Starting phenix.real_space_refine on Fri Aug 7 11:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13lq_77141/08_2026/13lq_77141.cif Found real_map, /net/cci-nas-00/data/ceres_data/13lq_77141/08_2026/13lq_77141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13lq_77141/08_2026/13lq_77141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13lq_77141/08_2026/13lq_77141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13lq_77141/08_2026/13lq_77141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13lq_77141/08_2026/13lq_77141.map" } resolution = 4.01 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= 0.010 sd= 0.021 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: 5 Type Number sf(0) Gaussians S 132 5.16 5 Na 3 4.78 5 C 13356 2.51 5 N 3408 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20559 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5139 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 14, 'TRANS': 616} Chain breaks: 2 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5139 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 14, 'TRANS': 616} Chain breaks: 2 Chain: "C" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5139 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 14, 'TRANS': 616} Chain breaks: 2 Chain: "D" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5139 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 14, 'TRANS': 616} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.90, per 1000 atoms: 0.19 Number of scatterers: 20559 At special positions: 0 Unit cell: (157.941, 157.941, 125.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 Na 3 11.00 O 3660 8.00 N 3408 7.00 C 13356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.05 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.05 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.05 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.05 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: 1.69 Conformation dependent library (CDL) restraints added in 839.1 milliseconds 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 64.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.571A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 4.296A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.650A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.729A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.797A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.630A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.653A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.688A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.752A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.560A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.647A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.923A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.236A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.594A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.906A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 462 removed outlier: 3.613A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.655A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.662A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.714A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.500A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 removed outlier: 4.175A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 608 removed outlier: 3.657A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.607A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 667 removed outlier: 3.534A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.511A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.578A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.804A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.570A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 4.296A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.650A pdb=" N LEU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.728A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.797A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.631A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.653A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.688A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.752A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.559A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.646A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.923A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.236A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.593A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.905A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 462 removed outlier: 3.613A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.655A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 507 " --> pdb=" O ILE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 540 removed outlier: 3.663A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.714A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.501A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 4.175A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.658A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.608A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.535A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.511A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.577A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.805A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 747 Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.571A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.295A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.649A pdb=" N LEU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.728A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.796A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 192 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.630A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.652A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.688A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.753A