Starting phenix.real_space_refine on Thu Feb 5 22:33:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5u_66597/02_2026/9x5u_66597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5u_66597/02_2026/9x5u_66597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5u_66597/02_2026/9x5u_66597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5u_66597/02_2026/9x5u_66597.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5u_66597/02_2026/9x5u_66597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5u_66597/02_2026/9x5u_66597.cif" } resolution = 3.19 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= 0.018 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13284 2.51 5 N 3328 2.21 5 O 3512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 20232 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5054 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5054 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 643} Chain breaks: 2 Chain: "C" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5054 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 643} Chain breaks: 2 Chain: "D" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5054 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'URE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'URE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'URE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'URE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.55, per 1000 atoms: 0.22 Number of scatterers: 20232 At special positions: 0 Unit cell: (156.48, 156.48, 117.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3512 8.00 N 3328 7.00 C 13284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 20 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 20 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 264 " - pdb=" SG CYS D 275 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 0 sheets defined 74.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.763A pdb=" N PHE A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLY A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.525A pdb=" N VAL A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.664A pdb=" N ILE A 99 " --> pdb=" O TRP A 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 4.070A pdb=" N PHE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 120 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 removed outlier: 4.205A pdb=" N LEU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.575A pdb=" N VAL A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 189 removed outlier: 3.708A pdb=" N PHE A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 3.783A pdb=" N PHE A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.687A pdb=" N VAL A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.716A pdb=" N VAL A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 4.060A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.697A pdb=" N VAL A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.635A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 321 Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.949A pdb=" N TYR A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 345 removed outlier: 3.734A pdb=" N LEU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.888A pdb=" N LEU A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 369 through 412 removed outlier: 8.925A pdb=" N LYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N SER A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 397 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 450 removed outlier: 3.770A pdb=" N LYS A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 454 removed outlier: 3.898A pdb=" N GLY A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.685A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.763A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 511 removed outlier: 3.913A pdb=" N THR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.904A pdb=" N LEU A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.185A pdb=" N PHE A 599 " --> pdb=" O TRP A 595 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.856A pdb=" N VAL A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 648 removed outlier: 3.538A pdb=" N GLY A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Proline residue: A 644 - end of helix Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.602A pdb=" N ALA A 678 " --> pdb=" O HIS A 674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 removed outlier: 3.898A pdb=" N GLU A 687 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 688 " --> pdb=" O PRO A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 63 removed outlier: 3.759A pdb=" N PHE B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLY B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.531A pdb=" N ILE B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.679A pdb=" N ILE B 99 " --> pdb=" O TRP B 95 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 4.068A pdb=" N PHE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 120 " --> pdb=" O TRP B 116 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 139 removed outlier: 4.164A pdb=" N LEU B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.597A pdb=" N VAL B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 189 removed outlier: 3.708A pdb=" N PHE B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS B 165 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 removed outlier: 3.715A pdb=" N PHE B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.726A pdb=" N VAL B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.714A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 4.052A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.703A pdb=" N VAL B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 311 removed outlier: 3.588A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 321 Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.940A pdb=" N TYR B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 removed outlier: 3.730A pdb=" N LEU B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.882A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 369 through 412 removed outlier: 8.898A pdb=" N LYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N SER B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 397 " --> pdb=" O MET B 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 450 removed outlier: 3.855A pdb=" N LYS B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 454 removed outlier: 3.905A pdb=" N GLY B 454 " --> pdb=" O ASN B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.686A pdb=" N LEU B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 468 " --> pdb=" O MET