Starting phenix.real_space_refine on Mon May 4 21:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unk_64354/05_2026/9unk_64354.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unk_64354/05_2026/9unk_64354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9unk_64354/05_2026/9unk_64354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unk_64354/05_2026/9unk_64354.map" model { file = "/net/cci-nas-00/data/ceres_data/9unk_64354/05_2026/9unk_64354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unk_64354/05_2026/9unk_64354.cif" } resolution = 3.37 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= 0.007 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 139 5.16 5 Cl 1 4.86 5 C 15085 2.51 5 N 3910 2.21 5 O 4313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23448 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 5848 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 35, 'TRANS': 768} Chain breaks: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 14, 'GLU:plan': 30, 'TRP:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 9, 'ASP:plan': 16, 'HIS:plan': 3, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5630 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 753 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 40, 'HIS:plan': 5, 'PHE:plan': 4, 'ARG:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 388 Chain: "C" Number of atoms: 5828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 5828 Classifications: {'peptide': 807} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 35, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 674 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 20, 'GLN:plan1': 7, 'GLU:plan': 31, 'HIS:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 16, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 380 Chain: "D" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5652 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 28, 'TRANS': 762} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 28, 'HIS:plan': 6, 'GLU:plan': 34, 'ARG:plan': 11, 'GLN:plan1': 4, 'PHE:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 395 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'NAG': 10} Classifications: {'peptide': 1, 'undetermined': 10} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 6} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'NAG': 10} Classifications: {'peptide': 1, 'undetermined': 10} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 93 Unusual residues: {'NAG': 6} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.68, per 1000 atoms: 0.24 Number of scatterers: 23448 At special positions: 0 Unit cell: (119.215, 141.37, 183.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 139 16.00 O 4313 8.00 N 3910 7.00 C 15085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 61 " " NAG A 902 " - " ASN A 203 " " NAG A 903 " - " ASN A 239 " " NAG A 904 " - " ASN A 276 " " NAG A 905 " - " ASN A 350 " " NAG A 906 " - " ASN A 368 " " NAG A 907 " - " ASN A 471 " " NAG A 908 " - " ASN A 771 " " NAG A 909 " - " ASN A 300 " " NAG A 910 " - " ASN A 440 " " NAG B 901 " - " ASN B 341 " " NAG B 902 " - " ASN B 348 " " NAG B 903 " - " ASN B 688 " " NAG B 904 " - " ASN B 74 " " NAG B 905 " - " ASN B 491 " " NAG B 906 " - " ASN B 542 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 239 " " NAG C 904 " - " ASN C 276 " " NAG C 905 " - " ASN C 350 " " NAG C 906 " - " ASN C 368 " " NAG C 907 " - " ASN C 471 " " NAG C 908 " - " ASN C 771 " " NAG C 909 " - " ASN C 300 " " NAG C 910 " - " ASN C 491 " " NAG D 901 " - " ASN D 341 " " NAG D 902 " - " ASN D 348 " " NAG D 903 " - " ASN D 688 " " NAG D 904 " - " ASN D 74 " " NAG D 905 " - " ASN D 491 " " NAG D 906 " - " ASN D 542 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5966 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 27 sheets defined 46.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.802A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.132A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.554A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.253A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.526A pdb=" N ASP A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 262 removed outlier: 4.019A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.833A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.368A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.085A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.075A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 584 removed outlier: 4.110A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 626 through 657 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.569A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 810 through 844 removed outlier: 4.781A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.945A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.778A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.521A pdb=" N MET B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.791A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 565 through 581 Processing helix chain 'B' and resid 601 through 615 Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.738A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 removed outlier: 3.612A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 699 through 706 removed outlier: 3.667A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 710 removed outlier: 3.675A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.442A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.821A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 804 removed outlier: 4.340A pdb=" N ASN B 803 " --> pdb=" O GLY B 799 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 804 " --> pdb=" O ILE B 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 799 through 804' Processing helix chain 'B' and resid 818 through 839 Processing helix chain 'C' and resid 35 through 53 removed outlier: 4.028A pdb=" N HIS C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.067A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.998A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.928A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.229A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.060A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 499 through 508 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 584 Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 626 through 657 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 709 removed outlier: 3.633A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 800 through 804 Processing helix chain 'C' and resid 814 through 843 removed outlier: 3.745A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 removed outlier: 4.502A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.877A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.787A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 331 through 341 removed outlier: 4.125A pdb=" N LEU D 335 " --> pdb=" O GLN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 546 through 551 removed outlier: 4.385A pdb=" N PHE D 550 " --> pdb=" O PRO D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 581 removed outlier: 4.197A pdb=" N LEU D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.678A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 669 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 708 removed outlier: 3.970A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 744 through 746 No H-bonds generated for 'chain 'D' and resid 744 through 746' Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.533A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 796 Processing helix chain 'D' and resid 799 through 804 Processing helix chain 'D' and resid 805 through 809 removed outlier: 3.575A pdb=" N VAL D 808 " --> pdb=" O LYS D 805 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET D 809 " --> pdb=" O ASN D 806 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 805 through 809' Processing helix chain 'D' and resid 814 through 842 removed outlier: 4.086A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.813A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.615A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.760A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.640A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 477 removed outlier: 7.067A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.534A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 683 removed outlier: 5.565A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.667A pdb=" N VAL B 39 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 205 removed outlier: 6.766A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU B 205 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR B 173 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 174 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU B 230 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB2, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.560A pdb=" N MET B 508 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.488A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 65 removed outlier: 8.667A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 121 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL C 92 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 193 through 197 removed outlier: 4.130A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 267 through 271 removed outlier: 4.049A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 473 through 478 removed outlier: 6.797A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.206A pdb=" N ILE C 540 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLU C 751 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 542 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 749 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 36 through 42 Processing sheet with id=AC4, first strand: chain 'D' and resid 97 through 99 removed outlier: 7.119A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.769A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 378 " --> pdb=" O GLN D 385 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC7, first strand: chain 'D' and resid 406 through 410 removed outlier: 7.052A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.585A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.585A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1162 hydrogen bonds defined for protein. 3372 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: 5.71 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5515 1.33 - 1.45: 4912 1.45 - 1.57: 13285 1.57 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 23952 Sorted by residual: bond pdb=" N ILE A 29 " pdb=" CA ILE A 29 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.81e+00 bond pdb=" N ASN A 28 " pdb=" CA ASN A 28 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.55e+00 bond pdb=" N GLY A 30 " pdb=" CA GLY A 30 " ideal model delta sigma weight residual 1.446 1.475 -0.030 1.30e-02 5.92e+03 5.15e+00 bond pdb=" N ALA A 31 " pdb=" CA ALA A 31 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.23e-02 6.61e+03 4.02e+00 bond pdb=" N VAL A 27 " pdb=" CA VAL A 27 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.71e+00 ... (remaining 23947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 32235 1.80 - 3.60: 439 3.60 - 5.41: 45 5.41 - 7.21: 10 7.21 - 9.01: 2 Bond angle restraints: 32731 Sorted by