pdb=" N LEU C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.560A pdb=" N HIS C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.646A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.923A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 4.236A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.593A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 423 through 436 removed outlier: 3.906A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 462 removed outlier: 3.612A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.655A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 507 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 removed outlier: 3.662A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.714A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.501A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.176A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 3.658A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 removed outlier: 3.608A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 667 removed outlier: 3.534A pdb=" N LEU C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.511A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.576A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.805A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 747 Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.571A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 4.296A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.649A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.728A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.797A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.631A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 3.652A pdb=" N GLU D 214 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.688A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 238 Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.752A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.559A pdb=" N HIS D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.647A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.923A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 4.236A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.593A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.905A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS D 435 " --> pdb=" O MET D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 462 removed outlier: 3.613A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.656A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 507 " --> pdb=" O ILE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 540 removed outlier: 3.662A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.715A pdb=" N VAL D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.501A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 removed outlier: 4.176A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 608 removed outlier: 3.657A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 635 removed outlier: 3.608A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 667 removed outlier: 3.535A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.511A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.576A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.805A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 747 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 7.124A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 388 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 734 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 390 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 731 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 7.124A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 388 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 734 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 390 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 731 " --> pdb=" O GLU B 719 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 7.124A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 388 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 734 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 390 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 731 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 7.124A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 388 " --> pdb=" O ILE D 734 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 734 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR D 390 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS D 731 " --> pdb=" O GLU D 719 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2532 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: 2.88 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5810 1.33 - 1.45: 3585 1.45 - 1.57: 11385 1.57 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 20996 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.335 1.408 -0.072 1.36e-02 5.41e+03 2.82e+01 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.335 1.408 -0.072 1.36e-02 5.41e+03 2.82e+01 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.36e-02 5.41e+03 2.80e+01 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.335 1.407 -0.071 1.36e-02 5.41e+03 2.74e+01 bond pdb=" C GLU D 423 " pdb=" N PRO D 424 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.24e-02 6.50e+03 1.37e+01 ... (remaining 20991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 26593 2.15 - 4.30: 1450 4.30 - 6.45: 217 6.45 - 8.60: 112 8.60 - 10.75: 12 Bond angle restraints: 28384 Sorted by residual: angle pdb=" N ILE A 199 " pdb=" CA ILE A 199 " pdb=" C ILE A 199 " ideal model delta sigma weight residual 112.83 107.13 5.70 9.90e-01 1.02e+00 3.31e+01 angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 112.83 107.14 5.69 9.90e-01 1.02e+00 3.30e+01 angle pdb=" N ILE B 199 " pdb=" CA ILE B 199 " pdb=" C ILE B 199 " ideal model delta sigma weight residual 112.83 107.15 5.68 9.90e-01 1.02e+00 3.29e+01 angle pdb=" N ILE D 199 " pdb=" CA ILE D 199 " pdb=" C ILE D 199 " ideal model delta sigma weight residual 112.83 107.16 