B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.765A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 511 removed outlier: 3.915A pdb=" N THR B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.896A pdb=" N LEU B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 605 removed outlier: 4.187A pdb=" N PHE B 599 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.861A pdb=" N VAL B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 648 removed outlier: 3.547A pdb=" N GLY B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B 637 " --> pdb=" O GLY B 633 " (cutoff:3.500A) Proline residue: B 644 - end of helix Processing helix chain 'B' and resid 649 through 658 Processing helix chain 'B' and resid 662 through 683 removed outlier: 3.617A pdb=" N ALA B 678 " --> pdb=" O HIS B 674 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 679 " --> pdb=" O ARG B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.892A pdb=" N GLU B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 688 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 63 removed outlier: 3.739A pdb=" N PHE C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 49 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.539A pdb=" N VAL C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 removed outlier: 3.662A pdb=" N ILE C 99 " --> pdb=" O TRP C 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 4.069A pdb=" N PHE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 120 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 139 removed outlier: 4.206A pdb=" N LEU C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 129 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.587A pdb=" N VAL C 149 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 189 removed outlier: 3.707A pdb=" N PHE C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS C 165 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 209 removed outlier: 3.733A pdb=" N PHE C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) Proline residue: C 200 - end of helix removed outlier: 3.701A pdb=" N VAL C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 231 removed outlier: 3.718A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.059A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.690A pdb=" N VAL C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.634A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 307 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 308 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 321 Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.917A pdb=" N TYR C 331 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 332 " --> pdb=" O HIS C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 345 removed outlier: 3.734A pdb=" N LEU C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.884A pdb=" N LEU C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 369 through 412 removed outlier: 8.926A pdb=" N LYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N SER C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 397 " --> pdb=" O MET C 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 450 removed outlier: 3.865A pdb=" N LYS C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 454 removed outlier: 3.908A pdb=" N GLY C 454 " --> pdb=" O ASN C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 454' Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 463 through 469 removed outlier: 3.685A pdb=" N LEU C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 468 " --> pdb=" O MET C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 removed outlier: 3.762A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 479 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 511 removed outlier: 3.911A pdb=" N THR C 494 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 496 " --> pdb=" O GLY C 492 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 511 " --> pdb=" O THR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.900A pdb=" N LEU C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 528 " --> pdb=" O GLY C 524 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.182A pdb=" N PHE C 599 " --> pdb=" O TRP C 595 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 601 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 612 removed outlier: 3.826A pdb=" N VAL C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 648 removed outlier: 3.538A pdb=" N GLY C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Proline residue: C 644 - end of helix Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 662 through 683 removed outlier: 3.573A pdb=" N ALA C 678 " --> pdb=" O HIS C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 695 removed outlier: 3.895A pdb=" N GLU C 687 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS C 688 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 63 removed outlier: 3.740A pdb=" N PHE D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLY D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 49 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.540A pdb=" N VAL D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 removed outlier: 3.653A pdb=" N ILE D 99 " --> pdb=" O TRP D 95 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.072A pdb=" N PHE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 120 " --> pdb=" O TRP D 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 139 removed outlier: 4.203A pdb=" N LEU D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY D 129 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.577A pdb=" N VAL D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.709A pdb=" N PHE D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 209 removed outlier: 3.726A pdb=" N PHE D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.731A pdb=" N VAL D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR D 207 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 231 removed outlier: 3.714A pdb=" N VAL D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 removed outlier: 4.059A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.695A pdb=" N VAL D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 311 removed outlier: 3.630A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY D 307 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR D 308 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 321 Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.915A pdb=" N TYR D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 345 removed outlier: 3.732A pdb=" N LEU D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.884A pdb=" N LEU D 354 " --> pdb=" O GLY D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 369 through 412 removed outlier: 8.923A pdb=" N LYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N SER