Starting phenix.real_space_refine on Sun Jul 5 05:29:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovw_70925/07_2026/9ovw_70925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovw_70925/07_2026/9ovw_70925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ovw_70925/07_2026/9ovw_70925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovw_70925/07_2026/9ovw_70925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ovw_70925/07_2026/9ovw_70925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovw_70925/07_2026/9ovw_70925.map" } resolution = 4.91 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= 0.013 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 16004 2.51 5 N 4196 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24938 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6240 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 26, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6203 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 767} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 11.82, per 1000 atoms: 0.47 Number of scatterers: 24938 At special positions: 0 Unit cell: (143.64, 131.67, 188.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 4616 8.00 N 4196 7.00 C 16004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.05 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 28 sheets defined 44.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.793A pdb=" N GLN A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 4.207A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 170 through 181 removed outlier: 3.856A pdb=" N ARG A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 208 removed outlier: 3.683A pdb=" N ALA A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.684A pdb=" N GLU A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.569A pdb=" N ILE A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.973A pdb=" N VAL A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 419 through 429 removed outlier: 4.045A pdb=" N ALA A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 removed outlier: 3.675A pdb=" N GLU A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.914A pdb=" N CYS A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.621A pdb=" N SER A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 596 through 626 removed outlier: 3.786A pdb=" N ILE A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.087A pdb=" N ARG A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.524A pdb=" N GLY A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 710 removed outlier: 5.360A pdb=" N TYR A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 708 " --> pdb=" O MET A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 removed outlier: 3.887A pdb=" N GLU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 763 removed outlier: 3.824A pdb=" N TRP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 800 Processing helix chain 'A' and resid 800 through 811 removed outlier: 3.525A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 4.269A pdb=" N ARG A 815 " --> pdb=" O TYR A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.518A pdb=" N ARG B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.865A pdb=" N LEU B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.130A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 4.084A pdb=" N VAL B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 removed outlier: 4.068A pdb=" N PHE B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.840A pdb=" N VAL B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.244A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.630A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.712A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.950A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.509A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.921A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 576 removed outlier: 3.591A pdb=" N SER B 576 " --> pdb=" O ILE B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 576' Processing helix chain 'B' and resid 577 through 585 removed outlier: 4.004A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.964A pdb=" N ARG B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.637A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 4.271A pdb=" N LEU B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 removed outlier: 3.878A pdb=" N SER B 785 " --> pdb=" O GLU B 782 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 786 " --> pdb=" O LYS B 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 782 through 786' Processing helix chain 'B' and resid 794 through 819 removed outlier: 4.051A pdb=" N LEU B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 800 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 819 " --> pdb=" O CYS B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 54 through 68 removed outlier: 3.793A pdb=" N GLN C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 4.207A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 92 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 170 through 181 removed outlier: 3.857A pdb=" N ARG C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 208 removed outlier: 3.684A pdb=" N ALA C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU C 207 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.684A pdb=" N GLU C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 removed outlier: 3.568A pdb=" N ILE C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 298 removed outlier: 3.973A pdb=" N VAL C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 296 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 331 Processing helix chain 'C' and resid 419 through 429 removed outlier: 4.045A pdb=" N ALA C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 removed outlier: 3.675A pdb=" N GLU C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.914A pdb=" N CYS C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 534 " --> pdb=" O ILE C 530 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 541 " --> pdb=" O PHE C 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 581 removed outlier: 3.620A pdb=" N SER C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 596 through 626 removed outlier: 3.785A pdb=" N ILE C 607 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C 608 " --> pdb=" O PHE C 604 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 609 " --> pdb=" O THR C 605 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 removed outlier: 4.087A pdb=" N ARG