Starting phenix.real_space_refine on Fri Feb 6 13:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l7p_62876/02_2026/9l7p_62876_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l7p_62876/02_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_62876/02_2026/9l7p_62876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l7p_62876/02_2026/9l7p_62876.map" model { file = "/net/cci-nas-00/data/ceres_data/9l7p_62876/02_2026/9l7p_62876_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l7p_62876/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 5.84, 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: 2.46 Conformation dependent library (CDL) restraints added in 995.4 milliseconds 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: 3.08 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: 4.58 Time building geometry restraints manager: 3.21 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: 3629 0.147 - 0.294: 381 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.160 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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= 0.788 Angle : 1.715 19.131 35577 Z= 1.175 Chirality : 0.088 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 covalent geometry : bond 0.01235 (25776) covalent geometry : angle 1.71200 (35571) hydrogen bonds : bond 0.29256 ( 921) hydrogen bonds : angle 7.15086 ( 2442) metal coordination : bond 0.11271 ( 4) metal coordination : angle 8.32740 ( 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 : 0.977 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: 0.2202 time to fit residues: 45.8686 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 : 1.153 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 272 GLN A 400 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.046354 restraints weight = 95939.605| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.76 r_work: 0.2772 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25780 Z= 0.154 Angle : 0.611 8.923 35577 Z= 0.346 Chirality : 0.043 0.185 4026 Planarity : 0.005 0.046 3987 Dihedral : 18.533 179.427 5160 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.69 % Rotamer: Outliers : 0.55 % Allowed : 4.73 % Favored : 94.72 % 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: -0.63 (0.15), residues: 2645 helix: 0.27 (0.15), residues: 1073 sheet: -0.57 (0.26), residues: 380 loop : -0.92 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 533 TYR 0.020 0.002 TYR C 246 PHE 0.017 0.001 PHE B 149 TRP 0.022 0.001 TRP D 245 HIS 0.006 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00299 (25776) covalent geometry : angle 0.60836 (35571) hydrogen bonds : bond 0.06003 ( 921) hydrogen bonds : angle 4.52653 ( 2442) metal coordination : bond 0.00198 ( 4) metal coordination : angle 4.50792 ( 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 106 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 537 MET cc_start: 0.8367 (mpp) cc_final: 0.8144 (mpp) REVERT: C 221 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8214 (ttm110) REVERT: D 279 MET cc_start: 0.3425 (mmm) cc_final: 0.3031 (pmm) REVERT: E 119 GLN cc_start: 0.8474 (mm110) cc_final: 0.7671 (pp30) REVERT: F 119 GLN cc_start: 0.9058 (mm110) cc_final: 0.8546 (tp40) REVERT: H 96 ASN cc_start: 0.7918 (m-40) cc_final: 0.7623 (p0) REVERT: H 215 PHE cc_start: 0.8746 (p90) cc_final: 0.8531 (t80) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.1708 time to fit residues: 29.3408 Evaluate side-chains 83 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain E residue 14 SER 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 81 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 182 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 84 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 181 optimal weight: 0.0870 chunk 173 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 overall best weight: 3.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 347 ASN E 46 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 = 0.3357 r_free = 0.3357 target = 0.062701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042698 restraints weight = 95381.414| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.85 r_work: 0.2660 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25780 Z= 0.213 Angle : 0.631 7.938 35577 Z= 0.358 Chirality : 0.045 0.179 4026 Planarity : 0.005 0.055 3987 Dihedral : 18.493 178.517 5154 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.01 % Allowed : 5.36 % Favored : 93.62 % 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: -0.75 (0.15), residues: 2645 helix: 0.61 (0.15), residues: 1061 sheet: -0.87 (0.26), residues: 378 loop : -1.35 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 160 TYR 0.021 0.002 TYR C 104 PHE 0.019 0.002 PHE C 149 TRP 0.023 0.001 TRP A 245 HIS 0.008 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00482 (25776) covalent geometry : angle 0.62969 (35571) hydrogen bonds : bond 0.07632 ( 921) hydrogen bonds : angle 4.48574 ( 2442) metal coordination : bond 0.00241 ( 