D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 396 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 397 " --> pdb=" O MET D 393 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 402 " --> pdb=" O ALA D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 450 removed outlier: 3.862A pdb=" N LYS D 430 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 445 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 448 " --> pdb=" O GLY D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 454 removed outlier: 3.908A pdb=" N GLY D 454 " --> pdb=" O ASN D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 451 through 454' Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 463 through 469 removed outlier: 3.686A pdb=" N LEU D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 468 " --> pdb=" O MET D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 481 removed outlier: 3.770A pdb=" N ALA D 476 " --> pdb=" O VAL D 472 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 479 " --> pdb=" O ILE D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 511 removed outlier: 3.913A pdb=" N THR D 494 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY D 496 " --> pdb=" O GLY D 492 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS D 497 " --> pdb=" O ALA D 493 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 511 " --> pdb=" O THR D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.897A pdb=" N LEU D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 528 " --> pdb=" O GLY D 524 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 605 removed outlier: 4.184A pdb=" N PHE D 599 " --> pdb=" O TRP D 595 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 3.841A pdb=" N VAL D 609 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 648 removed outlier: 3.531A pdb=" N GLY D 636 " --> pdb=" O TRP D 632 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER D 637 " --> pdb=" O GLY D 633 " (cutoff:3.500A) Proline residue: D 644 - end of helix Processing helix chain 'D' and resid 649 through 658 Processing helix chain 'D' and resid 662 through 683 removed outlier: 3.503A pdb=" N ASP D 671 " --> pdb=" O LYS D 667 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 678 " --> pdb=" O HIS D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 695 removed outlier: 3.894A pdb=" N GLU D 687 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS D 688 " --> pdb=" O PRO D 684 " (cutoff:3.500A) 1105 hydrogen bonds defined for protein. 3315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3048 1.28 - 1.41: 5368 1.41 - 1.55: 12105 1.55 - 1.68: 23 1.68 - 1.81: 172 Bond restraints: 20716 Sorted by residual: bond pdb=" CA TRP C 93 " pdb=" C TRP C 93 " ideal model delta sigma weight residual 1.521 1.414 0.108 1.31e-02 5.83e+03 6.77e+01 bond pdb=" CA TRP A 93 " pdb=" C TRP A 93 " ideal model delta sigma weight residual 1.521 1.415 0.107 1.31e-02 5.83e+03 6.63e+01 bond pdb=" CA TRP B 93 " pdb=" C TRP B 93 " ideal model delta sigma weight residual 1.521 1.415 0.107 1.31e-02 5.83e+03 6.63e+01 bond pdb=" CA TRP D 93 " pdb=" C TRP D 93 " ideal model delta sigma weight residual 1.521 1.415 0.106 1.31e-02 5.83e+03 6.58e+01 bond pdb=" C TRP B 93 " pdb=" O TRP B 93 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.33e-02 5.65e+03 4.95e+01 ... (remaining 20711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27775 2.13 - 4.27: 360 4.27 - 6.40: 50 6.40 - 8.54: 16 8.54 - 10.67: 7 Bond angle restraints: 28208 Sorted by residual: angle pdb=" N TYR A 415 " pdb=" CA TYR A 415 " pdb=" C TYR A 415 " ideal model delta sigma weight residual 114.75 106.69 8.06 1.26e+00 6.30e-01 4.09e+01 angle pdb=" C TRP A 93 " pdb=" CA TRP A 93 " pdb=" CB TRP A 93 " ideal model delta sigma weight residual 109.99 99.32 10.67 1.74e+00 3.30e-01 3.76e+01 angle pdb=" C TRP C 93 " pdb=" CA TRP C 93 " pdb=" CB TRP C 93 " ideal model delta sigma weight residual 109.99 99.45 10.54 1.74e+00 3.30e-01 3.67e+01 angle pdb=" C TRP D 93 " pdb=" CA TRP D 93 " pdb=" CB TRP D 93 " ideal model delta sigma weight residual 109.99 99.50 10.49 1.74e+00 3.30e-01 3.63e+01 angle pdb=" C TRP B 93 " pdb=" CA TRP B 93 " pdb=" CB TRP B 93 " ideal model delta sigma weight residual 109.99 99.53 10.46 1.74e+00 3.30e-01 3.61e+01 ... (remaining 28203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 9698 12.27 - 24.53: 1255 24.53 - 36.80: 640 36.80 - 49.07: 227 49.07 - 61.33: 68 Dihedral angle restraints: 11888 sinusoidal: 4352 harmonic: 7536 Sorted by residual: dihedral pdb=" CA ILE A 414 " pdb=" C ILE A 414 " pdb=" N TYR A 415 " pdb=" CA TYR A 415 " ideal model delta harmonic sigma weight residual 180.00 145.23 34.77 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA ILE D 414 " pdb=" C ILE D 414 " pdb=" N TYR D 415 " pdb=" CA TYR D 415 " ideal model delta harmonic sigma weight residual 180.00 146.34 33.66 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA ILE C 414 " pdb=" C ILE C 414 " pdb=" N TYR C 415 " pdb=" CA TYR C 415 " ideal model delta harmonic sigma weight residual 180.00 146.35 33.65 0 5.00e+00 4.00e-02 4.53e+01 ... (remaining 11885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1672 0.026 - 0.051: 1046 0.051 - 0.077: 434 0.077 - 0.102: 153 0.102 - 0.128: 43 Chirality restraints: 3348 Sorted by residual: chirality pdb=" CA TRP C 93 " pdb=" N TRP C 93 " pdb=" C TRP C 93 " pdb=" CB TRP C 93 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA TRP B 93 " pdb=" N TRP B 93 " pdb=" C TRP B 93 " pdb=" CB TRP B 93 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA TRP A 93 " pdb=" N TRP A 93 " pdb=" C TRP A 93 " pdb=" CB TRP A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 3345 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 376 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C ILE B 376 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 376 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 377 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 376 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ILE D 376 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE D 376 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA D 377 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 376 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C ILE C 376 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE C 376 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA C 377 " -0.011 2.00e-02 2.50e+03 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 9353 2.96 - 3.44: 20840 3.44 - 3.93: 30738 3.93 - 4.41: 35492 4.41 - 4.90: 58353 Nonbonded interactions: 154776 Sorted by model distance: nonbonded pdb=" O TRP A 93 " pdb=" CB TRP A 93 " model vdw 2.470 2.752 nonbonded pdb=" O TRP C 93 " pdb=" CB TRP C 93 " model vdw 2.473 2.752 nonbonded pdb=" O TRP D 93 " pdb=" CB TRP