residual: angle pdb=" CA LYS D 670 " pdb=" CB LYS D 670 " pdb=" CG LYS D 670 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.66e+00 angle pdb=" CA GLY A 30 " pdb=" C GLY A 30 " pdb=" O GLY A 30 " ideal model delta sigma weight residual 122.51 118.24 4.27 1.41e+00 5.03e-01 9.15e+00 angle pdb=" CB MET C 576 " pdb=" CG MET C 576 " pdb=" SD MET C 576 " ideal model delta sigma weight residual 112.70 121.71 -9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" C ASP D 676 " pdb=" N PHE D 677 " pdb=" CA PHE D 677 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.46e+00 angle pdb=" CA THR A 103 " pdb=" C THR A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 118.44 122.24 -3.80 1.59e+00 3.96e-01 5.72e+00 ... (remaining 32726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.44: 13736 22.44 - 44.89: 639 44.89 - 67.33: 98 67.33 - 89.78: 15 89.78 - 112.22: 8 Dihedral angle restraints: 14496 sinusoidal: 5246 harmonic: 9250 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 457 " pdb=" CB CYS B 457 " ideal model delta sinusoidal sigma weight residual -86.00 -166.72 80.72 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual -86.00 -158.10 72.10 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual 93.00 138.01 -45.01 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 14493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3343 0.056 - 0.112: 559 0.112 - 0.167: 71 0.167 - 0.223: 4 0.223 - 0.279: 3 Chirality restraints: 3980 Sorted by residual: chirality pdb=" C1 NAG A 910 " pdb=" ND2 ASN A 440 " pdb=" C2 NAG A 910 " pdb=" O5 NAG A 910 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG C 907 " pdb=" ND2 ASN C 471 " pdb=" C2 NAG C 907 " pdb=" O5 NAG C 907 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3977 not shown) Planarity restraints: 4155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 607 " -0.024 2.00e-02 2.50e+03 1.81e-02 8.17e+00 pdb=" CG TRP D 607 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP D 607 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 607 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 607 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 607 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 607 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 607 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 607 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 607 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 440 " 0.026 2.00e-02 2.50e+03 2.49e-02 7.74e+00 pdb=" CG ASN A 440 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 440 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 440 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG A 910 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 258 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO D 259 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 259 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 259 " -0.032 5.00e-02 4.00e+02 ... (remaining 4152 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2241 2.75 - 3.29: 24321 3.29 - 3.82: 40439 3.82 - 4.36: 44582 4.36 - 4.90: 77430 Nonbonded interactions: 189013 Sorted by model distance: nonbonded pdb=" O PHE D 114 " pdb=" NE2 GLN D 118 " model vdw 2.209 3.120 nonbonded pdb=" OD2 ASP D 732 " pdb=" OH TYR D 762 " model vdw 2.271 3.040 nonbonded pdb=" O LYS A 465 " pdb=" OG1 THR A 469 " model vdw 2.285 3.040 nonbonded pdb=" OG SER A 129 " pdb=" NH2 ARG A 139 " model vdw 2.301 3.120 nonbonded pdb=" O THR C 302 " pdb=" OG1 THR C 317 " model vdw 2.305 3.040 ... (remaining 189008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 43 or (resid 44 through 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 52 or (res \ id 53 and (name N or name CA or name C or name O or name CB )) or resid 54 throu \ gh 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or r \ esid 61 through 102 or (resid 103 and (name N or name CA or name C or name O or \ name CB )) or resid 104 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 292 or (resid 293 and (name N or \ name CA or name C or name O or name CB )) or resid 294 through 300 or (resid 30 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 302 through \ 322 or (resid 323 and (name N or name CA or name C or name O or name CB )) or re \ sid 324 through 336 or (resid 337 and (name N or name CA or name C or name O or \ name CB )) or resid 338 through 357 or (resid 358 through 360 and (name N or nam \ e CA or name C or name O or name CB )) or resid 361 through 369 or (resid 370 th \ rough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 376 or (resid 377 through 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 through 387 or (resid 388 and (name N or name CA or \ name C or name O or name CB )) or resid 389 or (resid 390 and (name N or name CA \ or name C or name O or name CB )) or resid 391 through 440 or (resid 441 and (n \ ame N or name CA or name C or name O or name CB )) or resid 442 through 467 or ( \ resid 468 and (name N or name CA or name C or name O or name CB )) or resid 469 \ through 501 or (resid 502 and (name N or name CA or name C or name O or name CB \ )) or resid 503 through 554 or (resid 555 through 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 through 676 or (resid 677 through 67 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 679 through \ 696 or (resid 697 through 698 and (name N or name CA or name C or name O or name \ CB )) or resid 699 through 703 or (resid 704 and (name N or name CA or name C o \ r name O or name CB )) or resid 705 through 706 or (resid 707 through 708 and (n \ ame N or name CA or name C or name O or name CB )) or resid 709 through 715 or ( \ resid 716 through 717 and (name N or name CA or name C or name O or name CB )) o \ r resid 