4) metal coordination : angle 3.66960 ( 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: 24 poor density : 80 time to evaluate : 0.944 Fit side-chains REVERT: A 537 MET cc_start: 0.8476 (mpp) cc_final: 0.8198 (mpp) REVERT: F 119 GLN cc_start: 0.9310 (mm110) cc_final: 0.8766 (tp40) REVERT: F 122 GLN cc_start: 0.8576 (mm110) cc_final: 0.8233 (mm110) REVERT: H 96 ASN cc_start: 0.7990 (m-40) cc_final: 0.7749 (p0) REVERT: H 215 PHE cc_start: 0.8741 (p90) cc_final: 0.8528 (t80) outliers start: 24 outliers final: 10 residues processed: 101 average time/residue: 0.1506 time to fit residues: 26.3425 Evaluate side-chains 83 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 175 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 224 optimal weight: 0.0050 chunk 169 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.043105 restraints weight = 94901.618| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.79 r_work: 0.2675 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25780 Z= 0.186 Angle : 0.573 8.245 35577 Z= 0.323 Chirality : 0.043 0.180 4026 Planarity : 0.005 0.058 3987 Dihedral : 18.462 179.935 5154 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 1.10 % Allowed : 6.25 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.15), residues: 2645 helix: 0.80 (0.16), residues: 1070 sheet: -0.84 (0.26), residues: 386 loop : -1.52 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.019 0.001 TYR C 104 PHE 0.016 0.002 PHE C 149 TRP 0.017 0.001 TRP A 245 HIS 0.006 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00422 (25776) covalent geometry : angle 0.57122 (35571) hydrogen bonds : bond 0.06438 ( 921) hydrogen bonds : angle 4.28788 ( 2442) metal coordination : bond 0.00230 ( 4) metal coordination : angle 3.55676 ( 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 103 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.957 Fit side-chains REVERT: A 537 MET cc_start: 0.8516 (mpp) cc_final: 0.8307 (mpp) REVERT: D 279 MET cc_start: 0.3278 (mmm) cc_final: 0.2729 (pmm) REVERT: F 119 GLN cc_start: 0.9386 (mm110) cc_final: 0.8817 (tp40) REVERT: F 122 GLN cc_start: 0.8564 (mm110) cc_final: 0.8229 (mm110) REVERT: H 20 GLN cc_start: 0.8516 (mp10) cc_final: 0.8232 (mp10) REVERT: H 215 PHE cc_start: 0.8765 (p90) cc_final: 0.8516 (t80) outliers start: 26 outliers final: 17 residues processed: 99 average time/residue: 0.1474 time to fit residues: 25.6045 Evaluate side-chains 91 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 341 ASP 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 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 Chi-restraints excluded: chain H residue 174 TYR Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 88 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 1 optimal weight: 0.0270 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN H 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043610 restraints weight = 94506.330| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.83 r_work: 0.2691 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25780 Z= 0.154 Angle : 0.534 9.048 35577 Z= 0.299 Chirality : 0.041 0.178 4026 Planarity : 0.005 0.052 3987 Dihedral : 18.356 179.503 5154 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.10 % Allowed : 7.05 % Favored : 91.85 % 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: -0.57 (0.16), residues: 2645 helix: 1.00 (0.16), residues: 1072 sheet: -0.76 (0.26), residues: 397 loop : -1.56 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 27 TYR 0.017 0.001 TYR C 104 PHE 0.014 0.001 PHE C 149 TRP 0.014 0.001 TRP A 245 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00339 (25776) covalent geometry : angle 0.53198 (35571) hydrogen bonds : bond 0.05697 ( 921) hydrogen bonds : angle 4.09860 ( 2442) metal coordination : bond 0.00247 ( 4) metal coordination : angle 3.23925 ( 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 107 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 1.016 Fit side-chains REVERT: F 119 GLN cc_start: 0.9429 (mm110) cc_final: 0.8863 (tp40) REVERT: F 122 GLN cc_start: 0.8582 (mm110) cc_final: 0.8212 (mm110) REVERT: H 215 PHE cc_start: 0.8750 (p90) cc_final: 0.8404 (p90) outliers start: 26 outliers final: 15 residues processed: 101 average time/residue: 0.1362 time to fit residues: 24.2250 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 : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 341 ASP 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 E residue 39 THR Chi-restraints excluded: chain E residue 175 CYS 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 Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 131 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 136 optimal weight: 0.3980 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.043137 restraints weight = 94638.684| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.83 r_work: 0.2673 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25780 Z= 0.165 Angle : 0.545 7.795 35577 Z= 0.305 Chirality : 0.041 0.176 4026 Planarity : 