D 93 " model vdw 2.474 2.752 nonbonded pdb=" O TRP B 93 " pdb=" CB TRP B 93 " model vdw 2.474 2.752 nonbonded pdb=" N TYR C 415 " pdb=" N ARG C 416 " model vdw 2.508 2.560 ... (remaining 154771 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.020 Find NCS groups from input model: 0.180 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 20724 Z= 0.240 Angle : 0.648 10.670 28224 Z= 0.383 Chirality : 0.040 0.128 3348 Planarity : 0.004 0.035 3420 Dihedral : 15.304 61.334 7064 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.78 % Allowed : 20.74 % Favored : 77.48 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.36 (0.16), residues: 2636 helix: -1.11 (0.12), residues: 1796 sheet: None (None), residues: 0 loop : -2.32 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 586 TYR 0.018 0.001 TYR D 415 PHE 0.008 0.001 PHE D 339 TRP 0.021 0.001 TRP C 591 HIS 0.002 0.000 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00427 (20716) covalent geometry : angle 0.64806 (28208) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.93292 ( 16) hydrogen bonds : bond 0.26159 ( 1105) hydrogen bonds : angle 8.59857 ( 3315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 ASP cc_start: 0.9115 (t0) cc_final: 0.8628 (t0) REVERT: A 385 LEU cc_start: 0.9373 (mt) cc_final: 0.9013 (pp) REVERT: A 393 MET cc_start: 0.9379 (tpp) cc_final: 0.9154 (tpt) REVERT: A 413 ASP cc_start: 0.7140 (m-30) cc_final: 0.6654 (m-30) REVERT: A 526 MET cc_start: 0.8850 (mmt) cc_final: 0.7718 (mmt) REVERT: B 363 ASP cc_start: 0.9129 (t0) cc_final: 0.8652 (t0) REVERT: B 385 LEU cc_start: 0.9372 (mt) cc_final: 0.9016 (pp) REVERT: B 402 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 413 ASP cc_start: 0.7062 (m-30) cc_final: 0.6615 (m-30) REVERT: B 526 MET cc_start: 0.8815 (mmt) cc_final: 0.7675 (mmt) REVERT: C 363 ASP cc_start: 0.9103 (t0) cc_final: 0.8621 (t0) REVERT: C 385 LEU cc_start: 0.9380 (mt) cc_final: 0.9015 (pp) REVERT: C 393 MET cc_start: 0.9374 (tpp) cc_final: 0.9149 (tpt) REVERT: C 413 ASP cc_start: 0.7091 (m-30) cc_final: 0.6639 (m-30) REVERT: C 526 MET cc_start: 0.8845 (mmt) cc_final: 0.7733 (mmt) REVERT: C 610 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8218 (mt) REVERT: D 91 SER cc_start: 0.9499 (OUTLIER) cc_final: 0.9252 (t) REVERT: D 363 ASP cc_start: 0.9125 (t0) cc_final: 0.8657 (t0) REVERT: D 385 LEU cc_start: 0.9385 (mt) cc_final: 0.9027 (pp) REVERT: D 393 MET cc_start: 0.9370 (tpp) cc_final: 0.9146 (tpt) REVERT: D 413 ASP cc_start: 0.7055 (m-30) cc_final: 0.6629 (m-30) REVERT: D 526 MET cc_start: 0.8846 (mmt) cc_final: 0.7731 (mmt) outliers start: 38 outliers final: 27 residues processed: 219 average time/residue: 0.1357 time to fit residues: 46.8594 Evaluate side-chains 172 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 637 SER Chi-restraints excluded: chain D residue 661 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066432 restraints weight = 50418.204| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.40 r_work: 0.2880 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20724 Z= 0.140 Angle : 0.596 10.764 28224 Z= 0.317 Chirality : 0.040 0.131 3348 Planarity : 0.005 0.042 3420 Dihedral : 5.572 59.796 2874 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.79 % Allowed : 20.13 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.56 (0.16), residues: 2636 helix: -0.42 (0.12), residues: 1840 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 586 TYR 0.013 0.001 TYR C 415 PHE 0.013 0.001 PHE A 48 TRP 0.015 0.001 TRP B 95 HIS 0.003 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00310 (20716) covalent geometry : angle 0.59571 (28208) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.72423 ( 16) hydrogen bonds : bond 0.05506 ( 1105) hydrogen bonds : angle 5.04755 ( 3315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 187 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TRP cc_start: 0.8617 (t-100) cc_final: 0.8168 (t-100) REVERT: A 236 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 363 ASP cc_start: 0.9121 (t0) cc_final: 0.8618 (t0) REVERT: A 385 LEU cc_start: 0.9348 (mt) cc_final: 0.8996 (pp) REVERT: A 393 MET cc_start: 0.9321 (tpp) cc_final: 0.9085 (tpt) REVERT: A 413 ASP cc_start: 0.7127 (m-30) cc_final: 0.6532 (m-30) REVERT: A 499 PHE cc_start: 0.8980 (m-80) cc_final: 0.8460 (m-10) REVERT: A 518 ASP cc_start: 0.9352 (OUTLIER) cc_final: 0.9085 (t70) REVERT: A 526 MET cc_start: 0.8885 (mmt) cc_final: 0.7721 (mmt) REVERT: A 692 LEU cc_start: 0.9631 (mt) cc_final: 0.9410 (pp) REVERT: B 93 TRP cc_start: 0.8625 (OUTLIER) cc_final: 0.8301 (t-100) REVERT: B 363 ASP cc_start: 0.9129 (t0) cc_final: 0.8667 (t0) REVERT: B 385 LEU cc_start: 0.9335 (mt) cc_final: 0.8983 (pp) REVERT: B 393 MET cc_start: 0.9332 (tpp) cc_final: 0.9082 (tpt) REVERT: B 413 ASP cc_start: 0.7007 (m-30) cc_final: 0.6462 (m-30) REVERT: B 499 PHE cc_start: 0.8972 (m-80) cc_final: 0.8409 (m-10) REVERT: B 526 MET cc_start: 0.8872 (mmt) cc_final: 0.7650 (mmt) REVERT: B 692 LEU cc_start: 0.9636 (mt) cc_final: 0.9422 (pp) REVERT: C 93 TRP cc_start: 0.8612 (t-100) cc_final: 0.8167 (t-100) REVERT: C 236 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8073 (tp) REVERT: C 363 ASP cc_start: 0.9110 (t0) cc_final: 0.8605 (t0) REVERT: C 385 LEU cc_start: 0.9344 (mt) cc_final: 0.8983 (pp) REVERT: C 393 MET cc_start: 0.9323 (tpp) cc_final: 0.9083 (tpt) REVERT: C 413 ASP cc_start: 0.6989 (m-30) cc_final: 0.6442 (m-30) REVERT: C 499 PHE cc_start: 0.8946 (m-80) cc_final: 0.8438 (m-10) REVERT: C 518 ASP cc_start: 0.9348 (OUTLIER) cc_final: 0.9083 (t70) REVERT: C 526 MET cc_start: 0.8910 (mmt) cc_final: 0.7747 (mmt) REVERT: C 692 LEU cc_start: 0.9635 (mt) cc_final: 0.9421 (pp) REVERT: D 93 TRP cc_start: 0.8598 (t-100) cc_final: 0.8166 (t-100) REVERT: D 236 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (tp) REVERT: D 363 ASP cc_start: 0.9123 (t0) cc_final: 0.8652 (t0) REVERT: D 385 LEU cc_start: 0.9346 (mt) cc_final: 0.8992 (pp) REVERT: D 393 MET cc_start: 0.9320 (tpp) cc_final: 0.9084 (tpt) REVERT: D 413 ASP cc_start: 0.6986 (m-30) cc_final: 0.6443 (m-30) REVERT: D 499 PHE cc_start: 0.8978 (m-80) cc_final: 0.8442 (m-10) REVERT: D 526 MET cc_start: 0.8915 (mmt) cc_final: 0.7754 (mmt) REVERT: D 692 LEU cc_start: 0.9640 (mt) cc_final: 0.9423 (pp) outliers start: 81 outliers final: 46 residues processed: 255 average time/residue: 0.1130 time to fit residues: 49.6859 Evaluate side-chains 212 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 638 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 679 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.093181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066215 restraints weight = 50479.913| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.37 r_work: 0.2878 