C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 681 through 692 removed outlier: 3.523A pdb=" N GLY C 685 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 692 " --> pdb=" O ARG C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 710 removed outlier: 5.359A pdb=" N TYR C 707 " --> pdb=" O THR C 703 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 removed outlier: 3.887A pdb=" N GLU C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 763 removed outlier: 3.823A pdb=" N TRP C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 800 Processing helix chain 'C' and resid 800 through 811 removed outlier: 3.525A pdb=" N ILE C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 815 removed outlier: 4.269A pdb=" N ARG C 815 " --> pdb=" O TYR C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 812 through 815' Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.518A pdb=" N ARG D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.865A pdb=" N LEU D 92 " --> pdb=" O PHE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.129A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 4.084A pdb=" N VAL D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 removed outlier: 4.068A pdb=" N PHE D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.841A pdb=" N VAL D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 removed outlier: 4.244A pdb=" N PHE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.630A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.712A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.950A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.510A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.921A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 576 removed outlier: 3.591A pdb=" N SER D 576 " --> pdb=" O ILE D 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 573 through 576' Processing helix chain 'D' and resid 577 through 585 removed outlier: 4.004A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.965A pdb=" N ARG D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 754 removed outlier: 3.637A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 4.270A pdb=" N LEU D 762 " --> pdb=" O VAL D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 786 removed outlier: 3.879A pdb=" N SER D 785 " --> pdb=" O GLU D 782 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 786 " --> pdb=" O LYS D 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 782 through 786' Processing helix chain 'D' and resid 794 through 819 removed outlier: 4.052A pdb=" N LEU D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 800 " --> pdb=" O PHE D 796 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 5.554A pdb=" N GLY A 16 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 96 " --> pdb=" O LEU A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.569A pdb=" N TYR A 137 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL A 189 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 134 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP A 191 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 136 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 221 removed outlier: 3.984A pdb=" N PHE A 241 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN A 220 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 476 through 477 removed outlier: 4.074A pdb=" N GLY A 727 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 728 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.937A pdb=" N ASP A 486 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.632A pdb=" N ALA A 697 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA9, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.104A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 132 through 134 removed outlier: 7.322A pdb=" N PHE B 133 " --> pdb=" O THR B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.511A pdb=" N GLN B 246 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 359 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 338 removed outlier: 3.551A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 502 through 503 removed outlier: 4.004A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 646 through 648 removed outlier: 7.430A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 15 through 18 removed outlier: 5.554A pdb=" N GLY C 16 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 96 " --> pdb=" O LEU C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.568A pdb=" N TYR C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL C 189 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 134 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP C 191 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE C 136 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 216 through 221 removed outlier: 3.984A pdb=" N PHE C 241 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 220 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 336 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 477 removed outlier: 4.074A pdb=" N GLY C 727 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 728 " --> pdb=" O MET C 492 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 486 through 487 removed outlier: 3.937A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.632A pdb=" N ALA C 697 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 500 through 501 Processing sheet with id=AC5, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.104A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 132 through 134 removed outlier: 7.321A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.511A pdb=" N GLN D 246 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 359 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 337 through 338 removed outlier: 3.551A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 502 through 503 removed outlier: 4.003A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 646 through 648 removed outlier: 7.429A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 786 hydrogen bonds defined for protein. 