718 through 722 or (resid 723 through 725 and (name N or name CA or name \ C or name O or name CB )) or resid 726 through 741 or (resid 742 through 743 an \ d (name N or name CA or name C or name O or name CB )) or resid 744 through 769 \ or (resid 770 and (name N or name CA or name C or name O or name CB )) or resid \ 771 through 793 or (resid 794 and (name N or name CA or name C or name O or name \ CB )) or resid 795 through 812 or (resid 813 through 814 and (name N or name CA \ or name C or name O or name CB )) or resid 815 through 838 or (resid 839 and (n \ ame N or name CA or name C or name O or name CB )) or resid 840 through 841 or ( \ resid 842 through 843 and (name N or name CA or name C or name O or name CB )) o \ r resid 901 through 909)) selection = (chain 'C' and (resid 27 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 100 or (re \ sid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 th \ rough 226 or (resid 227 through 229 and (name N or name CA or name C or name O o \ r name CB )) or resid 230 through 232 or (resid 233 through 237 and (name N or n \ ame CA or name C or name O or name CB )) or resid 238 through 252 or (resid 253 \ and (name N or name CA or name C or name O or name CB )) or resid 254 through 27 \ 2 or (resid 273 and (name N or name CA or name C or name O or name CB )) or resi \ d 274 through 282 or (resid 283 through 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 316 or (resid 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB )) or resid 344 through 414 or \ (resid 415 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 6 through 418 or (resid 419 and (name N or name CA or name C or name O or name C \ B )) or resid 420 through 424 or (resid 425 through 427 and (name N or name CA o \ r name C or name O or name CB )) or resid 428 or (resid 429 and (name N or name \ CA or name C or name O or name CB )) or resid 430 through 480 or (resid 481 and \ (name N or name CA or name C or name O or name CB )) or resid 482 through 489 or \ (resid 490 through 492 and (name N or name CA or name C or name O or name CB )) \ or resid 493 through 543 or (resid 544 through 546 and (name N or name CA or na \ me C or name O or name CB )) or resid 547 through 557 or (resid 558 through 559 \ and (name N or name CA or name C or name O or name CB )) or resid 560 through 56 \ 2 or (resid 563 through 564 and (name N or name CA or name C or name O or name C \ B )) or resid 565 through 586 or resid 601 through 801 or (resid 802 through 804 \ and (name N or name CA or name C or name O or name CB )) or resid 805 through 8 \ 24 or (resid 825 through 826 and (name N or name CA or name C or name O or name \ CB )) or resid 827 through 843 or resid 902 through 910)) } ncs_group { reference = (chain 'B' and (resid 34 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 101 or (resid 102 throu \ gh 104 and (name N or name CA or name C or name O or name CB )) or resid 105 thr \ ough 115 or (resid 116 through 117 and (name N or name CA or name C or name O or \ name CB )) or resid 118 through 129 or (resid 130 through 131 and (name N or na \ me CA or name C or name O or name CB )) or resid 132 through 193 or (resid 194 a \ nd (name N or name CA or name C or name O or name CB )) or resid 195 through 213 \ or (resid 214 and (name N or name CA or name C or name O or name CB )) or resid \ 215 through 220 or (resid 221 through 222 and (name N or name CA or name C or n \ ame O or name CB )) or resid 223 or (resid 224 and (name N or name CA or name C \ or name O or name CB )) or resid 225 through 323 or (resid 324 through 327 and ( \ name N or name CA or name C or name O or name CB )) or resid 328 through 329 or \ (resid 330 and (name N or name CA or name C or name O or name CB )) or resid 331 \ through 346 or (resid 347 and (name N or name CA or name C or name O or name CB \ )) or resid 348 through 425 or (resid 426 and (name N or name CA or name C or n \ ame O or name CB )) or resid 427 through 440 or (resid 441 and (name N or name C \ A or name C or name O or name CB )) or resid 442 through 469 or (resid 470 and ( \ name N or name CA or name C or name O or name CB )) or resid 471 through 545 or \ (resid 546 and (name N or name CA or name C or name O or name CB )) or resid 547 \ through 550 or (resid 551 through 552 and (name N or name CA or name C or name \ O or name CB )) or resid 553 through 560 or (resid 561 and (name N or name CA or \ name C or name O or name CB )) or resid 562 through 581 or resid 600 through 67 \ 4 or (resid 675 through 676 and (name N or name CA or name C or name O or name C \ B )) or resid 677 through 681 or (resid 682 and (name N or name CA or name C or \ name O or name CB )) or resid 683 through 696 or (resid 697 through 698 and (nam \ e N or name CA or name C or name O or name CB )) or resid 699 through 711 or (re \ sid 712 and (name N or name CA or name C or name O or name CB )) or resid 713 th \ rough 741 or (resid 742 through 744 and (name N or name CA or name C or name O o \ r name CB )) or resid 745 through 746 or (resid 747 and (name N or name CA or na \ me C or name O or name CB )) or resid 748 through 750 or (resid 751 and (name N \ or name CA or name C or name O or name CB )) or resid 752 through 773 or (resid \ 774 and (name N or name CA or name C or name O or name CB )) or resid 775 throug \ h 799 or (resid 800 and (name N or name CA or name C or name O or name CB )) or \ resid 801 through 804 or (resid 805 through 810 and (name N or name CA or name C \ or name O or name CB )) or resid 811 or (resid 812 and (name N or name CA or na \ me C or name O or name CB )) or resid 813 or (resid 814 and (name N or name CA o \ r name C or name O or name CB )) or resid 815 through 907)) selection = (chain 'D' and ((resid 34 through 35 and (name N or name CA or name C or name O \ or name CB )) or resid 36 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 or (resid 41 and (name N or name CA or na \ me C or name O or name CB )) or resid 42 through 44 or (resid 45 through 57 and \ (name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 th \ rough 62 and (name N or name CA or name C or name O or name CB )) or resid 63 th \ rough 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) o \ r resid 89 or (resid 90 through 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 139 or (resid 140 through 141 an \ d (name N or name CA or name C or name O or name CB )) or resid 142 through 206 \ or (resid 207 through 211 and (name N or name CA or name C or name O or name CB \ )) or resid 212 through 308 or (resid 309 and (name N or name CA or name C or na \ me O or name CB )) or resid 310 through 317 or (resid 318 through 321 and (name \ N or name CA or name C or name O or name CB )) or resid 322 through 369 or (resi \ d 370 through 372 and (name N or name CA or name C or name O or name CB )) or re \ sid 373 through 386 or (resid 387 and (name N or name CA or name C or name O or \ name CB )) or resid 388 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB )) or resid 391 through 393 or (resid 394 through 395 an \ d (name N or name CA or name C or name O or name CB )) or resid 396 through 482 \ or (resid 483 and (name N or name CA or name C or name O or name CB )) or resid \ 484 through 517 or (resid 518 and (name N or name CA or name C or name O or name \ CB )) or resid 519 through 530 or (resid 531 and (name N or name CA or name C o \ r name O or name CB )) or resid 532 through 539 or (resid 540 and (name N or nam \ e CA or name C or name O or name CB )) or resid 541 through 549 or (resid 550 th \ rough 552 and (name N or name CA or name C or name O or name CB )) or resid 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 through 558 or (resid 559 and (name N or name CA or name C or name O or name \ CB )) or resid 560 through 620 or (resid 621 and (name N or name CA or name C o \ r name O or name CB )) or resid 622 through 666 or (resid 667 and (name N or nam \ e CA or name C or name O or name CB )) or resid 668 through 721 or (resid 722 th \ rough 723 and (name N or name CA or name C or name O or name CB )) or resid 724 \ through 807 or (resid 808 through 810 and (name N or name CA or name C or name O \ or name CB )) or resid 811 through 839 or resid 901 through 907)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.060 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.003 0.045 23998 Z= 0.140 Angle : 0.524 10.502 32855 Z= 0.257 Chirality : 0.043 0.279 3980 Planarity : 0.003 0.057 4123 Dihedral : 13.150 112.224 8488 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3175 helix: 2.01 (0.14), residues: 1340 sheet: -0.60 (0.30), residues: 347 loop : -0.58 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.021 0.001 TYR D 287 PHE 0.025 0.001 PHE A 627 TRP 0.048 0.001 TRP D 607 HIS 0.007 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00273 (23952) covalent geometry : angle 0.49882 (32731) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.94492 ( 28) hydrogen bonds : bond 0.15497 ( 1158) hydrogen bonds : angle 6.26437 ( 3372) link_NAG-ASN : bond 0.00566 ( 32) link_NAG-ASN : angle 3.00181 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.810 Fit side-chains REVERT: B 631 MET cc_start: 0.8234 (tpp) cc_final: 0.8030 (tpt) REVERT: C 392 TYR cc_start: 0.8020 (t80) cc_final: 0.7751 (t80) REVERT: C 619 ILE cc_start: 0.8127 (mt) cc_final: 0.7897 (mt) REVERT: C 641 MET cc_start: 0.8805 (tmm) cc_final: 0.8220 (tmm) REVERT: C 818 MET cc_start: 0.5585 (mmp) cc_final: 0.3181 (tmm) REVERT: D 142 MET cc_start: 0.9041 (mmm) cc_final: 0.8753 (mtp) REVERT: D 565 MET cc_start: 0.4092 (ttt) cc_final: 0.3785 (tmm) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1406 time to fit residues: 52.2205 Evaluate side-chains 203 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 147 GLN A 363 GLN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 127 HIS D 615 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.100078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.082214 restraints weight = 85938.903| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.00 r_work: 0.3488 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23998 Z= 0.126 Angle : 0.534 11.728 32855 Z= 0.267 Chirality : 0.043 0.359 3980 Planarity : 0.004 0.059 4123 Dihedral : 6.174 62.114 4063 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.51 % Allowed : 6.55 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3175 helix: 1.87 (0.14), residues: 1357 sheet: -0.80 (0.29), residues: 352 loop : -0.58 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.026 0.001 TYR D 579 PHE 0.026 0.002 PHE B 677 TRP 0.031 0.001 TRP C 608 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00276 (23952) covalent geometry : angle 0.51026 (32731) SS BOND : bond 0.00185 ( 14) SS BOND : angle 1.02700 ( 28) hydrogen bonds : bond 0.03831 ( 1158) hydrogen bonds : angle 4.95239 ( 3372) link_NAG-ASN : bond 0.00793 ( 32) link_NAG-ASN : angle 2.90113 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 634 MET cc_start: 0.8353 (tpt) cc_final: 0.7586 (ptt) REVERT: C 196 GLN cc_start: 0.8188 (mm110) cc_final: 0.7985 (mm110) REVERT: C 392 TYR cc_start: 0.8273 (t80) cc_final: 0.7978 (t80) REVERT: C 641 MET cc_start: 0.8888 (tmm) cc_final: 0.8535 (tmm) REVERT: C 818 MET cc_start: 0.5942 (mmp) cc_final: 0.2968 (tmm) REVERT: D 142 MET cc_start: 0.9064 (mmm) cc_final: 0.8833 (mtp) REVERT: D 562 MET cc_start: 0.8223 (ttp) cc_final: 0.7830 (tmm) REVERT: D 565 MET cc_start: 0.4068 (ttt) cc_final: 0.3754 (tmm) REVERT: D 