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20724 Z= 0.129 Angle : 0.573 9.429 28224 Z= 0.298 Chirality : 0.040 0.130 3348 Planarity : 0.004 0.039 3420 Dihedral : 5.067 57.493 2854 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.03 % Allowed : 20.74 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.02 (0.17), residues: 2636 helix: 0.01 (0.13), residues: 1844 sheet: None (None), residues: 0 loop : -2.20 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 586 TYR 0.011 0.001 TYR C 415 PHE 0.014 0.001 PHE B 339 TRP 0.013 0.001 TRP A 95 HIS 0.004 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00295 (20716) covalent geometry : angle 0.57268 (28208) SS BOND : bond 0.00286 ( 8) SS BOND : angle 0.68735 ( 16) hydrogen bonds : bond 0.04532 ( 1105) hydrogen bonds : angle 4.41009 ( 3315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 152 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 93 TRP cc_start: 0.8746 (t-100) cc_final: 0.8164 (t-100) REVERT: A 236 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7936 (tp) REVERT: A 363 ASP cc_start: 0.9079 (t0) cc_final: 0.8579 (t0) REVERT: A 385 LEU cc_start: 0.9339 (mt) cc_final: 0.8983 (pp) REVERT: A 393 MET cc_start: 0.9340 (tpp) cc_final: 0.9096 (tpt) REVERT: A 413 ASP cc_start: 0.7218 (m-30) cc_final: 0.6620 (m-30) REVERT: A 499 PHE cc_start: 0.9017 (m-80) cc_final: 0.8453 (m-10) REVERT: A 518 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.9064 (t70) REVERT: A 526 MET cc_start: 0.8894 (mmt) cc_final: 0.7825 (mmt) REVERT: A 692 LEU cc_start: 0.9669 (mt) cc_final: 0.9440 (pp) REVERT: B 93 TRP cc_start: 0.8753 (OUTLIER) cc_final: 0.8314 (t-100) REVERT: B 236 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 289 MET cc_start: 0.8807 (mmm) cc_final: 0.8523 (tpp) REVERT: B 363 ASP cc_start: 0.9090 (t0) cc_final: 0.8632 (t0) REVERT: B 385 LEU cc_start: 0.9332 (mt) cc_final: 0.8979 (pp) REVERT: B 393 MET cc_start: 0.9361 (tpp) cc_final: 0.9117 (tpt) REVERT: B 499 PHE cc_start: 0.9012 (m-80) cc_final: 0.8425 (m-10) REVERT: B 526 MET cc_start: 0.8887 (mmt) cc_final: 0.7810 (mmt) REVERT: B 692 LEU cc_start: 0.9668 (mt) cc_final: 0.9455 (pp) REVERT: C 93 TRP cc_start: 0.8748 (t-100) cc_final: 0.8166 (t-100) REVERT: C 236 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7947 (tp) REVERT: C 363 ASP cc_start: 0.9071 (t0) cc_final: 0.8569 (t0) REVERT: C 385 LEU cc_start: 0.9344 (mt) cc_final: 0.8983 (pp) REVERT: C 393 MET cc_start: 0.9339 (tpp) cc_final: 0.9094 (tpt) REVERT: C 413 ASP cc_start: 0.7057 (m-30) cc_final: 0.6438 (m-30) REVERT: C 499 PHE cc_start: 0.9013 (m-80) cc_final: 0.8478 (m-10) REVERT: C 518 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9076 (t70) REVERT: C 526 MET cc_start: 0.8915 (mmt) cc_final: 0.7826 (mmt) REVERT: C 692 LEU cc_start: 0.9672 (mt) cc_final: 0.9448 (pp) REVERT: D 93 TRP cc_start: 0.8749 (t-100) cc_final: 0.8162 (t-100) REVERT: D 236 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (tp) REVERT: D 363 ASP cc_start: 0.9081 (t0) cc_final: 0.8607 (t0) REVERT: D 385 LEU cc_start: 0.9337 (mt) cc_final: 0.8988 (pp) REVERT: D 393 MET cc_start: 0.9343 (tpp) cc_final: 0.9099 (tpt) REVERT: D 499 PHE cc_start: 0.9021 (m-80) cc_final: 0.8453 (m-10) REVERT: D 526 MET cc_start: 0.8914 (mmt) cc_final: 0.7825 (mmt) REVERT: D 692 LEU cc_start: 0.9684 (mt) cc_final: 0.9469 (pp) outliers start: 86 outliers final: 55 residues processed: 228 average time/residue: 0.1168 time to fit residues: 46.1963 Evaluate side-chains 209 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 147 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 218 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.093403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066540 restraints weight = 50668.737| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.39 r_work: 0.2879 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20724 Z= 0.120 Angle : 0.556 10.385 28224 Z= 0.287 Chirality : 0.039 0.156 3348 Planarity : 0.004 0.039 3420 Dihedral : 4.803 55.364 2846 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.59 % Allowed : 21.11 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.66 (0.17), residues: 2636 helix: 0.27 (0.13), residues: 1860 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 586 TYR 0.009 0.001 TYR C 415 PHE 0.012 0.001 PHE B 339 TRP 0.012 0.001 TRP A 95 HIS 0.002 0.000 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00277 (20716) covalent geometry : angle 0.55560 (28208) SS BOND : bond 0.00278 ( 8) SS BOND : angle 0.63996 ( 16) hydrogen bonds : bond 0.03956 ( 1105) hydrogen bonds : angle 4.10062 ( 3315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 145 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 93 TRP cc_start: 0.8810 (t-100) cc_final: 0.8149 (t-100) REVERT: A 236 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7841 (tp) REVERT: A 363 ASP cc_start: 0.9048 (t0) cc_final: 0.8560 (t0) REVERT: A 385 LEU cc_start: 0.9328 (mt) cc_final: 0.8977 (pp) REVERT: A 393 MET cc_start: 0.9359 (tpp) cc_final: 0.9128 (tpt) REVERT: A 499 PHE cc_start: 0.9018 (m-80) cc_final: 0.8428 (m-10) REVERT: A 526 MET cc_start: 0.8837 (mmt) cc_final: 0.7735 (mmt) REVERT: A 597 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 93 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.8210 (t-100) REVERT: B 236 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7978 (tp) REVERT: B 363 ASP cc_start: 0.9025 (t0) cc_final: 0.8565 (t0) REVERT: B 385 LEU cc_start: 0.9331 (mt) cc_final: 0.8978 (pp) REVERT: B 393 MET cc_start: 0.9372 (tpp) cc_final: 0.9139 (tpt) REVERT: B 499 PHE cc_start: 0.9008 (m-80) cc_final: 0.8427 (m-10) REVERT: B 526 MET cc_start: 0.8861 (mmt) cc_final: 0.7778 (mmt) REVERT: B 692 LEU cc_start: 0.9703 (mt) cc_final: 0.9502 (pp) REVERT: C 91 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.9157 (t) REVERT: C 93 TRP cc_start: 0.8820 (t-100) cc_final: 0.8137 (t-100) REVERT: C 236 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7843 (tp) REVERT: C 363 ASP cc_start: 0.9040 (t0) cc_final: 0.8547 (t0) REVERT: C 385 LEU cc_start: 0.9338 (mt) cc_final: 0.8988 (pp) REVERT: C 393 MET cc_start: 0.9350 (tpp) cc_final: 0.9115 (tpt) REVERT: C 499 PHE cc_start: 0.9021 (m-80) cc_final: 0.8454 (m-10) REVERT: C 518 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.9065 (t70) REVERT: C 526 MET cc_start: 0.8878 (mmt) cc_final: 0.7783 (mmt) REVERT: D 93 TRP cc_start: 0.8817 (t-100) cc_final: 0.8156 (t-100) REVERT: D 236 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (tp) REVERT: D 363 ASP cc_start: 0.9039 (t0) cc_final: 0.8567 (t0) REVERT: D 385 LEU cc_start: 0.9334 (mt) cc_final: 0.8985 (pp) REVERT: D 393 MET cc_start: 0.9359 (tpp) cc_final: 0.9129 (tpt) REVERT: D 499 PHE cc_start: 0.9013 (m-80) cc_final: 0.8414 (m-10) REVERT: D 526 MET cc_start: 0.8902 (mmt) cc_final: 