5.67 9.90e-01 1.02e+00 3.28e+01 angle pdb=" N PRO C 613 " pdb=" CA PRO C 613 " pdb=" CB PRO C 613 " ideal model delta sigma weight residual 103.25 97.75 5.50 1.05e+00 9.07e-01 2.74e+01 ... (remaining 28379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 11496 16.21 - 32.42: 803 32.42 - 48.63: 221 48.63 - 64.84: 17 64.84 - 81.05: 23 Dihedral angle restraints: 12560 sinusoidal: 5116 harmonic: 7444 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.25 -80.25 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.20 -80.20 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.16 -80.16 1 1.00e+01 1.00e-02 7.96e+01 ... (remaining 12557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2543 0.060 - 0.120: 573 0.120 - 0.179: 77 0.179 - 0.239: 31 0.239 - 0.299: 12 Chirality restraints: 3236 Sorted by residual: chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE D 72 " pdb=" CA ILE D 72 " pdb=" CG1 ILE D 72 " pdb=" CG2 ILE D 72 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE C 72 " pdb=" CA ILE C 72 " pdb=" CG1 ILE C 72 " pdb=" CG2 ILE C 72 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 3233 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO B 181 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 181 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO D 181 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " -0.035 5.00e-02 4.00e+02 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5007 2.78 - 3.31: 19952 3.31 - 3.84: 34136 3.84 - 4.37: 38795 4.37 - 4.90: 63809 Nonbonded interactions: 161699 Sorted by model distance: nonbonded pdb=" O SER B 515 " pdb=" OG SER B 518 " model vdw 2.247 3.040 nonbonded pdb=" O SER A 515 " pdb=" OG SER A 518 " model vdw 2.248 3.040 nonbonded pdb=" O SER C 515 " pdb=" OG SER C 518 " model vdw 2.248 3.040 nonbonded pdb=" O SER D 515 " pdb=" OG SER D 518 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.270 3.040 ... (remaining 161694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 62 through 747) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.000 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.005 0.072 21000 Z= 0.282 Angle : 1.204 10.749 28392 Z= 0.720 Chirality : 0.054 0.299 3236 Planarity : 0.006 0.076 3532 Dihedral : 12.534 81.048 7708 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.52 % Favored : 87.60 % Rotamer: Outliers : 2.14 % Allowed : 7.70 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.51 (0.11), residues: 2500 helix: -3.70 (0.07), residues: 1420 sheet: -1.80 (0.56), residues: 80 loop : -3.56 (0.16), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 363 TYR 0.022 0.002 TYR B 390 PHE 0.030 0.002 PHE C 506 TRP 0.012 0.002 TRP C 433 HIS 0.008 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.28 (20996) covalent geometry : angle 1.20318 / 0.72 (28384) SS BOND : bond 0.01984 / 1.18 ( 4) SS BOND : angle 3.36374 / 2.02 ( 8) hydrogen bonds : bond 0.30208 / 19.86 ( 864) hydrogen bonds : angle 9.08160 / 6.32 ( 2532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 PHE cc_start: 0.7591 (t80) cc_final: 0.6973 (t80) REVERT: A 488 MET cc_start: 0.9326 (mmp) cc_final: 0.8824 (mmt) REVERT: A 495 MET cc_start: 0.9662 (mmp) cc_final: 0.9354 (mmm) REVERT: A 532 LEU cc_start: 0.9585 (mt) cc_final: 0.9157 (tp) REVERT: A 562 MET cc_start: 0.9587 (tpt) cc_final: 0.9136 (tpp) REVERT: B 159 MET cc_start: 0.9201 (tpt) cc_final: 0.8772 (mmt) REVERT: B 431 MET cc_start: 0.9222 (ttm) cc_final: 0.9020 (ttm) REVERT: B 488 MET cc_start: 0.9297 (mmp) cc_final: 0.8802 (mmt) REVERT: B 495 MET cc_start: 0.9571 (mmp) cc_final: 0.9286 (mmm) REVERT: B 532 LEU cc_start: 0.9626 (mt) cc_final: 0.9181 (tp) REVERT: B 562 MET cc_start: 0.9555 (tpt) cc_final: 0.8959 (tpp) REVERT: B 690 ARG cc_start: 0.9365 (mmt180) cc_final: 0.9106 (mtp-110) REVERT: C 159 MET cc_start: 0.9243 (tpt) cc_final: 0.8823 (mmt) REVERT: C 189 ILE cc_start: 0.9717 (mt) cc_final: 0.9482 (tp) REVERT: C 431 MET cc_start: 0.9242 (ttm) cc_final: 0.9037 (ttm) REVERT: C 488 MET cc_start: 0.9267 (mmp) cc_final: 0.8815 (mmt) REVERT: C 492 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9166 (pt) REVERT: C 495 MET cc_start: 0.9640 (mmp) cc_final: 0.9092 (mpp) REVERT: C 532 LEU cc_start: 0.9613 (mt) cc_final: 0.9136 (tp) REVERT: C 562 MET cc_start: 0.9557 (tpt) cc_final: 0.8877 (tpp) REVERT: C 690 ARG cc_start: 0.9370 (mmt180) cc_final: 0.9092 (mtp-110) REVERT: D 159 MET cc_start: 0.9277 (tpt) cc_final: 0.9011 (tpp) REVERT: D 173 MET cc_start: 0.8979 (ttm) cc_final: 0.8741 (ttm) REVERT: D 431 MET cc_start: 0.9217 (ttm) cc_final: 0.9011 (ttm) REVERT: D 488 MET cc_start: 0.9366 (mmp) cc_final: 0.8928 (mmt) REVERT: D 492 ILE cc_start: 0.9588 (OUTLIER) cc_final: 0.9175 (pt) REVERT: D 495 MET cc_start: 0.9655 (mmp) cc_final: 0.9147 (mpp) REVERT: D 532 LEU cc_start: 0.9532 (mt) cc_final: 0.9081 (tp) REVERT: D 664 LEU cc_start: 0.9627 (mm) cc_final: 0.9342 (tp) outliers start: 48 outliers final: 5 residues processed: 245 average time/residue: 0.1312 time to fit residues: 50.1342 Evaluate side-chains 134 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 242 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN A 646 GLN A 671 ASN B 150 HIS B 242 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN B 646 GLN B 671 ASN C 150 HIS C 242 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN C 646 GLN C 671 ASN D 150 HIS D 242 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN D 646 GLN D 671 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033019 restraints weight = 170558.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.033940 restraints weight = 102895.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034587 restraints weight = 72847.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035046 restraints weight = 57414.