2310 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: 4.15 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7912 1.34 - 1.46: 5902 1.46 - 1.58: 11462 1.58 - 1.70: 4 1.70 - 1.82: 200 Bond restraints: 25480 Sorted by residual: bond pdb=" C05 QUS C1301 " pdb=" O19 QUS C1301 " ideal model delta sigma weight residual 1.203 1.450 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C05 QUS A1301 " pdb=" O19 QUS A1301 " ideal model delta sigma weight residual 1.203 1.450 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C04 QUS B1301 " pdb=" O18 QUS B1301 " ideal model delta sigma weight residual 1.212 1.414 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 25475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 33612 2.62 - 5.23: 701 5.23 - 7.85: 121 7.85 - 10.47: 6 10.47 - 13.09: 4 Bond angle restraints: 34444 Sorted by residual: angle pdb=" N ALA D 786 " pdb=" CA ALA D 786 " pdb=" CB ALA D 786 " ideal model delta sigma weight residual 114.17 108.91 5.26 1.14e+00 7.69e-01 2.13e+01 angle pdb=" N ALA B 786 " pdb=" CA ALA B 786 " pdb=" CB ALA B 786 " ideal model delta sigma weight residual 114.17 108.93 5.24 1.14e+00 7.69e-01 2.11e+01 angle pdb=" C03 QUS C1301 " pdb=" N14 QUS C1301 " pdb=" O20 QUS C1301 " ideal model delta sigma weight residual 112.77 125.86 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C03 QUS A1301 " pdb=" N14 QUS A1301 " pdb=" O20 QUS A1301 " ideal model delta sigma weight residual 112.77 125.58 -12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C LYS C 183 " pdb=" N LYS C 184 " pdb=" CA LYS C 184 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 ... (remaining 34439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 14210 17.26 - 34.53: 790 34.53 - 51.79: 116 51.79 - 69.05: 14 69.05 - 86.31: 20 Dihedral angle restraints: 15150 sinusoidal: 6056 harmonic: 9094 Sorted by residual: dihedral pdb=" CA ASN A 407 " pdb=" C ASN A 407 " pdb=" N ALA A 408 " pdb=" CA ALA A 408 " ideal model delta harmonic sigma weight residual -180.00 -122.01 -57.99 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA ASN C 407 " pdb=" C ASN C 407 " pdb=" N ALA C 408 " pdb=" CA ALA C 408 " ideal model delta harmonic sigma weight residual -180.00 -122.07 -57.93 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLN D 112 " pdb=" C GLN D 112 " pdb=" N MET D 113 " pdb=" CA MET D 113 " ideal model delta harmonic sigma weight residual 180.00 125.61 54.39 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 15147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2641 0.049 - 0.099: 906 0.099 - 0.148: 214 0.148 - 0.198: 21 0.198 - 0.247: 8 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CB ILE C 392 " pdb=" CA ILE C 392 " pdb=" CG1 ILE C 392 " pdb=" CG2 ILE C 392 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A 392 " pdb=" CA ILE A 392 " pdb=" CG1 ILE A 392 " pdb=" CG2 ILE A 392 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C 400 " pdb=" N PRO C 400 " pdb=" C PRO C 400 " pdb=" CB PRO C 400 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3787 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 189 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C VAL A 189 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 189 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 190 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 189 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C VAL C 189 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL C 189 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C 190 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 215 " 0.026 2.00e-02 2.50e+03 2.10e-02 6.62e+00 pdb=" CG HIS A 215 " -0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 215 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS A 215 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 215 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 215 " 0.015 2.00e-02 2.50e+03 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 462 2.61 - 3.18: 25084 3.18 - 3.76: 39721 3.76 - 4.33: 57030 4.33 - 4.90: 85382 Nonbonded interactions: 207679 Sorted by model distance: nonbonded pdb=" O ILE B 612 " pdb=" OG SER B 615 " model vdw 2.038 3.040 nonbonded pdb=" O ILE D 612 " pdb=" OG SER D 615 " model vdw 2.038 3.040 nonbonded pdb=" O ILE C 608 " pdb=" OG SER C 611 " model vdw 2.091 3.040 nonbonded pdb=" O ILE A 608 " pdb=" OG SER A 611 " model vdw 2.092 3.040 nonbonded pdb=" O SER D 64 " pdb=" OG SER D 67 " model vdw 2.099 3.040 ... (remaining 207674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 1.200 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.008 0.247 25488 Z= 0.431 Angle : 0.992 13.086 34460 Z= 0.541 Chirality : 0.051 0.247 3790 Planarity : 0.006 0.060 4376 Dihedral : 11.415 86.314 9318 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 18.36 % Favored : 81.13 % Rotamer: Outliers : 0.23 % Allowed : 4.52 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.98 % 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: -4.92 (0.12), residues: 3138 helix: -3.08 (0.11), residues: 1092 sheet: -3.74 (0.33), residues: 174 loop : -3.50 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 599 TYR 0.021 0.002 TYR B 469 PHE 0.025 0.003 PHE B 101 TRP 0.019 0.003 TRP D 766 HIS 0.011 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.43 (25480) covalent geometry : angle 0.99180 / 0.54 (34444) SS BOND : bond 0.00836 / 0.39 ( 8) SS BOND : angle 1.47388 / 1.16 ( 16) hydrogen bonds : bond 0.30476 / 20.03 ( 786) hydrogen bonds : angle 9.76133 / 6.64 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9034 (mmm) cc_final: 0.8765 (mmt) REVERT: A 84 MET cc_start: 0.8164 (tmt) cc_final: 0.7931 (tmm) REVERT: A 175 MET cc_start: 0.8960 (mmp) cc_final: 0.8710 (tpp) REVERT: A 271 TRP cc_start: 0.6826 (m100) cc_final: 0.6599 (m-90) REVERT: A 459 MET cc_start: 0.8535 (mpt) cc_final: 0.8282 (mpp) REVERT: A 523 MET cc_start: 0.8402 (tpt) cc_final: 0.8112 (tpt) REVERT: A 666 MET cc_start: 0.9338 (mmt) cc_final: 0.8828 (tpp) REVERT: A 686 MET cc_start: 0.8183 (mtp) cc_final: 0.7593 (mmm) REVERT: A 704 MET cc_start: 0.8882 (ptp) cc_final: 0.8635 (ptp) REVERT: A 785 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5895 (tm) outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.1093 time to fit residues: 5.8812 Evaluate side-chains 29 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.241 Evaluate side-chains 31 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 LYS cc_start: 0.9138 (ptmt) cc_final: 0.8863 (ptmm) REVERT: B 292 MET cc_start: 0.8523 (mpp) cc_final: 0.7990 (mmp) REVERT: B 708 MET cc_start: 0.9203 (mtt) cc_final: 0.8990 (mtp) REVERT: B 721 MET cc_start: 0.9031 (tpp) cc_final: 0.8635 (tpt) REVERT: B 761 LYS cc_start: 0.9439 (mtpt) cc_final: 0.8971 (tptp) REVERT: B 781 LYS cc_start: 0.8432 (pttt) cc_final: 0.8038 (pttm) REVERT: B 807 MET cc_start: 0.8885 (mmt) cc_final: 0.8441 (mmm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1321 time to fit residues: 5.2379 Evaluate side-chains 23 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.0270 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.0770 overall best weight: 0.