.043 0.180 4026 Planarity : 0.005 0.056 3987 Dihedral : 18.489 179.700 5154 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 1.10 % Allowed : 7.64 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.16), residues: 2645 helix: 1.05 (0.16), residues: 1072 sheet: -0.89 (0.26), residues: 382 loop : -1.67 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.019 0.001 TYR C 104 PHE 0.016 0.002 PHE C 149 TRP 0.015 0.001 TRP A 245 HIS 0.006 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (25776) covalent geometry : angle 0.56385 / 0.32 (35571) hydrogen bonds : bond 0.06562 / 4.26 ( 921) hydrogen bonds : angle 4.20102 / 3.00 ( 2442) metal coordination : bond 0.00292 / 0.18 ( 4) metal coordination : angle 3.29092 / 1.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.831 Fit side-chains REVERT: F 119 GLN cc_start: 0.9402 (mm110) cc_final: 0.8870 (tp40) REVERT: F 122 GLN cc_start: 0.8580 (mm110) cc_final: 0.8289 (mm110) outliers start: 26 outliers final: 17 residues processed: 95 average time/residue: 0.1441 time to fit residues: 23.8718 Evaluate side-chains 90 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 174 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 228 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 247 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 224 optimal weight: 0.0370 chunk 206 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 159 optimal weight: 6.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045142 restraints weight = 94527.217| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.88 r_work: 0.2739 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25780 Z= 0.112 Angle : 0.498 11.197 35577 Z= 0.284 Chirality : 0.040 0.229 4026 Planarity : 0.004 0.050 3987 Dihedral : 18.409 179.992 5154 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 7.94 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.38 (0.16), residues: 2645 helix: 1.31 (0.16), residues: 1054 sheet: -0.79 (0.25), residues: 402 loop : -1.51 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 27 TYR 0.015 0.001 TYR C 104 PHE 0.015 0.001 PHE D 453 TRP 0.011 0.001 TRP A 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.11 (25776) covalent geometry : angle 0.49672 / 0.28 (35571) hydrogen bonds : bond 0.04521 / 2.95 ( 921) hydrogen bonds : angle 3.88954 / 2.77 ( 2442) metal coordination : bond 0.00227 / 0.15 ( 4) metal coordination : angle 2.99819 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.792 Fit side-chains REVERT: C 81 GLU cc_start: 0.8497 (mp0) cc_final: 0.8054 (mp0) REVERT: E 119 GLN cc_start: 0.8607 (mm110) cc_final: 0.8351 (mm-40) REVERT: F 119 GLN cc_start: 0.9404 (mm110) cc_final: 0.8862 (tp40) REVERT: F 122 GLN cc_start: 0.8560 (mm110) cc_final: 0.8255 (mm110) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 0.1323 time to fit residues: 21.5055 Evaluate side-chains 88 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 96 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.044711 restraints weight = 94433.062| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.84 r_work: 0.2725 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25780 Z= 0.120 Angle : 0.499 12.175 35577 Z= 0.283 Chirality : 0.040 0.186 4026 Planarity : 0.004 0.050 3987 Dihedral : 18.358 179.784 5154 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 0.68 % Allowed : 8.32 % Favored : 91.01 % 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: -0.32 (0.16), residues: 2645 helix: 1.31 (0.16), residues: 1074 sheet: -0.75 (0.26), residues: 404 loop : -1.47 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.016 0.001 TYR C 104 PHE 0.014 0.001 PHE D 453 TRP 0.011 0.001 TRP A 245 HIS 0.004 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (25776) covalent geometry : angle 0.49730 / 0.28 (35571) hydrogen bonds : bond 0.04831 / 3.15 ( 921) hydrogen bonds : angle 3.88571 / 2.77 ( 2442) metal coordination : bond 0.00218 / 0.14 ( 4) metal coordination : angle 2.97507 / 1.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.896 Fit side-chains REVERT: C 81 GLU cc_start: 0.8531 (mp0) cc_final: 0.8040 (mp0) REVERT: E 115 MET cc_start: 0.9048 (tpp) cc_final: 0.8830 (tmm) REVERT: E 119 GLN cc_start: 0.8642 (mm110) cc_final: 0.8373 (mm-40) REVERT: F 119 GLN cc_start: 0.9417 (mm110) cc_final: 0.8845 (tp40) REVERT: F 122 GLN cc_start: 0.8600 (mm110) cc_final: 0.8296 (mm110) outliers start: 16 outliers final: 15 residues processed: 89 average time/residue: 0.1441 time to fit residues: 22.3258 Evaluate side-chains 92 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 43 optimal weight: 0.0020 chunk 214 optimal weight: 5.9990 chunk 232 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 137 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046421 restraints weight = 95256.668| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.84 r_work: 0.2782 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25780 Z= 0.100 Angle : 0.473 10.839 35577 Z= 0.266 Chirality : 0.039 0.202 4026 Planarity : 0.004 0.049 3987 Dihedral : 18.296 179.594 5154 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 0.68 % Allowed : 8.36 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2645 helix: 1.45 (0.16), residues: 1075 sheet: -0.50 (0.25), residues: 404 loop : -1.38 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 171 TYR 0.014 0.001 TYR B 248 PHE 0.013 0.001 PHE B 149 TRP 0.009 0.001 TRP A 245 HIS 0.005 0.000 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.10 (25776) covalent geometry : angle 0.47208 / 0.27 (35571) hydrogen bonds : bond 0.03672 / 2.42 ( 921) hydrogen bonds : angle 3.70452 / 2.63 ( 2442) metal coordination : bond 0.00190 / 0.13 ( 4) metal coordination : angle 2.76531 / 1.50 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.948 Fit side-chains REVERT: C 81 GLU cc_start: 0.8500 (mp0) cc_final: 0.8036 (mp0) REVERT: E 115 MET cc_start: 0.9022 (tpp) cc_final: 0.8790 (tmm) REVERT: E 119 GLN cc_start: 0.8641 (mm110) cc_final: 0.8356 (mm-40) REVERT: F 119 GLN cc_start: 0.9430 (mm110) cc_final: 0.8864 (tp40) REVERT: F 122 GLN cc_start: 0.8582 (mm110) cc_final: 0.8271 (mm110) outliers start: 16 outliers final: 14 residues processed: 94 average time/residue: 0.1420 time to fit residues: 22.8041 Evaluate side-chains 91 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 75 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045688 restraints weight = 95433.292| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.92 r_work: 0.2758 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25780 Z= 0.107 Angle : 0.474 10.772 35577 Z= 0.267 Chirality : 0.039 0.183 4026 Planarity : 0.004 0.048 3987 Dihedral : 18.263 179.729 5154 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 0.59 % Allowed : 8.61 % Favored : 90.79 % 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: -0.03 (0.16), residues: 2645 helix: 1.55 (0.16), residues: 1075 sheet: -0.51 (0.26), residues: 400 loop : -1.37 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.015 0.001 TYR C 104 PHE 0.013 0.001 PHE D 453 TRP 0.009 0.001 TRP A 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (25776) covalent geometry : angle 0.47269 / 0.27 (35571) hydrogen bonds : bond 0.04170 / 2.73 ( 921) hydrogen bonds : angle 3.71786 / 2.65 ( 2442) metal coordination : bond 0.00186 / 0.12 ( 4) metal coordination : angle 2.63749 / 1.43 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6540.48 seconds wall clock time: 112 minutes 28.11 seconds (6748.11 seconds total)