566 LEU cc_start: 0.7348 (mp) cc_final: 0.7139 (mp) REVERT: D 818 MET cc_start: 0.7936 (mpp) cc_final: 0.7656 (mmt) outliers start: 11 outliers final: 8 residues processed: 215 average time/residue: 0.1396 time to fit residues: 49.7871 Evaluate side-chains 212 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 677 PHE Chi-restraints excluded: chain D residue 702 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 97 optimal weight: 0.0370 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 59 GLN A 358 ASN A 405 GLN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN C 571 HIS D 110 GLN D 767 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.099986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.081600 restraints weight = 83377.053| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.83 r_work: 0.3333 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23998 Z= 0.232 Angle : 0.603 11.391 32855 Z= 0.306 Chirality : 0.046 0.506 3980 Planarity : 0.004 0.057 4123 Dihedral : 5.426 59.111 4063 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.97 % Allowed : 10.52 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3175 helix: 1.46 (0.14), residues: 1363 sheet: -1.04 (0.29), residues: 355 loop : -0.70 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 139 TYR 0.023 0.002 TYR D 287 PHE 0.024 0.002 PHE C 321 TRP 0.025 0.002 TRP C 608 HIS 0.013 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00543 (23952) covalent geometry : angle 0.58233 (32731) SS BOND : bond 0.00411 ( 14) SS BOND : angle 0.93417 ( 28) hydrogen bonds : bond 0.04162 ( 1158) hydrogen bonds : angle 4.87026 ( 3372) link_NAG-ASN : bond 0.00521 ( 32) link_NAG-ASN : angle 2.94502 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 813 MET cc_start: 0.5886 (pmm) cc_final: 0.5672 (pmm) REVERT: A 829 PHE cc_start: 0.8860 (t80) cc_final: 0.8309 (m-80) REVERT: B 430 MET cc_start: 0.6469 (pmm) cc_final: 0.5746 (tmm) REVERT: B 659 TYR cc_start: 0.7617 (t80) cc_final: 0.7157 (t80) REVERT: C 194 VAL cc_start: 0.8944 (m) cc_final: 0.8483 (m) REVERT: C 196 GLN cc_start: 0.8271 (mm110) cc_final: 0.7928 (mm110) REVERT: C 392 TYR cc_start: 0.8323 (t80) cc_final: 0.7909 (t80) REVERT: C 641 MET cc_start: 0.8998 (tmm) cc_final: 0.8540 (tmm) REVERT: D 207 MET cc_start: 0.7279 (tpp) cc_final: 0.7076 (mmm) REVERT: D 386 MET cc_start: 0.8337 (mmm) cc_final: 0.8079 (mmm) REVERT: D 537 MET cc_start: 0.7771 (ttt) cc_final: 0.7423 (ttt) REVERT: D 565 MET cc_start: 0.4141 (ttt) cc_final: 0.3813 (tmm) REVERT: D 566 LEU cc_start: 0.7555 (mp) cc_final: 0.7235 (mt) REVERT: D 671 PHE cc_start: 0.7420 (m-80) cc_final: 0.6761 (m-80) REVERT: D 818 MET cc_start: 0.8224 (mpp) cc_final: 0.8010 (mmt) outliers start: 21 outliers final: 7 residues processed: 220 average time/residue: 0.1396 time to fit residues: 50.5577 Evaluate side-chains 210 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 312 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 81 optimal weight: 40.0000 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 245 optimal weight: 0.7980 chunk 277 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 262 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.099720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080273 restraints weight = 83775.315| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.85 r_work: 0.3367 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23998 Z= 0.122 Angle : 0.524 11.512 32855 Z= 0.261 Chirality : 0.043 0.352 3980 Planarity : 0.004 0.057 4123 Dihedral : 4.921 59.962 4063 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.06 % Allowed : 11.95 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3175 helix: 1.64 (0.14), residues: 1367 sheet: -1.01 (0.29), residues: 341 loop : -0.69 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.023 0.001 TYR D 579 PHE 0.027 0.001 PHE B 638 TRP 0.013 0.001 TRP D 197 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00274 (23952) covalent geometry : angle 0.50198 (32731) SS BOND : bond 0.00175 ( 14) SS BOND : angle 0.90646 ( 28) hydrogen bonds : bond 0.03493 ( 1158) hydrogen bonds : angle 4.63700 ( 3372) link_NAG-ASN : bond 0.00528 ( 32) link_NAG-ASN : angle 2.79353 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.765 Fit side-chains REVERT: B 430 MET cc_start: 0.6556 (pmm) cc_final: 0.5798 (tmm) REVERT: C 194 VAL cc_start: 0.8950 (m) cc_final: 0.8485 (m) REVERT: C 196 GLN cc_start: 0.8280 (mm110) cc_final: 0.7959 (mm110) REVERT: C 392 TYR cc_start: 0.8262 (t80) cc_final: 0.7894 (t80) REVERT: C 563 TRP cc_start: 0.8470 (m100) cc_final: 0.8061 (m100) REVERT: C 576 MET cc_start: 0.8774 (tmm) cc_final: 0.8186 (tmm) REVERT: C 641 MET cc_start: 0.8941 (tmm) cc_final: 0.8290 (tmm) REVERT: C 818 MET cc_start: 0.6066 (mmp) cc_final: 0.3068 (tmm) REVERT: D 386 MET cc_start: 0.8323 (mmm) cc_final: 0.8111 (mmm) REVERT: D 565 MET cc_start: 0.3887 (ttt) cc_final: 0.3667 (tmm) REVERT: D 671 PHE cc_start: 0.7459 (m-80) cc_final: 0.6997 (m-10) REVERT: D 818 MET cc_start: 0.8199 (mpp) cc_final: 0.7988 (mmt) outliers start: 23 outliers final: 14 residues processed: 221 average time/residue: 0.1424 time to fit residues: 51.8376 Evaluate side-chains 209 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.098465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079387 restraints weight = 84030.380| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.90 r_work: 0.3342 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23998 Z= 0.144 Angle : 0.534 11.511 32855 Z= 0.268 Chirality : 0.043 0.401 3980 Planarity : 0.004 0.065 4123 Dihedral : 4.735 59.939 4063 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.43 % Allowed : 13.24 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3175 helix: 1.58 (0.14), residues: 