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 131 GLN A 257 GLN ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 583 GLN A 638 GLN B 24 GLN B 46 HIS B 93 HIS B 207 GLN B 344 ASN B 350 ASN B 435 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.043394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.034931 restraints weight = 58262.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036131 restraints weight = 37969.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036962 restraints weight = 27954.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037537 restraints weight = 22314.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.037922 restraints weight = 18909.275| |-----------------------------------------------------------------------------| r_work (final): 0.3002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.040027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.032460 restraints weight = 62490.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.033359 restraints weight = 41657.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033993 restraints weight = 30905.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034447 restraints weight = 24779.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.034769 restraints weight = 21066.285| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25488 Z= 0.161 Angle : 0.782 10.178 34460 Z= 0.418 Chirality : 0.047 0.176 3790 Planarity : 0.006 0.054 4376 Dihedral : 8.860 81.501 3474 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 15.49 % Favored : 84.13 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.17 (0.13), residues: 3138 helix: -1.85 (0.13), residues: 1238 sheet: -2.68 (0.35), residues: 176 loop : -3.65 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 599 TYR 0.024 0.002 TYR C 434 PHE 0.019 0.002 PHE A 575 TRP 0.050 0.002 TRP A 602 HIS 0.013 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (25480) covalent geometry : angle 0.78194 / 0.42 (34444) SS BOND : bond 0.00083 / 0.04 ( 8) SS BOND : angle 0.72456 / 0.54 ( 16) hydrogen bonds : bond 0.05185 / 3.44 ( 786) hydrogen bonds : angle 5.93790 / 4.10 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 58 MET cc_start: 0.9342 (mmm) cc_final: 0.8402 (mmm) REVERT: C 666 MET cc_start: 0.8887 (mmt) cc_final: 0.8371 (mtp) REVERT: C 670 MET cc_start: 0.9118 (mtm) cc_final: 0.8364 (mtt) REVERT: C 704 MET cc_start: 0.8882 (ptp) cc_final: 0.8543 (ptm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1210 time to fit residues: 5.0570 Evaluate side-chains 23 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.296 Evaluate side-chains 33 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.9225 (mtt) cc_final: 0.8731 (mtp) REVERT: D 503 MET cc_start: 0.7718 (ttp) cc_final: 0.7368 (ptm) REVERT: D 721 MET cc_start: 0.8887 (tpp) cc_final: 0.8311 (tpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1143 time to fit residues: 5.0135 Evaluate side-chains 21 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 242 optimal weight: 9.9990 chunk 305 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 193 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 24 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 134 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 118 GLN C 157 ASN C 257 GLN C 266 HIS C 326 GLN C 361 HIS C 638 GLN D 24 GLN D 46 HIS D 60 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.043755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035354 restraints weight = 58015.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.036512 restraints weight = 38573.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037257 restraints weight = 28797.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.037798 restraints weight = 23538.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.038195 restraints weight = 20219.361| |-----------------------------------------------------------------------------| r_work (final): 0.3010 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032369 restraints weight = 63977.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.033366 restraints weight = 42064.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.034039 restraints weight = 30758.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034491 restraints weight = 24476.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034824 restraints weight = 20712.653| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25488 Z= 0.133 Angle : 0.717 10.115 34460 Z= 0.376 Chirality : 0.045 0.177 3790 Planarity : 0.005 0.082 4376 Dihedral : 7.923 84.377 3474 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.00 % Favored : 83.75 % Rotamer: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.64 (0.13), residues: 3138 helix: -1.21 (0.13), residues: 1232 sheet: -2.57 (0.35), residues: 186 loop : -3.48 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 259 TYR 0.018 0.001 TYR C 434 PHE 0.012 0.001 PHE B 237 TRP 0.022 0.002 TRP D 606 HIS 0.011 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (25480) covalent geometry : angle 0.71710 / 0.38 (34444) SS BOND : bond 0.00075 / 0.04 ( 8) SS BOND : angle 0.65451 / 0.52 ( 16) hydrogen bonds : bond 0.04439 / 2.95 ( 786) hydrogen bonds : angle 5.27841 / 3.65 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: C 58 MET cc_start: 0.9311 (mmm) cc_final: 0.8511 (mmm) REVERT: C 525 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8546 (tt) REVERT: C 666 MET cc_start: 0.8860 (mmt) cc_final: 0.8451 (mtp) REVERT: C 670 MET cc_start: 0.9053 (mtm) cc_final: 0.8319 (mtt) REVERT: C 686 MET cc_start: 0.8587 (ttt) cc_final: 0.8007 (mtp) REVERT: C 704 MET cc_start: 0.8938 (ptp) cc_final: 0.8638 (ptm) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0985 time to fit residues: 3.8389 Evaluate side-chains 23 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.353 Evaluate side-chains 26 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.9339 (mtt) cc_final: 0.8815 (mtp) REVERT: D 361 MET cc_start: 0.7297 (ptp) cc_final: 0.6751 (pmm) REVERT: D 503 MET cc_start: 0.7766 (ttp) cc_final: 0.7268 (ptm) REVERT: D 527 MET cc_start: 0.7997 (ttm) cc_final: 0.7788 (tpp) REVERT: D 670 MET cc_start: 0.9697 (mtm) cc_final: 0.9188 (mtp) REVERT: D 721 MET cc_start: 0.9019 (tpp) cc_final: 0.8493 (tpp) REVERT: D 807 MET cc_start: 0.8844 (mmt) cc_final: 0.8405 (mmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0972 time to fit residues: 3.5186 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 291 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 299 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 305 optimal weight: 0.0980 chunk 182 optimal weight: 2.9990 chunk 266 optimal weight: 0.0000 chunk 134 optimal weight: 0.0020 chunk 289 optimal weight: 2.