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.035364 restraints weight = 48434.973| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21000 Z= 0.179 Angle : 0.696 6.767 28392 Z= 0.367 Chirality : 0.042 0.195 3236 Planarity : 0.005 0.044 3532 Dihedral : 5.847 34.998 2740 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.24 % Favored : 87.52 % Rotamer: Outliers : 0.18 % Allowed : 3.65 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.07 (0.14), residues: 2500 helix: -1.26 (0.11), residues: 1528 sheet: -1.85 (0.75), residues: 40 loop : -3.32 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 375 TYR 0.019 0.002 TYR A 390 PHE 0.018 0.002 PHE C 506 TRP 0.011 0.002 TRP B 559 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (20996) covalent geometry : angle 0.69632 / 0.37 (28384) SS BOND : bond 0.00124 / 0.07 ( 4) SS BOND : angle 0.33164 / 0.17 ( 8) hydrogen bonds : bond 0.04333 / 2.81 ( 864) hydrogen bonds : angle 4.62697 / 3.20 ( 2532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8990 (ttm) cc_final: 0.8776 (ttm) REVERT: A 351 MET cc_start: 0.9406 (mmp) cc_final: 0.9145 (tpp) REVERT: A 431 MET cc_start: 0.8941 (ttt) cc_final: 0.8665 (ttt) REVERT: A 488 MET cc_start: 0.9216 (mmp) cc_final: 0.8815 (mmt) REVERT: A 495 MET cc_start: 0.9717 (mmp) cc_final: 0.9339 (mmm) REVERT: A 578 MET cc_start: 0.9464 (mtm) cc_final: 0.9049 (ptm) REVERT: A 677 MET cc_start: 0.9337 (mtm) cc_final: 0.8911 (mpp) REVERT: B 159 MET cc_start: 0.9397 (tpt) cc_final: 0.9109 (mmt) REVERT: B 173 MET cc_start: 0.8816 (ttm) cc_final: 0.8298 (ppp) REVERT: B 357 LEU cc_start: 0.9670 (tt) cc_final: 0.9449 (mt) REVERT: B 419 MET cc_start: 0.9357 (mtt) cc_final: 0.9101 (mmt) REVERT: B 431 MET cc_start: 0.8995 (ttm) cc_final: 0.8747 (ttm) REVERT: B 488 MET cc_start: 0.9160 (mmp) cc_final: 0.8772 (mmt) REVERT: B 495 MET cc_start: 0.9694 (mmp) cc_final: 0.9321 (mmm) REVERT: B 677 MET cc_start: 0.9448 (mtm) cc_final: 0.8926 (mtm) REVERT: C 159 MET cc_start: 0.9410 (tpt) cc_final: 0.9120 (mmt) REVERT: C 173 MET cc_start: 0.8943 (ttm) cc_final: 0.8431 (ppp) REVERT: C 351 MET cc_start: 0.9111 (tpp) cc_final: 0.8618 (tpp) REVERT: C 357 LEU cc_start: 0.9652 (tt) cc_final: 0.9433 (mt) REVERT: C 419 MET cc_start: 0.9345 (mtt) cc_final: 0.9025 (mmt) REVERT: C 431 MET cc_start: 0.9057 (ttm) cc_final: 0.8778 (ttm) REVERT: C 488 MET cc_start: 0.9242 (mmp) cc_final: 0.8835 (mmt) REVERT: C 495 MET cc_start: 0.9691 (mmp) cc_final: 0.9330 (mmm) REVERT: C 677 MET cc_start: 0.9474 (mtm) cc_final: 0.8956 (mtm) REVERT: D 72 ILE cc_start: 0.4718 (tp) cc_final: 0.4508 (tp) REVERT: D 159 MET cc_start: 0.9453 (tpt) cc_final: 0.9108 (mmt) REVERT: D 173 MET cc_start: 0.8948 (ttm) cc_final: 0.8666 (ttm) REVERT: D 351 MET cc_start: 0.8832 (ttm) cc_final: 0.8574 (ttp) REVERT: D 357 LEU cc_start: 0.9618 (tt) cc_final: 0.9396 (mt) REVERT: D 419 MET cc_start: 0.9313 (mtt) cc_final: 0.9014 (mmt) REVERT: D 431 MET cc_start: 0.9044 (ttm) cc_final: 0.8753 (ttm) REVERT: D 488 MET cc_start: 0.9288 (mmp) cc_final: 0.8864 (mmt) REVERT: D 492 ILE cc_start: 0.9651 (OUTLIER) cc_final: 0.9271 (pt) REVERT: D 495 MET cc_start: 0.9689 (mmp) cc_final: 0.9337 (mtp) REVERT: D 562 MET cc_start: 0.9555 (tpp) cc_final: 0.9259 (tpp) outliers start: 4 outliers final: 1 residues processed: 152 average time/residue: 0.1382 time to fit residues: 33.6719 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 224 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 647 ASN B 150 HIS B 452 ASN B 647 ASN C 150 HIS ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 647 ASN D 150 HIS D 647 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.032789 restraints weight = 173310.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.033718 restraints weight = 104559.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034372 restraints weight = 74740.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034814 restraints weight = 59506.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035091 restraints weight = 50839.303| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21000 Z= 0.158 Angle : 0.632 6.095 28392 Z= 0.331 Chirality : 0.040 0.180 3236 Planarity : 0.004 0.041 3532 Dihedral : 5.299 30.950 2740 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.16 % Favored : 87.68 % Rotamer: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.96 (0.16), residues: 2500 helix: -0.18 (0.12), residues: 1520 sheet: None (None), residues: 0 loop : -3.17 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 698 TYR 0.016 0.002 TYR C 260 PHE 0.013 0.001 PHE A 261 TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (20996) covalent geometry : angle 0.63157 / 0.33 (28384) SS BOND : bond 0.00196 / 0.12 ( 4) SS BOND : angle 0.79605 / 0.43 ( 8) hydrogen bonds : bond 0.03638 / 2.36 ( 864) hydrogen bonds : angle 4.08943 / 2.81 ( 2532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8960 (ttm) cc_final: 0.8741 (ttm) REVERT: A 351 MET cc_start: 0.9402 (mmp) cc_final: 0.9167 (mpp) REVERT: A 357 LEU cc_start: 0.9577 (tt) cc_final: 0.9371 (mt) REVERT: A 431 MET cc_start: 0.8881 (ttt) cc_final: 0.8548 (ttt) REVERT: A 488 MET cc_start: 0.9181 (mmp) cc_final: 0.8760 (mmt) REVERT: A 495 MET cc_start: 0.9714 (mmp) cc_final: 0.9384 (mtp) REVERT: A 562 MET cc_start: 0.9505 (tpp) cc_final: 0.9207 (tpp) REVERT: A 578 MET cc_start: 0.9335 (mtm) cc_final: 0.9048 (ptm) REVERT: A 677 MET cc_start: 0.9411 (mtm) cc_final: 0.9078 (mtm) REVERT: B 159 MET cc_start: 0.9451 (tpt) cc_final: 0.9160 (mmt) REVERT: B 173 MET cc_start: 0.8870 (ttm) cc_final: 0.8351 (ppp) REVERT: B 357 LEU cc_start: 0.9624 (tt) cc_final: 0.9374 (mt) REVERT: B 431 MET cc_start: 0.8984 (ttm) cc_final: 0.8768 (ttp) REVERT: B 488 MET cc_start: 0.9130 (mmp) cc_final: 0.8728 (mmt) REVERT: B 495 MET cc_start: 0.9704 (mmp) cc_final: 0.9370 (mtp) REVERT: C 159 MET cc_start: 0.9447 (tpt) cc_final: 0.9151 (mmt) REVERT: C 173 MET cc_start: 0.8932 (ttm) cc_final: 0.8417 (ppp) REVERT: C 357 LEU cc_start: 0.9604 (tt) cc_final: 0.9372 (mt) REVERT: C 431 MET cc_start: 0.8955 (ttm) cc_final: 0.8731 (ttp) REVERT: C 495 MET cc_start: 0.9682 (mmp) cc_final: 0.9375 (mtp) REVERT: C 572 MET cc_start: 0.9216 (tpp) cc_final: 0.8962 (tpt) REVERT: D 159 MET cc_start: 0.9476 (tpt) cc_final: 0.9123 (mmt) REVERT: D 173 MET cc_start: 0.8943 (ttm) cc_final: 0.8673 (ttm) REVERT: D 351 MET cc_start: 0.8768 (ttm) cc_final: 0.8479 (ttp) REVERT: D 357 LEU cc_start: 0.9609 (tt) cc_final: 0.9372 (mt) REVERT: D 431 MET cc_start: 0.8949 (ttm) cc_final: 0.8691 (ttm) REVERT: D 495 MET cc_start: 0.9675 (mmp) cc_final: 0.9405 (mtp) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.1217 time to fit residues: 27.9740 Evaluate side-chains 111 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 30.0000 chunk 245 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN C 346 GLN D 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032871 restraints weight = 175158.