0.005 0.054 3987 Dihedral : 18.340 179.599 5154 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 7.60 % 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: -0.57 (0.16), residues: 2645 helix: 1.07 (0.16), residues: 1071 sheet: -0.80 (0.27), residues: 379 loop : -1.61 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.018 0.001 TYR C 104 PHE 0.017 0.001 PHE D 291 TRP 0.014 0.001 TRP A 245 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00370 (25776) covalent geometry : angle 0.54352 (35571) hydrogen bonds : bond 0.06003 ( 921) hydrogen bonds : angle 4.11562 ( 2442) metal coordination : bond 0.00237 ( 4) metal coordination : angle 3.27649 ( 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 105 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.892 Fit side-chains REVERT: F 119 GLN cc_start: 0.9474 (mm110) cc_final: 0.8886 (tp40) REVERT: F 122 GLN cc_start: 0.8633 (mm110) cc_final: 0.8244 (mm110) REVERT: H 215 PHE cc_start: 0.8726 (p90) cc_final: 0.8363 (p90) outliers start: 27 outliers final: 18 residues processed: 99 average time/residue: 0.1492 time to fit residues: 26.0447 Evaluate side-chains 94 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 341 ASP 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 49 ASP 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 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 Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 104 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043631 restraints weight = 94509.325| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.87 r_work: 0.2691 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25780 Z= 0.144 Angle : 0.520 8.619 35577 Z= 0.289 Chirality : 0.040 0.175 4026 Planarity : 0.004 0.054 3987 Dihedral : 18.278 179.441 5154 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 1.10 % Allowed : 8.02 % Favored : 90.88 % 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: -0.51 (0.16), residues: 2645 helix: 1.15 (0.16), residues: 1075 sheet: -0.76 (0.26), residues: 389 loop : -1.62 (0.16), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.017 0.001 TYR C 104 PHE 0.021 0.001 PHE D 291 TRP 0.012 0.001 TRP A 245 HIS 0.004 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00317 (25776) covalent geometry : angle 0.51849 (35571) hydrogen bonds : bond 0.05400 ( 921) hydrogen bonds : angle 4.00776 ( 2442) metal coordination : bond 0.00242 ( 4) metal coordination : angle 3.12012 ( 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 103 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 1.043 Fit side-chains REVERT: F 119 GLN cc_start: 0.9482 (mm110) cc_final: 0.8889 (tp40) REVERT: F 122 GLN cc_start: 0.8609 (mm110) cc_final: 0.8179 (mm110) REVERT: H 215 PHE cc_start: 0.8764 (p90) cc_final: 0.8492 (t80) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.1482 time to fit residues: 25.5565 Evaluate side-chains 95 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 495 LEU 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 341 ASP 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 49 ASP 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 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 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: 3.9990 chunk 61 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 224 optimal weight: 0.0010 chunk 206 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 137 optimal weight: 0.0070 chunk 159 optimal weight: 4.9990 overall best weight: 2.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.043894 restraints weight = 94415.113| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.84 r_work: 0.2700 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25780 Z= 0.136 Angle : 0.509 9.897 35577 Z= 0.282 Chirality : 0.040 0.173 4026 Planarity : 0.004 0.053 3987 Dihedral : 18.225 179.304 5154 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 0.89 % Allowed : 8.32 % 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: -0.43 (0.16), residues: 2645 helix: 1.24 (0.16), residues: 1074 sheet: -0.69 (0.26), residues: 394 loop : -1.61 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.017 0.001 TYR C 104 PHE 0.021 0.001 PHE D 291 TRP 0.011 0.001 TRP A 245 HIS 0.004 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00296 (25776) covalent geometry : angle 0.50781 (35571) hydrogen bonds : bond 0.05155 ( 921) hydrogen bonds : angle 3.94032 ( 2442) metal coordination : bond 0.00229 ( 4) metal coordination : angle 3.02483 ( 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 96 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.983 Fit side-chains REVERT: F 119 GLN cc_start: 0.9486 (mm110) cc_final: 0.8871 (tp40) REVERT: F 122 GLN cc_start: 0.8621 (mm110) cc_final: 0.8215 (mm110) REVERT: H 215 PHE cc_start: 0.8769 (p90) cc_final: 0.8495 (t80) outliers start: 21 outliers final: 15 residues processed: 92 average time/residue: 0.1487 time to fit residues: 24.2739 Evaluate side-chains 90 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 495 LEU 