0.7803 (mmt) outliers start: 98 outliers final: 69 residues processed: 227 average time/residue: 0.1129 time to fit residues: 45.2459 Evaluate side-chains 219 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 142 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 646 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 122 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 523 ASN C 523 ASN D 523 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067628 restraints weight = 50504.280| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.40 r_work: 0.2898 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20724 Z= 0.102 Angle : 0.550 12.313 28224 Z= 0.279 Chirality : 0.038 0.153 3348 Planarity : 0.004 0.038 3420 Dihedral : 4.675 54.083 2846 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.56 % Allowed : 22.43 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.17), residues: 2636 helix: 0.44 (0.13), residues: 1860 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 586 TYR 0.007 0.001 TYR C 415 PHE 0.010 0.001 PHE B 128 TRP 0.010 0.001 TRP A 95 HIS 0.001 0.000 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00233 (20716) covalent geometry : angle 0.54953 (28208) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.54015 ( 16) hydrogen bonds : bond 0.03524 ( 1105) hydrogen bonds : angle 3.94752 ( 3315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 91 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9104 (t) REVERT: A 93 TRP cc_start: 0.8807 (t-100) cc_final: 0.8172 (t-100) REVERT: A 236 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7808 (tp) REVERT: A 363 ASP cc_start: 0.9021 (t0) cc_final: 0.8556 (t0) REVERT: A 385 LEU cc_start: 0.9338 (mt) cc_final: 0.8991 (pp) REVERT: A 393 MET cc_start: 0.9353 (tpp) cc_final: 0.9138 (tpt) REVERT: A 499 PHE cc_start: 0.9021 (m-80) cc_final: 0.8420 (m-10) REVERT: A 526 MET cc_start: 0.8823 (mmt) cc_final: 0.7759 (mmt) REVERT: B 93 TRP cc_start: 0.8780 (OUTLIER) cc_final: 0.8229 (t-100) REVERT: B 236 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7884 (tp) REVERT: B 363 ASP cc_start: 0.8995 (t0) cc_final: 0.8541 (t0) REVERT: B 385 LEU cc_start: 0.9325 (mt) cc_final: 0.8976 (pp) REVERT: B 393 MET cc_start: 0.9361 (tpp) cc_final: 0.9136 (tpt) REVERT: B 499 PHE cc_start: 0.9023 (m-80) cc_final: 0.8402 (m-10) REVERT: B 526 MET cc_start: 0.8834 (mmt) cc_final: 0.7729 (mmt) REVERT: C 91 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9137 (t) REVERT: C 93 TRP cc_start: 0.8814 (t-100) cc_final: 0.8169 (t-100) REVERT: C 236 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7810 (tp) REVERT: C 363 ASP cc_start: 0.9022 (t0) cc_final: 0.8557 (t0) REVERT: C 385 LEU cc_start: 0.9341 (mt) cc_final: 0.8992 (pp) REVERT: C 393 MET cc_start: 0.9344 (tpp) cc_final: 0.9124 (tpt) REVERT: C 499 PHE cc_start: 0.9019 (m-80) cc_final: 0.8407 (m-10) REVERT: C 526 MET cc_start: 0.8834 (mmt) cc_final: 0.7711 (mmt) REVERT: D 93 TRP cc_start: 0.8804 (t-100) cc_final: 0.8178 (t-100) REVERT: D 236 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7812 (tp) REVERT: D 289 MET cc_start: 0.8775 (mmm) cc_final: 0.8444 (tpp) REVERT: D 363 ASP cc_start: 0.9023 (t0) cc_final: 0.8576 (t0) REVERT: D 385 LEU cc_start: 0.9335 (mt) cc_final: 0.8988 (pp) REVERT: D 393 MET cc_start: 0.9340 (tpp) cc_final: 0.9124 (tpt) REVERT: D 499 PHE cc_start: 0.9011 (m-80) cc_final: 0.8406 (m-10) REVERT: D 526 MET cc_start: 0.8852 (mmt) cc_final: 0.7712 (mmt) outliers start: 76 outliers final: 51 residues processed: 210 average time/residue: 0.1148 time to fit residues: 42.0875 Evaluate side-chains 201 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 65 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 126 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066523 restraints weight = 50192.854| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.38 r_work: 0.2879 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20724 Z= 0.123 Angle : 0.558 12.726 28224 Z= 0.284 Chirality : 0.039 0.145 3348 Planarity : 0.004 0.038 3420 Dihedral : 4.667 53.297 2846 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.70 % Allowed : 22.10 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2636 helix: 0.54 (0.13), residues: 1836 sheet: None (None), residues: 0 loop : -2.02 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 586 TYR 0.008 0.001 TYR C 415 PHE 0.013 0.001 PHE B 339 TRP 0.013 0.001 TRP D 95 HIS 0.002 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00290 (20716) covalent geometry : angle 0.55757 (28208) SS BOND : bond 0.00271 ( 8) SS BOND : angle 0.59998 ( 16) hydrogen bonds : bond 0.03728 ( 1105) hydrogen bonds : angle 3.91476 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 138 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 91 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.9130 (t) REVERT: A 93 TRP cc_start: 0.8851 (t-100) cc_final: 0.8119 (t60) REVERT: A 236 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 363 ASP cc_start: 0.9007 (t0) cc_final: 0.8578 (t0) REVERT: A 385 LEU cc_start: 0.9328 (mt) cc_final: 0.8980 (pp) REVERT: A 393 MET cc_start: 0.9366 (tpp) cc_final: 0.9141 (tpt) REVERT: A 499 PHE cc_start: 0.9029 (m-80) cc_final: 0.8420 (m-10) REVERT: A 526 MET cc_start: 0.8785 (mmt) cc_final: 0.7732 (mmt) REVERT: B 93 TRP cc_start: 0.8842 (OUTLIER) cc_final: 0.8259 (t-100) REVERT: B 236 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7823 (tp) REVERT: B 363 ASP cc_start: 0.9004 (t0) cc_final: 0.8595 (t0) REVERT: B 385 LEU cc_start: 0.9332 (mt) cc_final: 0.8983 (pp) REVERT: B 393 MET cc_start: 0.9366 (tpp) cc_final: 0.9130 (tpt) REVERT: B 499 PHE cc_start: 0.9018 (m-80) cc_final: 0.8373 (m-10) REVERT: B 526 MET cc_start: 0.8850 (mmt) cc_final: 0.7784 (mmt) REVERT: C 93 TRP cc_start: 0.8848 (t-100) cc_final: 0.8112 (t60) REVERT: C 236 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7801 (tp) REVERT: C 363 ASP cc_start: 0.9005 (t0) cc_final: 0.8578 (t0) REVERT: C 385 LEU cc_start: 0.9330 (mt) cc_final: 0.8979 (pp) REVERT: C 393 MET cc_start: 0.9365 (tpp) cc_final: 0.9138 (tpt) REVERT: C 499 PHE cc_start: 0.9018 (m-80) cc_final: 0.8405 (m-10) REVERT: C 526 MET cc_start: 0.8832 (mmt) cc_final: 0.7739 (mmt) REVERT: D 93 TRP cc_start: 0.8896 (t-100) cc_final: 0.8142 (t-100) REVERT: D 236 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7822 (tp) REVERT: D 363 ASP cc_start: 0.9002 (t0) cc_final: 0.8594 (t0) REVERT: D 385 LEU cc_start: 0.9329 (mt) cc_final: 0.8986 (pp) REVERT: D 393 MET cc_start: 0.9360 (tpp) cc_final: 0.9136 (tpt) REVERT: D 499 PHE cc_start: 0.9024 (m-80) cc_final: 0.8376 (m-10) REVERT: D 526 MET cc_start: 0.8833 (mmt) cc_final: 0.7738 (mmt) outliers start: 79 outliers final: 60 residues processed: 204 average time/residue: 0.1131 time to fit residues: 