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033805 restraints weight = 104806.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034452 restraints weight = 74757.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034899 restraints weight = 59586.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.035213 restraints weight = 50881.397| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21000 Z= 0.144 Angle : 0.608 6.001 28392 Z= 0.315 Chirality : 0.041 0.190 3236 Planarity : 0.004 0.042 3532 Dihedral : 5.066 29.640 2740 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.80 % Favored : 87.00 % Rotamer: Outliers : 0.13 % Allowed : 3.60 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2500 helix: 0.28 (0.13), residues: 1572 sheet: 0.23 (0.69), residues: 56 loop : -3.10 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 416 TYR 0.011 0.001 TYR A 260 PHE 0.015 0.001 PHE B 261 TRP 0.011 0.001 TRP A 521 HIS 0.003 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (20996) covalent geometry : angle 0.60770 / 0.32 (28384) SS BOND : bond 0.00091 / 0.05 ( 4) SS BOND : angle 0.61811 / 0.33 ( 8) hydrogen bonds : bond 0.03276 / 2.13 ( 864) hydrogen bonds : angle 3.93098 / 2.70 ( 2532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8948 (ttm) cc_final: 0.8738 (ttm) REVERT: A 351 MET cc_start: 0.9417 (mmp) cc_final: 0.9193 (mpp) REVERT: A 357 LEU cc_start: 0.9638 (tt) cc_final: 0.9406 (mt) REVERT: A 488 MET cc_start: 0.9169 (mmp) cc_final: 0.8728 (mmt) REVERT: A 495 MET cc_start: 0.9670 (mmp) cc_final: 0.9425 (mtm) REVERT: A 572 MET cc_start: 0.9155 (tpp) cc_final: 0.8669 (tpt) REVERT: A 578 MET cc_start: 0.9417 (mtm) cc_final: 0.9102 (ptm) REVERT: A 717 MET cc_start: 0.7887 (mmp) cc_final: 0.7537 (mmt) REVERT: B 159 MET cc_start: 0.9486 (tpt) cc_final: 0.8947 (mtp) REVERT: B 173 MET cc_start: 0.8878 (ttm) cc_final: 0.8387 (ppp) REVERT: B 346 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.9144 (pm20) REVERT: B 431 MET cc_start: 0.9021 (ttm) cc_final: 0.8688 (ttm) REVERT: B 488 MET cc_start: 0.9112 (mmp) cc_final: 0.8656 (mmt) REVERT: B 495 MET cc_start: 0.9673 (mmp) cc_final: 0.9429 (mtp) REVERT: B 562 MET cc_start: 0.9464 (tpp) cc_final: 0.9187 (tpp) REVERT: C 159 MET cc_start: 0.9485 (tpt) cc_final: 0.8933 (mtp) REVERT: C 173 MET cc_start: 0.8933 (ttm) cc_final: 0.8475 (ppp) REVERT: C 346 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.9141 (pm20) REVERT: C 351 MET cc_start: 0.9192 (tpp) cc_final: 0.8678 (tpp) REVERT: C 357 LEU cc_start: 0.9629 (tt) cc_final: 0.9408 (mt) REVERT: C 431 MET cc_start: 0.9006 (ttm) cc_final: 0.8677 (ttm) REVERT: C 495 MET cc_start: 0.9659 (mmp) cc_final: 0.9422 (mtp) REVERT: C 562 MET cc_start: 0.9476 (tpp) cc_final: 0.9178 (tpp) REVERT: D 159 MET cc_start: 0.9527 (tpt) cc_final: 0.8996 (mtp) REVERT: D 173 MET cc_start: 0.8929 (ttm) cc_final: 0.8686 (ttm) REVERT: D 346 GLN cc_start: 0.9556 (OUTLIER) cc_final: 0.9080 (pm20) REVERT: D 351 MET cc_start: 0.8823 (ttm) cc_final: 0.8483 (ttm) REVERT: D 357 LEU cc_start: 0.9617 (tt) cc_final: 0.9362 (mt) REVERT: D 431 MET cc_start: 0.8994 (ttm) cc_final: 0.8697 (ttm) REVERT: D 495 MET cc_start: 0.9646 (mmp) cc_final: 0.9431 (mtp) REVERT: D 562 MET cc_start: 0.9557 (tpp) cc_final: 0.9294 (tpp) REVERT: D 572 MET cc_start: 0.9298 (tpp) cc_final: 0.9007 (tpt) REVERT: D 574 MET cc_start: 0.9232 (pmm) cc_final: 0.8850 (pmm) REVERT: D 677 MET cc_start: 0.9446 (mtm) cc_final: 0.8971 (mpp) outliers start: 3 outliers final: 0 residues processed: 134 average time/residue: 0.1135 time to fit residues: 25.8838 Evaluate side-chains 117 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 34 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 67 optimal weight: 50.0000 chunk 225 optimal weight: 40.0000 chunk 175 optimal weight: 0.0470 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.041247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.032751 restraints weight = 170315.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033639 restraints weight = 104394.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034271 restraints weight = 74854.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.034701 restraints weight = 59430.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.035016 restraints weight = 50646.227| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21000 Z= 0.157 Angle : 0.610 5.984 28392 Z= 0.315 Chirality : 0.041 0.189 3236 Planarity : 0.004 0.051 3532 Dihedral : 4.923 28.831 2740 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.24 % Favored : 87.56 % Rotamer: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2500 helix: 0.64 (0.13), residues: 1548 sheet: 0.28 (0.68), residues: 56 loop : -2.95 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 416 TYR 0.019 0.001 TYR C 661 PHE 0.014 0.001 PHE C 249 TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (20996) covalent geometry : angle 0.61014 / 0.32 (28384) SS BOND : bond 0.00096 / 0.06 ( 4) SS BOND : angle 0.43041 / 0.23 ( 8) hydrogen bonds : bond 0.03238 / 2.09 ( 864) hydrogen bonds : angle 3.85515 / 2.65 ( 2532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLN cc_start: 0.9540 (OUTLIER) cc_final: 0.9092 (pm20) REVERT: A 431 MET cc_start: 0.8853 (ttt) cc_final: 0.8443 (ttt) REVERT: B 173 MET cc_start: 0.8883 (ttm) cc_final: 0.8447 (ppp) REVERT: B 431 MET cc_start: 0.9053 (ttm) cc_final: 0.8720 (ttm) REVERT: B 488 MET cc_start: 0.9087 (mmp) cc_final: 0.8627 (mmt) REVERT: B 562 MET cc_start: 0.9491 (tpp) cc_final: 0.9223 (tpp) REVERT: B 677 MET cc_start: 0.9512 (mtm) cc_final: 0.9035 (mtm) REVERT: C 159 MET cc_start: 0.9507 (tpt) cc_final: 0.9191 (ttt) REVERT: C 173 MET cc_start: 0.8960 (ttm) cc_final: 0.8453 (ppp) REVERT: C 431 MET cc_start: 0.9026 (ttm) cc_final: 0.8697 (ttm) REVERT: C 562 MET cc_start: 0.9485 (tpp) cc_final: 0.9183 (tpp) REVERT: D 173 MET cc_start: 0.8955 (ttm) cc_final: 0.8731 (ttm) REVERT: D 351 MET cc_start: 0.8873 (ttm) cc_final: 0.8507 (ttm) REVERT: D 431 MET cc_start: 0.9012 (ttm) cc_final: 0.8712 (ttm) REVERT: D 562 MET cc_start: 0.9530 (tpp) cc_final: 0.9234 (tpp) REVERT: D 574 MET cc_start: 0.9332 (pmm) cc_final: 0.9128 (pmm) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1155 time to fit residues: 25.0896 Evaluate side-chains 113 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 175 optimal weight: 0.4980 chunk 176 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 735 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.042116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.033596 restraints weight = 167552.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034501 restraints weight = 103232.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.035140 restraints weight = 74108.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035588 restraints weight = 58797.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035884 restraints weight = 49951.526| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21000 Z= 0.114 Angle : 0.578 6.307 28392 Z= 0.297 Chirality : 0.040 0.198 3236 Planarity : 0.004 0.059 3532 Dihedral : 4.802 27.874 2740 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.72 % Favored : 88.04 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2500 helix: 0.79 (0.13), residues: 1552 sheet: 0.65 (0.68), residues: 56 loop : -2.94 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 696 TYR 0.017 0.001 TYR D 213 PHE 0.015 0.001 PHE D 249 TRP 0.010 0.001 TRP C 521 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (20996) covalent geometry : angle 0.57778 / 0.30 (28384) SS BOND : bond 0.00148 / 0.09 ( 4) SS BOND : angle 0.93863 / 0.50 ( 8) hydrogen bonds : bond 0.03005 / 1.95 ( 864) hydrogen bonds : angle 3.73835 / 2.56 ( 2532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8988 (ttm) cc_final: 0.8767 (ttm) REVERT: A 351 MET cc_start: 0.9379 (mmp) cc_final: 0.9152 (tpp) REVERT: A 357 LEU cc_start: 0.9622 (tt) cc_final: 0.9357 (mt) REVERT: A 431 MET cc_start: 0.8906 (ttt) cc_final: 0.8604 (ttt) REVERT: A 488 MET cc_start: 0.9169 (mmp) cc_final: 0.8767 (mmt) REVERT: A 495 MET cc_start: 0.9566 (mtp) cc_final: 0.9326 (mtp) REVERT: B 159 MET cc_start: 0.9534 (tpt) cc_final: 0.8951 (mtp) REVERT: B 173 MET cc_start: 0.8881 (ttm) cc_final: 0.8444 (ppp) REVERT: B 315 ASP cc_start: 0.8788 (p0) cc_final: 0.8585 (p0) REVERT: B 419 MET cc_start: 0.9187 (mmt) cc_final: 0.8697 (mmt) REVERT: B 431 MET cc_start: 0.9049 (ttm) cc_final: 0.8722 (ttm) REVERT: B 488 MET cc_start: 0.9076 (mmp) cc_final: 0.8624 (mmt) REVERT: B 495 MET cc_start: 0.9548 (mtp) cc_final: 0.9295 (mtp) REVERT: B 562 MET cc_start: 0.9459 (tpp) cc_final: 0.9215 (tpp) REVERT: C 159 MET cc_start: 0.9524 (tpt) cc_final: 0.8950 (mtp) REVERT: C 173 MET cc_start: 0.8946 (ttm) cc_final: 0.8512 (ppp) REVERT: C 351 MET cc_start: 0.9172 (tpp) cc_final: 0.8701 (tpp) REVERT: C 357 LEU cc_start: 0.9625 (tt) cc_final: 0.9388 (mt) REVERT: C 431 MET cc_start: 0.9053 (ttm) cc_final: 0.8702 (ttm) REVERT: C 495 MET cc_start: 0.9546 (mtp) cc_final: 0.9285 (mtp) REVERT: C 562 MET cc_start: 0.9457 (tpp) cc_final: 0.9179 (tpp) REVERT: C 578 MET cc_start: 0.9510 (ptt) cc_final: 0.9304 (ptt) REVERT: C 677 MET cc_start: 0.9509 (mtm) cc_final: 0.9024 (mtm) REVERT: D 159 MET cc_start: 0.9326 (tpp) cc_final: 0.9069 (mtt) REVERT: D 351 MET cc_start: 0.8614 (ttm) cc_final: 0.8331 (ttt) REVERT: D 357 LEU cc_start: 0.9618 (tt) cc_final: 0.9360 (mt) REVERT: D 431 MET cc_start: 0.9050 (ttm) cc_final: 0.8728 (ttm) REVERT: D 495 MET cc_start: 0.9546 (mtp) cc_final: 0.9301 (mtp) REVERT: D 562 MET cc_start: 0.9499 (tpp) cc_final: 0.9208 (tpp) REVERT: D 574 MET cc_start: 0.9447 (pmm) cc_final: 0.9191 (pmm) REVERT: D 578 MET cc_start: 0.9598 (ptt) cc_final: 0.9273 (ptt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1289 time to fit residues: 29.8653 Evaluate side-chains 118 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 223 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 227 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 211 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN C 227 GLN D 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033875 restraints weight = 171471.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034805 restraints weight = 105616.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.035452 restraints weight = 76175.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035839 restraints weight = 60706.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036175 restraints weight = 52690.938| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21000 Z= 0.109 Angle : 0.585 7.147 28392 Z= 0.297 Chirality : 0.040 0.195 3236 Planarity : 0.004 0.064 3532 Dihedral : 4.693 30.430 2740 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.68 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2500 helix: 0.90 (0.13), residues: 1544 sheet: 0.79 (0.70), residues: 56 loop : -2.74 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 696 TYR 0.009 0.001 TYR D 208 PHE 0.015 0.001 PHE C 261 TRP 0.010 0.001 TRP B 521 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (20996) covalent geometry : angle 0.58337 / 0.30 (28384) SS BOND : bond 0.00594 / 0.35 ( 4) SS BOND : angle 2.74570 / 1.56 ( 8) hydrogen bonds : bond 0.02958 / 1.92 ( 864) hydrogen bonds : angle 3.76502 / 2.59 ( 2532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8957 (ttm) cc_final: 0.8734 (ttm) REVERT: A 351 MET cc_start: 0.9375 (mmp) cc_final: 0.9136 (tpp) REVERT: A 357 LEU cc_start: 0.9614 (tt) cc_final: 0.9354 (mt) REVERT: A 431 MET cc_start: 0.8864 (ttt) cc_final: 0.8571 (ttt) REVERT: A 488 MET cc_start: 0.9153 (mmp) cc_final: 0.8749 (mmt) REVERT: A 495 MET cc_start: 0.9552 (mtp) cc_final: 0.9315 (mtp) REVERT: B 159 MET cc_start: 0.9512 (tpt) cc_final: 0.8945 (mtp) REVERT: B 173 MET cc_start: 0.8882 (ttm) cc_final: 0.8491 (ppp) REVERT: B 315 ASP cc_start: 0.8748 (p0) cc_final: 0.8535 (p0) REVERT: B 351 MET cc_start: 0.9280 (tpp) cc_final: 0.8903 (tpp) REVERT: B 488 MET cc_start: 0.9070 (mmp) cc_final: 0.8617 (mmt) REVERT: B 495 MET cc_start: 0.9560 (mtp) cc_final: 0.9311 (mtp) REVERT: B 562 MET cc_start: 0.9418 (tpp) cc_final: 0.9212 (tpp) REVERT: B 677 MET cc_start: 0.9462 (mtm) cc_final: 0.9005 (mtm) REVERT: C 159 MET cc_start: 0.9497 (tpt) cc_final: 0.8943 (mtp) REVERT: C 173 MET cc_start: 0.8952 (ttm) cc_final: 0.8546 (ppp) REVERT: C 351 MET cc_start: 0.9188 (tpp) cc_final: 0.8703 (tpp) REVERT: C 357 LEU cc_start: 0.9577 (tt) cc_final: 0.9346 (mt) REVERT: C 495 MET cc_start: 0.9528 (mtp) cc_final: 0.9327 (mtp) REVERT: C 562 MET cc_start: 0.9424 (tpp) cc_final: 0.9188 (tpp) REVERT: C 677 MET cc_start: 0.9487 (mtm) cc_final: 0.9001 (mtm) REVERT: D 159 MET cc_start: 0.9324 (tpp) cc_final: 0.9063 (mtt) REVERT: D 351 MET cc_start: 0.8602 (ttm) cc_final: 0.8350 (ttt) REVERT: D 357 LEU cc_start: 0.9625 (tt) cc_final: 0.9371 (mt) REVERT: D 495 MET cc_start: 0.9550 (mtp) cc_final: 0.9330 (mtp) REVERT: D 562 MET cc_start: 0.9469 (tpp) cc_final: 0.9195 (tpp) REVERT: D 574 MET cc_start: 0.9471 (pmm) cc_final: 0.9231 (pmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1147 time to fit residues: 27.6652 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** 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 = 0.3154 r_free = 0.3154 target = 0.042276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033752 restraints weight = 169402.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034657 restraints weight = 105080.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035296 restraints weight = 75692.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.035742 restraints weight = 60145.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036060 restraints weight = 51097.959| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21000 Z= 0.124 Angle : 0.596 7.287 28392 Z= 0.302 Chirality : 0.040 0.190 3236 Planarity : 0.004 0.051 3532 Dihedral : 4.682 29.818 2740 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.96 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2500 helix: 0.91 (0.13), residues: 1544 sheet: 0.67 (0.69), residues: 56 loop : -2.73 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.009 0.001 TYR C 390 PHE 0.017 0.001 PHE A 261 TRP 0.010 0.001 TRP B 521 HIS 0.003 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20996) covalent geometry : angle 0.59420 / 0.30 (28384) SS BOND : bond 0.00421 / 0.25 ( 4) SS BOND : angle 2.50246 / 1.44 ( 8) hydrogen bonds : bond 0.03023 / 1.96 ( 864) hydrogen bonds : angle 3.85324 / 2.65 ( 2532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.9373 (mmp) cc_final: 0.9079 (mmm) REVERT: A 357 LEU cc_start: 0.9608 (tt) cc_final: 0.9342 (mt) REVERT: A 431 MET cc_start: 0.8875 (ttt) cc_final: 0.8660 (ttt) REVERT: A 488 MET cc_start: 0.9121 (mmp) cc_final: 0.8740 (mmt) REVERT: A 495 MET cc_start: 0.9538 (mtp) cc_final: 0.9329 (mtp) REVERT: B 159 MET cc_start: 0.9523 (tpt) cc_final: 0.8961 (mtp) REVERT: B 315 ASP cc_start: 0.8748 (p0) cc_final: 0.8543 (p0) REVERT: B 488 MET cc_start: 0.9077 (mmp) cc_final: 0.8630 (mmt) REVERT: B 495 MET cc_start: 0.9563 (mtp) cc_final: 0.9315 (mtp) REVERT: B 562 MET cc_start: 0.9413 (tpp) cc_final: 0.9207 (tpp) REVERT: B 677 MET cc_start: 0.9458 (mtm) cc_final: 0.8982 (mtm) REVERT: B 717 MET cc_start: 0.7321 (tpp) cc_final: 0.6890 (tpp) REVERT: C 159 MET cc_start: 0.9511 (tpt) cc_final: 0.8953 (mtp) REVERT: C 173 MET cc_start: 0.8930 (ttm) cc_final: 0.8593 (ppp) REVERT: C 357 LEU cc_start: 0.9590 (tt) cc_final: 0.9370 (mt) REVERT: C 562 MET cc_start: 0.9432 (tpp) cc_final: 0.9202 (tpp) REVERT: C 677 MET cc_start: 0.9490 (mtm) cc_final: 0.9008 (mtm) REVERT: C 717 MET cc_start: 0.7166 (tpp) cc_final: 0.6917 (tpp) REVERT: D 159 MET cc_start: 0.9313 (tpp) cc_final: 0.9066 (mtt) REVERT: D 351 MET cc_start: 0.8622 (ttm) cc_final: 0.8335 (ttt) REVERT: D 357 LEU cc_start: 0.9582 (tt) cc_final: 0.9337 (mt) REVERT: D 495 MET cc_start: 0.9522 (mtp) cc_final: 0.9308 (mtp) REVERT: D 562 MET cc_start: 0.9462 (tpp) cc_final: 0.9187 (tpp) REVERT: D 677 MET cc_start: 0.9412 (mtm) cc_final: 0.8986 (mpp) REVERT: D 706 MET cc_start: 0.9163 (mtm) cc_final: 0.8841 (ptp) REVERT: D 717 MET cc_start: 0.7248 (tpp) cc_final: 0.6839 (tpp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1160 time to fit residues: 26.6785 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 167 optimal weight: 5.9990 chunk 113 optimal weight: 0.0170 chunk 91 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 241 optimal weight: 0.0770 chunk 141 optimal weight: 7.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 735 ASN B 242 ASN B 735 ASN C 735 ASN D 242 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034974 restraints weight = 167112.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.035934 restraints weight = 101998.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036598 restraints weight = 73077.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037074 restraints weight = 57887.