1374 sheet: -1.10 (0.29), residues: 349 loop : -0.71 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.022 0.001 TYR D 579 PHE 0.026 0.001 PHE A 829 TRP 0.030 0.001 TRP C 636 HIS 0.008 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00333 (23952) covalent geometry : angle 0.51337 (32731) SS BOND : bond 0.00217 ( 14) SS BOND : angle 0.86797 ( 28) hydrogen bonds : bond 0.03528 ( 1158) hydrogen bonds : angle 4.58632 ( 3372) link_NAG-ASN : bond 0.00570 ( 32) link_NAG-ASN : angle 2.75619 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 430 MET cc_start: 0.6666 (pmm) cc_final: 0.5835 (tmm) REVERT: B 503 MET cc_start: 0.7853 (ppp) cc_final: 0.7331 (ptp) REVERT: C 194 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8462 (m) REVERT: C 196 GLN cc_start: 0.8266 (mm110) cc_final: 0.7925 (mm110) REVERT: C 392 TYR cc_start: 0.8280 (t80) cc_final: 0.7929 (t80) REVERT: C 563 TRP cc_start: 0.8507 (m100) cc_final: 0.8112 (m100) REVERT: C 641 MET cc_start: 0.8942 (tmm) cc_final: 0.8323 (tmm) REVERT: C 818 MET cc_start: 0.6168 (mmp) cc_final: 0.2932 (tmm) REVERT: D 207 MET cc_start: 0.7324 (tpp) cc_final: 0.7052 (mmm) REVERT: D 386 MET cc_start: 0.8364 (mmm) cc_final: 0.8133 (mmm) REVERT: D 537 MET cc_start: 0.7656 (ttt) cc_final: 0.7355 (ttt) REVERT: D 562 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8000 (tmm) REVERT: D 565 MET cc_start: 0.4178 (ttt) cc_final: 0.3883 (tmm) REVERT: D 566 LEU cc_start: 0.7362 (mp) cc_final: 0.7026 (mp) REVERT: D 671 PHE cc_start: 0.7467 (m-80) cc_final: 0.7017 (m-10) REVERT: D 818 MET cc_start: 0.8258 (mpp) cc_final: 0.8027 (mmt) outliers start: 31 outliers final: 20 residues processed: 229 average time/residue: 0.1354 time to fit residues: 51.4802 Evaluate side-chains 227 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 275 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 chunk 223 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.100072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082427 restraints weight = 83781.146| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.77 r_work: 0.3342 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23998 Z= 0.136 Angle : 0.552 14.572 32855 Z= 0.270 Chirality : 0.043 0.311 3980 Planarity : 0.004 0.057 4123 Dihedral : 4.647 59.318 4063 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.38 % Allowed : 14.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3175 helix: 1.61 (0.14), residues: 1368 sheet: -1.08 (0.29), residues: 349 loop : -0.71 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 139 TYR 0.022 0.001 TYR D 579 PHE 0.030 0.001 PHE B 638 TRP 0.019 0.001 TRP D 607 HIS 0.007 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00312 (23952) covalent geometry : angle 0.52206 (32731) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.85927 ( 28) hydrogen bonds : bond 0.03437 ( 1158) hydrogen bonds : angle 4.53144 ( 3372) link_NAG-ASN : bond 0.00592 ( 32) link_NAG-ASN : angle 3.32024 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 441 ASP cc_start: 0.6406 (p0) cc_final: 0.6182 (p0) REVERT: B 430 MET cc_start: 0.6778 (pmm) cc_final: 0.5959 (tmm) REVERT: C 194 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8476 (m) REVERT: C 196 GLN cc_start: 0.8252 (mm110) cc_final: 0.7901 (mm110) REVERT: C 209 MET cc_start: 0.8436 (mmt) cc_final: 0.8234 (mmm) REVERT: C 392 TYR cc_start: 0.8271 (t80) cc_final: 0.7887 (t80) REVERT: C 563 TRP cc_start: 0.8520 (m100) cc_final: 0.8196 (m100) REVERT: C 641 MET cc_start: 0.8939 (tmm) cc_final: 0.8333 (tmm) REVERT: D 89 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7396 (mpp) REVERT: D 207 MET cc_start: 0.7200 (tpp) cc_final: 0.6917 (mmm) REVERT: D 386 MET cc_start: 0.8373 (mmm) cc_final: 0.8129 (mmm) REVERT: D 537 MET cc_start: 0.7664 (ttt) cc_final: 0.7395 (ttt) REVERT: D 565 MET cc_start: 0.4133 (ttt) cc_final: 0.3922 (tmm) REVERT: D 643 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8372 (mm) REVERT: D 671 PHE cc_start: 0.7452 (m-80) cc_final: 0.6986 (m-10) REVERT: D 818 MET cc_start: 0.8256 (mpp) cc_final: 0.8045 (mmt) outliers start: 30 outliers final: 20 residues processed: 230 average time/residue: 0.1355 time to fit residues: 51.8283 Evaluate side-chains 225 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 193 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 297 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 163 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 477 HIS ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.099917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.081353 restraints weight = 83478.928| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.97 r_work: 0.3360 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23998 Z= 0.107 Angle : 0.557 16.278 32855 Z= 0.267 Chirality : 0.043 0.319 3980 Planarity : 0.004 0.059 4123 Dihedral : 5.922 127.101 4063 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.61 % Allowed : 15.27 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3175 helix: 1.69 (0.14), residues: 1369 sheet: -1.11 (0.28), residues: 359 loop : -0.69 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.022 0.001 TYR D 579 PHE 0.033 0.001 PHE A 829 TRP 0.021 0.001 TRP D 607 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00235 (23952) covalent geometry : angle 0.52652 (32731) SS BOND : bond 0.00155 ( 14) SS BOND : angle 0.87163 ( 28) hydrogen bonds : bond 0.03258 ( 1158) hydrogen bonds : angle 4.45475 ( 3372) link_NAG-ASN : bond 0.00507 ( 32) link_NAG-ASN : angle 3.37294 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8214 (tpt) cc_final: 0.7959 (tpp) REVERT: A 441 ASP cc_start: 0.6473 (p0) cc_final: 0.6270 (p0) REVERT: B 430 MET cc_start: 0.6759 (pmm) cc_final: 0.5978 (tmm) REVERT: B 470 