40.0675 Evaluate side-chains 202 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 136 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 216 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.094640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067875 restraints weight = 50368.448| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.40 r_work: 0.2909 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20724 Z= 0.098 Angle : 0.544 11.576 28224 Z= 0.274 Chirality : 0.038 0.129 3348 Planarity : 0.003 0.037 3420 Dihedral : 4.594 51.706 2846 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.42 % Allowed : 22.28 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.25 (0.17), residues: 2636 helix: 0.60 (0.13), residues: 1840 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 586 TYR 0.007 0.001 TYR D 415 PHE 0.010 0.001 PHE C 128 TRP 0.011 0.001 TRP D 95 HIS 0.001 0.000 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00223 (20716) covalent geometry : angle 0.54385 (28208) SS BOND : bond 0.00194 ( 8) SS BOND : angle 0.48751 ( 16) hydrogen bonds : bond 0.03300 ( 1105) hydrogen bonds : angle 3.83768 ( 3315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 91 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.9032 (t) REVERT: A 93 TRP cc_start: 0.8810 (t-100) cc_final: 0.8076 (t60) REVERT: A 236 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 363 ASP cc_start: 0.8996 (t0) cc_final: 0.8570 (t0) REVERT: A 385 LEU cc_start: 0.9321 (mt) cc_final: 0.8992 (pp) REVERT: A 393 MET cc_start: 0.9355 (tpp) cc_final: 0.9133 (tpt) REVERT: A 499 PHE cc_start: 0.9023 (m-80) cc_final: 0.8438 (m-10) REVERT: A 526 MET cc_start: 0.8734 (mmt) cc_final: 0.7744 (mmt) REVERT: B 93 TRP cc_start: 0.8825 (OUTLIER) cc_final: 0.8205 (t-100) REVERT: B 236 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 363 ASP cc_start: 0.8990 (t0) cc_final: 0.8582 (t0) REVERT: B 385 LEU cc_start: 0.9334 (mt) cc_final: 0.8993 (pp) REVERT: B 393 MET cc_start: 0.9354 (tpp) cc_final: 0.9132 (tpt) REVERT: B 413 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6461 (m-30) REVERT: B 499 PHE cc_start: 0.9010 (m-80) cc_final: 0.8392 (m-10) REVERT: B 526 MET cc_start: 0.8766 (mmt) cc_final: 0.7762 (mmt) REVERT: C 91 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9029 (t) REVERT: C 93 TRP cc_start: 0.8802 (t-100) cc_final: 0.8123 (t60) REVERT: C 236 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7763 (tp) REVERT: C 363 ASP cc_start: 0.8981 (t0) cc_final: 0.8556 (t0) REVERT: C 385 LEU cc_start: 0.9319 (mt) cc_final: 0.8990 (pp) REVERT: C 393 MET cc_start: 0.9346 (tpp) cc_final: 0.9127 (tpt) REVERT: C 499 PHE cc_start: 0.9013 (m-80) cc_final: 0.8375 (m-10) REVERT: C 526 MET cc_start: 0.8784 (mmt) cc_final: 0.7734 (mmt) REVERT: D 93 TRP cc_start: 0.8816 (t-100) cc_final: 0.8061 (t-100) REVERT: D 236 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7775 (tp) REVERT: D 363 ASP cc_start: 0.8973 (t0) cc_final: 0.8568 (t0) REVERT: D 385 LEU cc_start: 0.9336 (mt) cc_final: 0.9002 (pp) REVERT: D 393 MET cc_start: 0.9339 (tpp) cc_final: 0.9119 (tpt) REVERT: D 499 PHE cc_start: 0.9010 (m-80) cc_final: 0.8379 (m-10) REVERT: D 526 MET cc_start: 0.8811 (mmt) cc_final: 0.7773 (mmt) outliers start: 73 outliers final: 55 residues processed: 209 average time/residue: 0.1112 time to fit residues: 40.7345 Evaluate side-chains 202 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 139 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.093085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066489 restraints weight = 50020.155| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.36 r_work: 0.2878 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20724 Z= 0.128 Angle : 0.560 11.581 28224 Z= 0.283 Chirality : 0.039 0.164 3348 Planarity : 0.004 0.038 3420 Dihedral : 4.585 50.883 2844 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.93 % Allowed : 21.82 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.22 (0.17), residues: 2636 helix: 0.61 (0.13), residues: 1868 sheet: None (None), residues: 0 loop : -1.96 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.008 0.001 TYR C 415 PHE 0.014 0.001 PHE C 128 TRP 0.014 0.001 TRP D 95 HIS 0.003 0.001 HIS D 227 Details of bonding type rmsd covalent geometry : bond 0.00304 (20716) covalent geometry : angle 0.55978 (28208) SS BOND : bond 0.00277 ( 8) SS BOND : angle 0.59532 ( 16) hydrogen bonds : bond 0.03681 ( 1105) hydrogen bonds : angle 3.84832 ( 3315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 131 time to evaluate : 0.662 Fit side-chains REVERT: A 91 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9071 (t) REVERT: A 93 TRP cc_start: 0.8842 (t-100) cc_final: 0.8124 (t-100) REVERT: A 236 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7849 (tp) REVERT: A 363 ASP cc_start: 0.9016 (t0) cc_final: 0.8578 (t0) REVERT: A 385 LEU cc_start: 0.9342 (mt) cc_final: 0.8997 (pp) REVERT: A 393 MET cc_start: 0.9400 (tpp) cc_final: 0.9166 (tpt) REVERT: A 413 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: A 499 PHE cc_start: 0.9039 (m-80) cc_final: 0.8446 (m-10) REVERT: A 526 MET cc_start: 0.8781 (mmt) cc_final: 0.7789 (mmt) REVERT: B 93 TRP cc_start: 0.8905 (t-100) cc_final: 0.8216 (t-100) REVERT: B 236 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (tp) REVERT: B 363 ASP cc_start: 0.8983 (t0) cc_final: 0.8562 (t0) REVERT: B 385 LEU cc_start: 0.9351 (mt) cc_final: 0.8999 (pp) REVERT: B 393 MET cc_start: 0.9382 (tpp) cc_final: 0.9148 (tpt) REVERT: B 402 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8208 (mm-30) REVERT: B 526 MET cc_start: 0.8806 (mmt) cc_final: 0.7761 (mmt) REVERT: C 93 TRP cc_start: 0.8837 (t-100) cc_final: 0.8123 (t-100) REVERT: C 236 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7845 (tp) REVERT: C 363 ASP cc_start: 0.9000 (t0) cc_final: 0.8561 (t0) REVERT: C 385 LEU cc_start: 0.9338 (mt) cc_final: 0.8993 (pp) REVERT: C 393 MET cc_start: 0.9386 (tpp) cc_final: 0.9150 (tpt) REVERT: C 526 MET cc_start: 0.8802 (mmt) cc_final: 0.7774 (mmt) REVERT: D 93 TRP cc_start: 0.8901 (t-100) cc_final: 0.8101 (t-100) REVERT: D 236 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7866 (tp) REVERT: D 363 ASP cc_start: 0.8985 (t0) cc_final: 0.8560 (t0) REVERT: D 385 LEU cc_start: 0.9356 (mt) cc_final: 0.9010 (pp) REVERT: D 393 MET cc_start: 0.9376 (tpp) cc_final: 0.9143 (tpt) REVERT: D 526 MET cc_start: 0.8810 (mmt) cc_final: 0.7769 (mmt) outliers start: 84 outliers final: 67 residues processed: 204 average time/residue: 0.1084 time to fit residues: 38.5951 Evaluate side-chains 202 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 165 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.094131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067564 restraints weight = 