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 147 GLN C 257 GLN C 361 HIS D 46 HIS D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.043912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035499 restraints weight = 57633.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036629 restraints weight = 38765.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037420 restraints weight = 29107.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.037960 restraints weight = 23471.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.038340 restraints weight = 20061.479| |-----------------------------------------------------------------------------| r_work (final): 0.3010 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031916 restraints weight = 62462.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.032962 restraints weight = 40288.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.033630 restraints weight = 29136.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.034123 restraints weight = 23047.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034473 restraints weight = 19371.393| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25488 Z= 0.123 Angle : 0.679 9.443 34460 Z= 0.356 Chirality : 0.044 0.167 3790 Planarity : 0.005 0.073 4376 Dihedral : 7.271 87.524 3474 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.30 % Favored : 84.45 % Rotamer: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.34 (0.14), residues: 3138 helix: -0.79 (0.14), residues: 1250 sheet: -2.58 (0.38), residues: 178 loop : -3.46 (0.13), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 259 TYR 0.015 0.001 TYR C 434 PHE 0.013 0.001 PHE D 237 TRP 0.066 0.002 TRP A 602 HIS 0.010 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (25480) covalent geometry : angle 0.67889 / 0.36 (34444) SS BOND : bond 0.00318 / 0.14 ( 8) SS BOND : angle 0.71837 / 0.56 ( 16) hydrogen bonds : bond 0.03561 / 2.39 ( 786) hydrogen bonds : angle 4.98293 / 3.44 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.246 Fit side-chains REVERT: C 58 MET cc_start: 0.9309 (mmm) cc_final: 0.8597 (mmt) REVERT: C 525 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8566 (tt) REVERT: C 666 MET cc_start: 0.8933 (mmt) cc_final: 0.8605 (mtp) REVERT: C 670 MET cc_start: 0.9006 (mtm) cc_final: 0.8393 (mtt) REVERT: C 686 MET cc_start: 0.8514 (ttt) cc_final: 0.7881 (mtp) REVERT: C 704 MET cc_start: 0.8738 (ptp) cc_final: 0.8355 (ptm) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0778 time to fit residues: 3.0346 Evaluate side-chains 23 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.242 Evaluate side-chains 23 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: D 33 MET cc_start: 0.9440 (mtt) cc_final: 0.8948 (mtp) REVERT: D 361 MET cc_start: 0.7142 (ptp) cc_final: 0.6800 (pmm) REVERT: D 408 MET cc_start: 0.7461 (ptm) cc_final: 0.6934 (mtm) REVERT: D 463 MET cc_start: 0.8302 (ptp) cc_final: 0.8068 (pmm) REVERT: D 503 MET cc_start: 0.7725 (ttp) cc_final: 0.7361 (ptm) REVERT: D 670 MET cc_start: 0.9763 (mtm) cc_final: 0.9020 (mtp) REVERT: D 721 MET cc_start: 0.8984 (tpp) cc_final: 0.8512 (tpp) REVERT: D 807 MET cc_start: 0.8878 (mmt) cc_final: 0.8404 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0578 time to fit residues: 2.0817 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 268 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 121 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 23 optimal weight: 0.0000 chunk 269 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 0.0050 chunk 188 optimal weight: 20.0000 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 257 GLN C 361 HIS C 583 GLN D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.044374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035865 restraints weight = 56908.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037032 restraints weight = 37965.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.037865 restraints weight = 28287.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038426 restraints weight = 22667.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.038818 restraints weight = 19244.871| |-----------------------------------------------------------------------------| r_work (final): 0.3023 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.040404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032356 restraints weight = 64199.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033387 restraints weight = 41381.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034115 restraints weight = 30139.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034612 restraints weight = 23796.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034954 restraints weight = 20044.983| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.880 25488 Z= 0.649 Angle : 0.714 24.174 34460 Z= 0.365 Chirality : 0.044 0.236 3790 Planarity : 0.005 0.065 4376 Dihedral : 6.963 86.259 3474 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.30 % Favored : 84.51 % Rotamer: Outliers : 0.15 % Allowed : 2.33 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.20 (0.14), residues: 3138 helix: -0.57 (0.14), residues: 1266 sheet: -2.48 (0.38), residues: 172 loop : -3.50 (0.13), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 309 TYR 0.012 0.001 TYR C 434 PHE 0.011 0.001 PHE B 237 TRP 0.048 0.002 TRP C 602 HIS 0.010 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.01841 / 0.65 (25480) covalent geometry : angle 0.71436 / 0.37 (34444) SS BOND : bond 0.00152 / 0.08 ( 8) SS BOND : angle 0.77722 / 0.62 ( 16) hydrogen bonds : bond 0.03610 / 2.36 ( 786) hydrogen bonds : angle 4.86694 / 3.39 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.258 Fit side-chains REVERT: C 58 MET cc_start: 0.9222 (mmm) cc_final: 0.8553 (mmt) REVERT: C 523 MET cc_start: 0.8457 (mtt) cc_final: 0.7797 (mmp) REVERT: C 666 MET cc_start: 0.8906 (mmt) cc_final: 0.8558 (mtp) REVERT: C 670 MET cc_start: 0.8961 (mtm) cc_final: 0.8337 (mtt) REVERT: C 686 MET cc_start: 0.8495 (ttt) cc_final: 0.7854 (mtp) REVERT: C 704 MET cc_start: 0.8671 (ptp) cc_final: 0.8297 (ptm) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.0818 time to fit residues: 3.1368 Evaluate side-chains 22 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.219 Evaluate side-chains 23 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: D 33 MET cc_start: 0.9445 (mtt) cc_final: 0.8995 (mtp) REVERT: D 361 MET cc_start: 0.7243 (ptp) cc_final: 0.6995 (pmm) REVERT: D 408 MET cc_start: 0.7445 (ptm) cc_final: 0.6892 (mtm) REVERT: D 503 MET cc_start: 0.7651 (ttp) cc_final: 0.7228 (ptm) REVERT: D 670 MET cc_start: 0.9746 (mtm) cc_final: 0.9129 (mpp) REVERT: D 674 MET cc_start: 0.8311 (ptp) cc_final: 0.7869 (ppp) REVERT: D 708 MET cc_start: 0.8868 (mtp) cc_final: 0.8648 (mtp) REVERT: D 721 MET cc_start: 0.8992 (tpp) cc_final: 0.8504 (tpp) REVERT: D 807 MET cc_start: 0.8847 (mmt) cc_final: 0.8451 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0721 time to fit residues: 2.5638 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 4 optimal weight: 0.0270 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 257 GLN C 361 HIS D 219 HIS D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.043319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034911 restraints weight = 56503.