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.037416 restraints weight = 49012.422| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21000 Z= 0.100 Angle : 0.607 10.087 28392 Z= 0.298 Chirality : 0.040 0.203 3236 Planarity : 0.003 0.043 3532 Dihedral : 4.553 29.700 2740 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.68 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2500 helix: 0.84 (0.13), residues: 1568 sheet: 0.87 (0.69), residues: 56 loop : -2.72 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 567 TYR 0.016 0.001 TYR B 661 PHE 0.012 0.001 PHE D 447 TRP 0.010 0.001 TRP B 521 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (20996) covalent geometry : angle 0.60649 / 0.30 (28384) SS BOND : bond 0.00475 / 0.28 ( 4) SS BOND : angle 1.96098 / 1.12 ( 8) hydrogen bonds : bond 0.02872 / 1.85 ( 864) hydrogen bonds : angle 3.77588 / 2.60 ( 2532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.9398 (mmp) cc_final: 0.9166 (tpp) REVERT: A 357 LEU cc_start: 0.9585 (tt) cc_final: 0.9365 (mt) REVERT: A 431 MET cc_start: 0.8876 (ttt) cc_final: 0.8529 (ttt) REVERT: A 488 MET cc_start: 0.9131 (mmp) cc_final: 0.8713 (mmt) REVERT: A 495 MET cc_start: 0.9541 (mtp) cc_final: 0.9333 (mtp) REVERT: B 159 MET cc_start: 0.9526 (tpt) cc_final: 0.9102 (mtp) REVERT: B 488 MET cc_start: 0.9066 (mmp) cc_final: 0.8594 (mmt) REVERT: B 677 MET cc_start: 0.9397 (mtm) cc_final: 0.8954 (mtm) REVERT: C 159 MET cc_start: 0.9515 (tpt) cc_final: 0.9096 (mtp) REVERT: C 351 MET cc_start: 0.9126 (tpp) cc_final: 0.8684 (tpp) REVERT: C 357 LEU cc_start: 0.9583 (tt) cc_final: 0.9354 (mt) REVERT: C 562 MET cc_start: 0.9369 (tpp) cc_final: 0.9158 (tpp) REVERT: C 677 MET cc_start: 0.9414 (mtm) cc_final: 0.8966 (mtm) REVERT: D 159 MET cc_start: 0.9270 (tpp) cc_final: 0.9030 (mtt) REVERT: D 173 MET cc_start: 0.8867 (ptt) cc_final: 0.8336 (ppp) REVERT: D 351 MET cc_start: 0.8580 (ttm) cc_final: 0.8362 (ttt) REVERT: D 357 LEU cc_start: 0.9570 (tt) cc_final: 0.9346 (mt) REVERT: D 562 MET cc_start: 0.9411 (tpp) cc_final: 0.9145 (tpp) REVERT: D 578 MET cc_start: 0.9508 (ptt) cc_final: 0.9303 (ptt) REVERT: D 706 MET cc_start: 0.9039 (mtm) cc_final: 0.8815 (ptp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1160 time to fit residues: 27.8860 Evaluate side-chains 116 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 chunk 239 optimal weight: 0.0020 chunk 233 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034061 restraints weight = 170156.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035012 restraints weight = 103422.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035684 restraints weight = 73876.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036149 restraints weight = 58525.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036484 restraints weight = 49685.374| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21000 Z= 0.117 Angle : 0.615 11.517 28392 Z= 0.304 Chirality : 0.041 0.215 3236 Planarity : 0.003 0.044 3532 Dihedral : 4.491 29.647 2740 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.24 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2500 helix: 1.00 (0.13), residues: 1540 sheet: 0.66 (0.69), residues: 56 loop : -2.61 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.010 0.001 TYR B 661 PHE 0.018 0.001 PHE A 261 TRP 0.010 0.001 TRP C 559 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (20996) covalent geometry : angle 0.61409 / 0.30 (28384) SS BOND : bond 0.00348 / 0.21 ( 4) SS BOND : angle 1.92919 / 1.11 ( 8) hydrogen bonds : bond 0.02947 / 1.91 ( 864) hydrogen bonds : angle 3.79483 / 2.60 ( 2532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5000 Ramachandran restraints generated. 2500 Oldfield, 0 Emsley, 2500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 MET cc_start: 0.9423 (mmp) cc_final: 0.9152 (mmm) REVERT: A 357 LEU cc_start: 0.9597 (tt) cc_final: 0.9364 (mt) REVERT: A 488 MET cc_start: 0.9149 (mmp) cc_final: 0.8747 (mmt) REVERT: A 495 MET cc_start: 0.9545 (mtp) cc_final: 0.9339 (mtp) REVERT: A 717 MET cc_start: 0.7911 (mmp) cc_final: 0.7674 (mmt) REVERT: B 159 MET cc_start: 0.9524 (tpt) cc_final: 0.9114 (mtp) REVERT: B 351 MET cc_start: 0.9281 (tpp) cc_final: 0.8892 (tpp) REVERT: B 488 MET cc_start: 0.9065 (mmp) cc_final: 0.8623 (mmt) REVERT: B 495 MET cc_start: 0.9566 (mtp) cc_final: 0.9360 (mtp) REVERT: B 555 MET cc_start: 0.9210 (mmm) cc_final: 0.8874 (mmt) REVERT: B 562 MET cc_start: 0.9461 (tpp) cc_final: 0.9194 (tpp) REVERT: B 677 MET cc_start: 0.9401 (mtm) cc_final: 0.8907 (mtm) REVERT: C 159 MET cc_start: 0.9540 (tpt) cc_final: 0.9078 (mtp) REVERT: C 351 MET cc_start: 0.9132 (tpp) cc_final: 0.8679 (tpp) REVERT: C 357 LEU cc_start: 0.9593 (tt) cc_final: 0.9381 (mt) REVERT: C 562 MET cc_start: 0.9412 (tpp) cc_final: 0.9198 (tpp) REVERT: C 574 MET cc_start: 0.9493 (pmm) cc_final: 0.9291 (pmm) REVERT: C 677 MET cc_start: 0.9424 (mtm) cc_final: 0.8980 (mtm) REVERT: D 159 MET cc_start: 0.9319 (tpp) cc_final: 0.9119 (mtt) REVERT: D 173 MET cc_start: 0.8806 (ptt) cc_final: 0.7903 (ppp) REVERT: D 357 LEU cc_start: 0.9582 (tt) cc_final: 0.9362 (mt) REVERT: D 562 MET cc_start: 0.9448 (tpp) cc_final: 0.9189 (tpp) REVERT: D 578 MET cc_start: 0.9518 (ptt) cc_final: 0.9293 (ptt) REVERT: D 706 MET cc_start: 0.9132 (mtm) cc_final: 0.8897 (ptp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1212 time to fit residues: 27.6197 Evaluate side-chains 114 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 129 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 GLN B 695 GLN C 695 GLN D 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.041795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033244 restraints weight = 169129.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034139 restraints weight = 104772.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034780 restraints weight = 75390.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035224 restraints weight = 59904.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035543 restraints weight = 50846.924| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21000 Z= 0.154 Angle : 0.642 8.913 28392 Z= 0.321 Chirality : 0.041 0.214 3236 Planarity : 0.004 0.053 3532 Dihedral : 4.656 29.262 2740 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.12 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2500 helix: 0.97 (0.13), residues: 1540 sheet: 0.49 (0.70), residues: 56 loop : -2.68 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 696 TYR 0.016 0.001 TYR C 661 PHE 0.017 0.001 PHE C 447 TRP 0.010 0.001 TRP B 521 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (20996) covalent geometry : angle 0.64174 / 0.32 (28384) SS BOND : bond 0.00332 / 0.20 ( 4) SS BOND : angle 1.82410 / 1.04 ( 8) hydrogen bonds : bond 0.03089 / 2.00 ( 864) hydrogen bonds : angle 3.97897 / 2.73 ( 2532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.03 seconds wall clock time: 54 minutes 55.79 seconds (3295.79 seconds total)