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 254 VAL 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 175 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 174 TYR 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: 3.9990 chunk 225 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.043494 restraints weight = 94849.232| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.86 r_work: 0.2686 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25780 Z= 0.149 Angle : 0.522 9.687 35577 Z= 0.290 Chirality : 0.040 0.172 4026 Planarity : 0.004 0.055 3987 Dihedral : 18.226 179.554 5150 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 0.84 % Allowed : 8.49 % Favored : 90.67 % 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: -0.47 (0.16), residues: 2645 helix: 1.23 (0.16), residues: 1075 sheet: -0.74 (0.26), residues: 389 loop : -1.65 (0.16), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.018 0.001 TYR C 104 PHE 0.024 0.001 PHE D 291 TRP 0.012 0.001 TRP A 245 HIS 0.005 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00330 (25776) covalent geometry : angle 0.52021 (35571) hydrogen bonds : bond 0.05522 ( 921) hydrogen bonds : angle 3.98093 ( 2442) metal coordination : bond 0.00241 ( 4) metal coordination : angle 3.03520 ( 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 95 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.960 Fit side-chains REVERT: F 119 GLN cc_start: 0.9497 (mm110) cc_final: 0.8874 (tp40) REVERT: F 122 GLN cc_start: 0.8627 (mm110) cc_final: 0.8209 (mm110) REVERT: H 215 PHE cc_start: 0.8774 (p90) cc_final: 0.8327 (p90) outliers start: 20 outliers final: 17 residues processed: 89 average time/residue: 0.1443 time to fit residues: 22.9525 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 : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 495 LEU 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 254 VAL 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 175 CYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 35 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 232 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.063683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.043948 restraints weight = 94763.655| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.82 r_work: 0.2702 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25780 Z= 0.134 Angle : 0.510 10.130 35577 Z= 0.281 Chirality : 0.040 0.171 4026 Planarity : 0.004 0.053 3987 Dihedral : 18.187 179.421 5150 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 0.93 % Allowed : 8.36 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2645 helix: 1.34 (0.16), residues: 1068 sheet: -0.69 (0.26), residues: 395 loop : -1.60 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.017 0.001 TYR C 104 PHE 0.028 0.001 PHE D 291 TRP 0.011 0.001 TRP A 245 HIS 0.004 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00291 (25776) covalent geometry : angle 0.50860 (35571) hydrogen bonds : bond 0.05058 ( 921) hydrogen bonds : angle 3.91047 ( 2442) metal coordination : bond 0.00234 ( 4) metal coordination : angle 2.98927 ( 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 97 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.074 Fit side-chains REVERT: F 119 GLN cc_start: 0.9500 (mm110) cc_final: 0.8843 (tp40) REVERT: F 122 GLN cc_start: 0.8611 (mm110) cc_final: 0.8214 (mm110) REVERT: H 215 PHE cc_start: 0.8783 (p90) cc_final: 0.8305 (p90) outliers start: 22 outliers final: 19 residues processed: 93 average time/residue: 0.1422 time to fit residues: 23.7574 Evaluate side-chains 93 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 341 ASP 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 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 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 81 SER Chi-restraints excluded: chain H residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 75 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 246 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044121 restraints weight = 94705.259| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.87 r_work: 0.2710 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25780 Z= 0.126 Angle : 0.499 10.209 35577 Z= 0.274 Chirality : 0.039 0.170 4026 Planarity : 0.004 0.052 3987 Dihedral : 18.139 179.316 5150 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 0.89 % Allowed : 8.53 % Favored : 90.58 % 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: 1.38 (0.16), residues: 1075 sheet: -0.76 (0.25), residues: 404 loop : -1.56 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.016 0.001 TYR C 104 PHE 0.027 0.001 PHE D 291 TRP 0.011 0.001 TRP A 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00273 (25776) covalent geometry : angle 0.49725 (35571) hydrogen bonds : bond 0.04814 ( 921) hydrogen bonds : angle 3.84614 ( 2442) metal coordination : bond 0.00222 ( 4) metal coordination : angle 2.88036 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7374.47 seconds wall clock time: 126 minutes 35.04 seconds (7595.04 seconds total)