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.035983 restraints weight = 38726.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036743 restraints weight = 29381.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037283 restraints weight = 23882.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037668 restraints weight = 20387.407| |-----------------------------------------------------------------------------| r_work (final): 0.2981 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.039645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031522 restraints weight = 63142.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032569 restraints weight = 40797.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033249 restraints weight = 29569.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.033766 restraints weight = 23474.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034082 restraints weight = 19741.377| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25488 Z= 0.149 Angle : 0.661 9.200 34460 Z= 0.347 Chirality : 0.043 0.198 3790 Planarity : 0.005 0.065 4376 Dihedral : 6.792 84.507 3474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.85 % Favored : 84.89 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.14), residues: 3138 helix: -0.28 (0.14), residues: 1262 sheet: -2.43 (0.38), residues: 196 loop : -3.40 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 599 TYR 0.011 0.001 TYR C 434 PHE 0.018 0.001 PHE B 584 TRP 0.019 0.002 TRP A 602 HIS 0.010 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (25480) covalent geometry : angle 0.66089 / 0.35 (34444) SS BOND : bond 0.00216 / 0.11 ( 8) SS BOND : angle 0.60011 / 0.47 ( 16) hydrogen bonds : bond 0.03376 / 2.23 ( 786) hydrogen bonds : angle 4.72504 / 3.24 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.263 Fit side-chains REVERT: C 58 MET cc_start: 0.9269 (mmm) cc_final: 0.8588 (mmt) REVERT: C 523 MET cc_start: 0.8482 (mtt) cc_final: 0.7843 (mmp) REVERT: C 666 MET cc_start: 0.8982 (mmt) cc_final: 0.8612 (mtp) REVERT: C 670 MET cc_start: 0.9018 (mtm) cc_final: 0.8393 (mtt) REVERT: C 686 MET cc_start: 0.8663 (ttt) cc_final: 0.8037 (mtp) REVERT: C 704 MET cc_start: 0.8745 (ptp) cc_final: 0.8347 (ptm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0811 time to fit residues: 2.9077 Evaluate side-chains 21 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.262 Evaluate side-chains 22 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.9473 (mtt) cc_final: 0.8991 (mtp) REVERT: D 361 MET cc_start: 0.7239 (ptp) cc_final: 0.6998 (pmm) REVERT: D 380 MET cc_start: 0.8401 (tpp) cc_final: 0.8058 (tpp) REVERT: D 503 MET cc_start: 0.7729 (ttp) cc_final: 0.7359 (ptm) REVERT: D 670 MET cc_start: 0.9754 (mtm) cc_final: 0.9113 (mpp) REVERT: D 674 MET cc_start: 0.8291 (ptp) cc_final: 0.7917 (ppp) REVERT: D 708 MET cc_start: 0.8882 (mtp) cc_final: 0.8676 (mtp) REVERT: D 721 MET cc_start: 0.9031 (tpp) cc_final: 0.8586 (tpp) REVERT: D 807 MET cc_start: 0.8974 (mmt) cc_final: 0.8518 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0591 time to fit residues: 2.1412 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 108 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 245 optimal weight: 0.0970 chunk 92 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.044075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035731 restraints weight = 56642.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036817 restraints weight = 38437.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037551 restraints weight = 29186.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038103 restraints weight = 23587.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038481 restraints weight = 20151.990| |-----------------------------------------------------------------------------| r_work (final): 0.3007 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.040347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032186 restraints weight = 64294.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.033245 restraints weight = 41369.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033972 restraints weight = 30045.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034470 restraints weight = 23719.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.034790 restraints weight = 19991.095| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25488 Z= 0.113 Angle : 0.648 10.720 34460 Z= 0.335 Chirality : 0.043 0.180 3790 Planarity : 0.005 0.060 4376 Dihedral : 6.674 87.346 3474 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.85 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 3138 helix: -0.08 (0.14), residues: 1258 sheet: -2.27 (0.39), residues: 196 loop : -3.36 (0.13), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 141 TYR 0.012 0.001 TYR D 218 PHE 0.012 0.001 PHE C 580 TRP 0.011 0.001 TRP D 606 HIS 0.009 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (25480) covalent geometry : angle 0.64787 / 0.33 (34444) SS BOND : bond 0.00152 / 0.08 ( 8) SS BOND : angle 0.66279 / 0.52 ( 16) hydrogen bonds : bond 0.03019 / 2.03 ( 786) hydrogen bonds : angle 4.55235 / 3.13 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: C 58 MET cc_start: 0.9272 (mmm) cc_final: 0.8555 (mmt) REVERT: C 523 MET cc_start: 0.8425 (mtt) cc_final: 0.7764 (mmp) REVERT: C 666 MET cc_start: 0.8971 (mmt) cc_final: 0.8604 (mtp) REVERT: C 670 MET cc_start: 0.9023 (mtm) cc_final: 0.8463 (mtt) REVERT: C 686 MET cc_start: 0.8578 (ttt) cc_final: 0.7979 (mtp) REVERT: C 704 MET cc_start: 0.8689 (ptp) cc_final: 0.8267 (ptm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0888 time to fit residues: 3.1895 Evaluate