49905.959| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.36 r_work: 0.2899 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20724 Z= 0.102 Angle : 0.553 11.626 28224 Z= 0.277 Chirality : 0.038 0.174 3348 Planarity : 0.003 0.037 3420 Dihedral : 4.535 49.879 2844 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.51 % Allowed : 22.38 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.04 (0.17), residues: 2636 helix: 0.73 (0.13), residues: 1840 sheet: None (None), residues: 0 loop : -1.78 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 586 TYR 0.007 0.001 TYR C 415 PHE 0.011 0.001 PHE B 128 TRP 0.012 0.001 TRP C 95 HIS 0.001 0.000 HIS D 227 Details of bonding type rmsd covalent geometry : bond 0.00235 (20716) covalent geometry : angle 0.55313 (28208) SS BOND : bond 0.00216 ( 8) SS BOND : angle 0.50247 ( 16) hydrogen bonds : bond 0.03368 ( 1105) hydrogen bonds : angle 3.79924 ( 3315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 140 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 91 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.9033 (t) REVERT: A 93 TRP cc_start: 0.8821 (t-100) cc_final: 0.8076 (t-100) REVERT: A 236 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7847 (tp) REVERT: A 363 ASP cc_start: 0.9003 (t0) cc_final: 0.8561 (t0) REVERT: A 385 LEU cc_start: 0.9342 (mt) cc_final: 0.9003 (pp) REVERT: A 393 MET cc_start: 0.9389 (tpp) cc_final: 0.9163 (tpt) REVERT: A 499 PHE cc_start: 0.9033 (m-80) cc_final: 0.8440 (m-10) REVERT: A 526 MET cc_start: 0.8753 (mmt) cc_final: 0.7796 (mmt) REVERT: B 93 TRP cc_start: 0.8888 (t-100) cc_final: 0.8194 (t-100) REVERT: B 236 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7886 (tp) REVERT: B 363 ASP cc_start: 0.8981 (t0) cc_final: 0.8550 (t0) REVERT: B 385 LEU cc_start: 0.9347 (mt) cc_final: 0.8998 (pp) REVERT: B 393 MET cc_start: 0.9380 (tpp) cc_final: 0.9154 (tpt) REVERT: B 413 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6426 (m-30) REVERT: B 526 MET cc_start: 0.8781 (mmt) cc_final: 0.7774 (mmt) REVERT: C 91 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9031 (t) REVERT: C 93 TRP cc_start: 0.8865 (t-100) cc_final: 0.8117 (t-100) REVERT: C 236 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7836 (tp) REVERT: C 363 ASP cc_start: 0.8972 (t0) cc_final: 0.8526 (t0) REVERT: C 385 LEU cc_start: 0.9336 (mt) cc_final: 0.8997 (pp) REVERT: C 393 MET cc_start: 0.9379 (tpp) cc_final: 0.9157 (tpt) REVERT: C 499 PHE cc_start: 0.9024 (m-80) cc_final: 0.8516 (m-10) REVERT: C 526 MET cc_start: 0.8767 (mmt) cc_final: 0.7760 (mmt) REVERT: D 93 TRP cc_start: 0.8873 (t-100) cc_final: 0.8060 (t-100) REVERT: D 236 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7853 (tp) REVERT: D 363 ASP cc_start: 0.8941 (t0) cc_final: 0.8512 (t0) REVERT: D 385 LEU cc_start: 0.9356 (mt) cc_final: 0.9016 (pp) REVERT: D 393 MET cc_start: 0.9374 (tpp) cc_final: 0.9150 (tpt) REVERT: D 413 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6409 (m-30) REVERT: D 499 PHE cc_start: 0.9033 (m-80) cc_final: 0.8530 (m-10) REVERT: D 526 MET cc_start: 0.8784 (mmt) cc_final: 0.7763 (mmt) outliers start: 75 outliers final: 63 residues processed: 203 average time/residue: 0.1046 time to fit residues: 37.0682 Evaluate side-chains 207 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 136 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 174 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064888 restraints weight = 50540.779| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.28 r_work: 0.2842 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20724 Z= 0.181 Angle : 0.600 11.294 28224 Z= 0.306 Chirality : 0.041 0.161 3348 Planarity : 0.004 0.039 3420 Dihedral : 4.688 49.218 2844 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.42 % Allowed : 22.80 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.21 (0.17), residues: 2636 helix: 0.60 (0.13), residues: 1872 sheet: None (None), residues: 0 loop : -1.94 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.010 0.001 TYR B 461 PHE 0.019 0.001 PHE B 128 TRP 0.018 0.001 TRP A 95 HIS 0.003 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00430 (20716) covalent geometry : angle 0.59987 (28208) SS BOND : bond 0.00388 ( 8) SS BOND : angle 0.79911 ( 16) hydrogen bonds : bond 0.04247 ( 1105) hydrogen bonds : angle 3.93858 ( 3315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 0.719 Fit side-chains REVERT: A 93 TRP cc_start: 0.8954 (t-100) cc_final: 0.8207 (t-100) REVERT: A 236 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 363 ASP cc_start: 0.8995 (t0) cc_final: 0.8570 (t0) REVERT: A 385 LEU cc_start: 0.9378 (mt) cc_final: 0.9021 (pp) REVERT: A 526 MET cc_start: 0.8810 (mmt) cc_final: 0.7837 (mmt) REVERT: B 236 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8030 (tp) REVERT: B 363 ASP cc_start: 0.9005 (t0) cc_final: 0.8584 (t0) REVERT: B 385 LEU cc_start: 0.9375 (mt) cc_final: 0.9011 (pp) REVERT: B 526 MET cc_start: 0.8846 (mmt) cc_final: 0.7853 (mmt) REVERT: C 236 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7952 (tp) REVERT: C 363 ASP cc_start: 0.8999 (t0) cc_final: 0.8574 (t0) REVERT: C 385 LEU cc_start: 0.9368 (mt) cc_final: 0.9005 (pp) REVERT: C 526 MET cc_start: 0.8852 (mmt) cc_final: 0.7867 (mmt) REVERT: D 236 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7961 (tp) REVERT: D 363 ASP cc_start: 0.9017 (t0) cc_final: 0.8588 (t0) REVERT: D 385 LEU cc_start: 0.9372 (mt) cc_final: 0.9011 (pp) REVERT: D 526 MET cc_start: 0.8860 (mmt) cc_final: 0.7861 (mmt) outliers start: 73 outliers final: 66 residues processed: 191 average time/residue: 0.1049 time to fit residues: 35.2858 Evaluate side-chains 195 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 67 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.065391 restraints weight = 50371.020| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.29 r_work: 0.2852 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20724 Z= 0.155 Angle : 0.584 11.272 28224 Z= 0.297 Chirality : 0.040 0.148 3348 Planarity : 0.004 0.040 3420 Dihedral : 4.669 47.822 2844 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.56 % Allowed : 22.89 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.16 (0.17), residues: 2636 helix: 0.64 (0.13), residues: 1876 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 586 TYR 0.009 0.001 TYR C 415 PHE 0.016 0.001 PHE D 128 TRP 0.015 0.001 TRP A 95 HIS 0.003 0.001 HIS D 227 Details of bonding type rmsd covalent geometry : bond 0.00368 (20716) covalent geometry : angle 0.58378 (28208) SS BOND : bond 0.00312 ( 8) SS BOND : angle 0.63670 ( 16) hydrogen bonds : bond 0.03953 ( 1105) hydrogen bonds : angle 3.91250 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.97 seconds wall clock time: 76 minutes 14.21 seconds (4574.21 seconds total)