side-chains 22 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.250 Evaluate side-chains 23 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: D 33 MET cc_start: 0.9455 (mtt) cc_final: 0.9025 (mtp) REVERT: D 113 MET cc_start: 0.6605 (mmm) cc_final: 0.6351 (mmm) REVERT: D 361 MET cc_start: 0.7335 (ptp) cc_final: 0.7027 (pmm) REVERT: D 380 MET cc_start: 0.8424 (tpp) cc_final: 0.8167 (tpp) REVERT: D 408 MET cc_start: 0.7533 (ptm) cc_final: 0.6886 (mtm) REVERT: D 463 MET cc_start: 0.7861 (pmm) cc_final: 0.7646 (pmm) REVERT: D 503 MET cc_start: 0.7594 (ttp) cc_final: 0.7217 (ptm) REVERT: D 670 MET cc_start: 0.9724 (mtm) cc_final: 0.9107 (mpp) REVERT: D 674 MET cc_start: 0.8290 (ptp) cc_final: 0.7834 (ppp) REVERT: D 721 MET cc_start: 0.8955 (tpp) cc_final: 0.8474 (tpp) REVERT: D 807 MET cc_start: 0.8889 (mmt) cc_final: 0.8474 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0767 time to fit residues: 2.7659 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 69 optimal weight: 0.0000 chunk 199 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 235 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.043563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034949 restraints weight = 57131.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036052 restraints weight = 38692.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036857 restraints weight = 28904.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037422 restraints weight = 23379.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037835 restraints weight = 19904.120| |-----------------------------------------------------------------------------| r_work (final): 0.2982 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.031851 restraints weight = 62645.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032878 restraints weight = 40392.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033596 restraints weight = 29453.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034084 restraints weight = 23264.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034427 restraints weight = 19603.982| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25488 Z= 0.120 Angle : 0.651 10.027 34460 Z= 0.335 Chirality : 0.043 0.172 3790 Planarity : 0.005 0.060 4376 Dihedral : 6.552 86.196 3474 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.72 % Favored : 85.15 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.15), residues: 3138 helix: 0.06 (0.15), residues: 1276 sheet: -2.17 (0.39), residues: 196 loop : -3.33 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 264 TYR 0.011 0.001 TYR A 60 PHE 0.011 0.001 PHE B 237 TRP 0.015 0.001 TRP D 605 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (25480) covalent geometry : angle 0.65045 / 0.34 (34444) SS BOND : bond 0.00216 / 0.11 ( 8) SS BOND : angle 0.93797 / 0.74 ( 16) hydrogen bonds : bond 0.02920 / 1.97 ( 786) hydrogen bonds : angle 4.48855 / 3.08 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: C 58 MET cc_start: 0.9280 (mmm) cc_final: 0.8575 (mmt) REVERT: C 523 MET cc_start: 0.8426 (mtt) cc_final: 0.7765 (mmp) REVERT: C 666 MET cc_start: 0.9047 (mmt) cc_final: 0.8653 (mtp) REVERT: C 670 MET cc_start: 0.9056 (mtm) cc_final: 0.8486 (mtt) REVERT: C 686 MET cc_start: 0.8636 (ttt) cc_final: 0.8045 (mtp) REVERT: C 704 MET cc_start: 0.8705 (ptp) cc_final: 0.8307 (ptm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0793 time to fit residues: 2.9593 Evaluate side-chains 22 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.272 Evaluate side-chains 22 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 MET cc_start: 0.9485 (mtt) cc_final: 0.9080 (mtp) REVERT: D 503 MET cc_start: 0.7623 (ttp) cc_final: 0.7304 (ptm) REVERT: D 670 MET cc_start: 0.9731 (mtm) cc_final: 0.9157 (mtp) REVERT: D 674 MET cc_start: 0.8256 (ptp) cc_final: 0.7816 (ppp) REVERT: D 721 MET cc_start: 0.8961 (tpp) cc_final: 0.8439 (tpp) REVERT: D 807 MET cc_start: 0.8923 (mmt) cc_final: 0.8493 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0604 time to fit residues: 2.2105 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 41 optimal weight: 0.0670 chunk 281 optimal weight: 9.9990 chunk 211 optimal weight: 0.0770 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 221 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 273 optimal weight: 8.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 GLN D 344 ASN D 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035949 restraints weight = 55472.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037017 restraints weight = 37841.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037764 restraints weight = 28732.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038270 restraints weight = 23360.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.038676 restraints weight = 20044.032| |-----------------------------------------------------------------------------| r_work (final): 0.3016 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032540 restraints weight = 63566.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.033604 restraints weight = 40758.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034306 restraints weight = 29517.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.034832 restraints weight = 23336.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.035163 restraints weight = 19615.825| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25488 Z= 0.109 Angle : 0.662 9.500 34460 Z= 0.336 Chirality : 0.043 0.176 3790 Planarity : 0.005 0.062 4376 Dihedral : 6.433 88.025 3474 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.21 % Favored : 85.66 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.15), residues: 3138 helix: 0.11 (0.15), residues: 1280 sheet: -2.09 (0.40), residues: 196 loop : -3.29 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.010 0.001 TYR A 60 PHE 0.014 0.001 PHE D 109 TRP 0.016 0.001 TRP D 605 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (25480) covalent geometry : angle 0.66139 / 0.34 (34444) SS BOND : bond 0.00271 / 0.14 ( 8) SS BOND : angle 1.25787 / 0.98 ( 16) hydrogen bonds : bond 0.02808 / 1.89 ( 786) hydrogen bonds : angle 4.34785 / 2.98 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: C 58 MET cc_start: 0.9200 (mmm) cc_final: 0.8484 (mmt) REVERT: C 288 MET cc_start: 0.9002 (ptm) cc_final: 0.8785 (ptm) REVERT: C 523 MET cc_start: 0.8413 (mtt) cc_final: 0.7763 (mmp) REVERT: C 666 MET cc_start: 0.8914 (mmt) cc_final: 0.8653 (mtp) REVERT: C 670 MET cc_start: 0.9049 (mtm) cc_final: 0.8469 (mtt) REVERT: C 704 MET cc_start: 0.8577 (ptp) cc_final: 0.8183 (ptm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0739 time to fit residues: 2.7422 Evaluate side-chains 22 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.194 Evaluate side-chains 22 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 408 MET cc_start: 0.7500 (ptm) cc_final: 0.6894 (mtm) REVERT: D 463 MET cc_start: 0.7714 (pmm) cc_final: 0.7486 (pmm) REVERT: D 670 MET cc_start: 0.9706 (mtm) cc_final: 0.9077 (mpp) REVERT: D 674 MET cc_start: 0.8238 (ptp) cc_final: 0.7747 (ppp) REVERT: D 708 MET cc_start: 0.8810 (mtp) cc_final: 0.8598 (mtp) REVERT: D 721 MET cc_start: 0.8868 (tpp) cc_final: 0.8352 (tpp) REVERT: D 807 MET cc_start: 0.8826 (mmt) cc_final: 0.8396 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0636 time to fit residues: 2.2567 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.4980 chunk 50 optimal weight: 0.0570 chunk 255 optimal weight: 0.0060 chunk 95 optimal weight: 0.4980 chunk 206 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 194 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 107 optimal weight: 0.0670 chunk 204 optimal weight: 0.0570 overall best weight: 0.0570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.045025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036414 restraints weight = 56896.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037456 restraints weight = 39520.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038229 restraints weight = 30204.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038767 restraints weight = 24672.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039136 restraints weight = 21147.545| |-----------------------------------------------------------------------------| r_work (final): 0.3027 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.041172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.033064 restraints weight = 63519.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034128 restraints weight = 41165.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.034818 restraints weight = 30019.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035354 restraints weight = 23848.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035718 restraints weight = 19987.033| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25488 Z= 0.114 Angle : 0.661 9.343 34460 Z= 0.334 Chirality : 0.043 0.193 3790 Planarity : 0.005 0.061 4376 Dihedral : 6.260 88.832 3474 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.28 % Favored : 85.66 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.15), residues: 3138 helix: 0.16 (0.15), residues: 1296 sheet: -1.90 (0.42), residues: 180 loop : -3.30 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 264 TYR 0.014 0.001 TYR B 218 PHE 0.023 0.001 PHE D 109 TRP 0.018 0.001 TRP D 605 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (25480) covalent geometry : angle 0.66035 / 0.33 (34444) SS BOND : bond 0.00152 / 0.08 ( 8) SS BOND : angle 1.10389 / 0.85 ( 16) hydrogen bonds : bond 0.02713 / 1.82 ( 786) hydrogen bonds : angle 4.30667 / 2.95 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: C 58 MET cc_start: 0.9165 (mmm) cc_final: 0.8848 (mmt) REVERT: C 288 MET cc_start: 0.8933 (ptm) cc_final: 0.8731 (ptm) REVERT: C 523 MET cc_start: 0.8397 (mtt) cc_final: 0.7795 (mmp) REVERT: C 666 MET cc_start: 0.8868 (mmt) cc_final: 0.8665 (mtp) REVERT: C 670 MET cc_start: 0.9042 (mtm) cc_final: 0.8459 (mtt) REVERT: C 686 MET cc_start: 0.8498 (ttm) cc_final: 0.7946 (mtp) REVERT: C 704 MET cc_start: 0.8701 (ptp) cc_final: 0.8300 (ptm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0762 time to fit residues: 2.7232 Evaluate side-chains 21 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.249 Evaluate side-chains 23 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: D 33 MET cc_start: 0.9401 (mtt) cc_final: 0.9125 (ptm) REVERT: D 408 MET cc_start: 0.7567 (ptm) cc_final: 0.7004 (mtm) REVERT: D 670 MET cc_start: 0.9686 (mtm) cc_final: 0.9112 (mpp) REVERT: D 674 MET cc_start: 0.8236 (ptp) cc_final: 0.7760 (ppp) REVERT: D 708 MET cc_start: 0.8799 (mtp) cc_final: 0.8587 (mtp) REVERT: D 721 MET cc_start: 0.8806 (tpp) cc_final: 0.8307 (tpp) REVERT: D 807 MET cc_start: 0.8803 (mmt) cc_final: 0.8380 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0757 time to fit residues: 2.6951 Evaluate side-chains 20 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 299 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 98 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 201 optimal weight: 0.2980 chunk 177 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 350 ASN D 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.044390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035818 restraints weight = 57078.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036868 restraints weight = 39565.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037569 restraints weight = 30128.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038117 restraints weight = 24864.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038495 restraints weight = 21328.389| |-----------------------------------------------------------------------------| r_work (final): 0.3003 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.032638 restraints weight = 62284.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033675 restraints weight = 40403.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034394 restraints weight = 29404.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034892 restraints weight = 23258.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035222 restraints weight = 19526.121| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25488 Z= 0.112 Angle : 0.659 10.031 34460 Z= 0.332 Chirality : 0.043 0.183 3790 Planarity : 0.005 0.062 4376 Dihedral : 6.174 88.926 3474 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.72 % Favored : 85.21 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 3138 helix: 0.30 (0.15), residues: 1282 sheet: -2.02 (0.40), residues: 198 loop : -3.27 (0.13), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.010 0.001 TYR C 60 PHE 0.009 0.001 PHE D 237 TRP 0.022 0.001 TRP D 605 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (25480) covalent geometry : angle 0.65847 / 0.33 (34444) SS BOND : bond 0.00170 / 0.09 ( 8) SS BOND : angle 0.91840 / 0.71 ( 16) hydrogen bonds : bond 0.02668 / 1.81 ( 786) hydrogen bonds : angle 4.28705 / 2.93 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.50 seconds wall clock time: 44 minutes 40.23 seconds (2680.23 seconds total)