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8157 (mppt) REVERT: B 503 MET cc_start: 0.7672 (ppp) cc_final: 0.6929 (ptp) REVERT: B 561 MET cc_start: 0.8050 (ppp) cc_final: 0.7817 (mtt) REVERT: C 194 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8500 (m) REVERT: C 196 GLN cc_start: 0.8202 (mm110) cc_final: 0.7863 (mm110) REVERT: C 392 TYR cc_start: 0.8257 (t80) cc_final: 0.7939 (t80) REVERT: C 563 TRP cc_start: 0.8520 (m100) cc_final: 0.8208 (m100) REVERT: C 632 LEU cc_start: 0.8387 (pp) cc_final: 0.8114 (tt) REVERT: C 641 MET cc_start: 0.8921 (tmm) cc_final: 0.8359 (tmm) REVERT: C 818 MET cc_start: 0.6123 (mmp) cc_final: 0.3260 (tmm) REVERT: D 89 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: D 207 MET cc_start: 0.7211 (tpp) cc_final: 0.6926 (mmm) REVERT: D 386 MET cc_start: 0.8349 (mmm) cc_final: 0.8120 (mmm) REVERT: D 537 MET cc_start: 0.7671 (ttt) cc_final: 0.7440 (ttt) REVERT: D 562 MET cc_start: 0.8182 (ttt) cc_final: 0.7966 (tmm) REVERT: D 565 MET cc_start: 0.3915 (ttt) cc_final: 0.3581 (tmm) REVERT: D 566 LEU cc_start: 0.7805 (pp) cc_final: 0.7423 (mp) REVERT: D 643 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8372 (mm) REVERT: D 671 PHE cc_start: 0.7452 (m-80) cc_final: 0.7035 (m-10) outliers start: 35 outliers final: 22 residues processed: 227 average time/residue: 0.1362 time to fit residues: 51.9898 Evaluate side-chains 228 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 313 optimal weight: 0.1980 chunk 291 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN D 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.099604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080201 restraints weight = 83390.136| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.48 r_work: 0.3385 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23998 Z= 0.114 Angle : 0.540 13.242 32855 Z= 0.262 Chirality : 0.042 0.305 3980 Planarity : 0.003 0.058 4123 Dihedral : 5.686 120.456 4063 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.57 % Allowed : 15.59 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3175 helix: 1.72 (0.14), residues: 1369 sheet: -1.13 (0.28), residues: 375 loop : -0.68 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.022 0.001 TYR D 579 PHE 0.034 0.001 PHE C 639 TRP 0.016 0.001 TRP B 610 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00257 (23952) covalent geometry : angle 0.51758 (32731) SS BOND : bond 0.00168 ( 14) SS BOND : angle 0.84137 ( 28) hydrogen bonds : bond 0.03235 ( 1158) hydrogen bonds : angle 4.42124 ( 3372) link_NAG-ASN : bond 0.00509 ( 32) link_NAG-ASN : angle 2.86134 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.8095 (mmm) cc_final: 0.7870 (mmp) REVERT: A 639 PHE cc_start: 0.8485 (t80) cc_final: 0.8231 (t80) REVERT: B 430 MET cc_start: 0.6898 (pmm) cc_final: 0.6151 (tmm) REVERT: B 503 MET cc_start: 0.7768 (ppp) cc_final: 0.7120 (ptp) REVERT: B 561 MET cc_start: 0.8075 (ppp) cc_final: 0.7844 (mtt) REVERT: C 392 TYR cc_start: 0.8194 (t80) cc_final: 0.7852 (t80) REVERT: C 563 TRP cc_start: 0.8463 (m100) cc_final: 0.8178 (m100) REVERT: C 632 LEU cc_start: 0.8411 (pp) cc_final: 0.8026 (tt) REVERT: C 641 MET cc_start: 0.8908 (tmm) cc_final: 0.8401 (tmm) REVERT: C 818 MET cc_start: 0.6175 (mmp) cc_final: 0.3187 (tmm) REVERT: D 89 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7156 (mpp) REVERT: D 207 MET cc_start: 0.7155 (tpp) cc_final: 0.6680 (mmm) REVERT: D 386 MET cc_start: 0.8340 (mmm) cc_final: 0.8104 (mmm) REVERT: D 430 MET cc_start: 0.7449 (tmm) cc_final: 0.6893 (tmm) REVERT: D 562 MET cc_start: 0.8092 (ttt) cc_final: 0.7851 (tmm) REVERT: D 565 MET cc_start: 0.3853 (ttt) cc_final: 0.3552 (tmm) REVERT: D 566 LEU cc_start: 0.7716 (pp) cc_final: 0.7246 (mp) REVERT: D 643 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8361 (mm) REVERT: D 671 PHE cc_start: 0.7327 (m-80) cc_final: 0.6948 (m-10) outliers start: 34 outliers final: 22 residues processed: 224 average time/residue: 0.1375 time to fit residues: 51.3335 Evaluate side-chains 224 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 111 optimal weight: 8.9990 chunk 216 optimal weight: 0.0050 chunk 175 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 189 optimal weight: 0.0670 chunk 110 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN C 616 ASN C 650 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.094726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076886 restraints weight = 83258.322| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.66 r_work: 0.3396 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23998 Z= 0.099 Angle : 0.533 13.575 32855 Z= 0.258 Chirality : 0.042 0.305 3980 Planarity : 0.003 0.060 4123 Dihedral : 5.332 114.148 4063 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.25 % Allowed : 16.10 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3175 helix: 1.80 (0.14), residues: 1363 sheet: -1.12 (0.27), residues: 382 loop : -0.58 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.022 0.001 TYR D 579 PHE 0.037 0.001 PHE C 639 TRP 0.017 0.001 TRP B 610 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00215 (23952) covalent geometry : angle 0.51373 (32731) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.84910 ( 28) hydrogen bonds : bond 0.03112 ( 1158) hydrogen bonds : angle 4.34602 ( 3372) link_NAG-ASN : bond 0.00533 ( 32) link_NAG-ASN : angle 2.68218 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8325 (tpp) cc_final: 0.8024 (tpp) REVERT: A 354 MET cc_start: 0.8057 (mmm) cc_final: 0.7848 (mmp) REVERT: B 89 MET cc_start: 0.8113 (mmm) cc_final: 0.7858 (mmm) REVERT: B 430 MET cc_start: 0.6735 (pmm) cc_final: 0.6017 (tmm) REVERT: B 503 MET cc_start: 0.7749 (ppp) cc_final: 0.7084 (ptp) REVERT: B 561 MET cc_start: 0.8091 (ppp) cc_final: 0.7855 (mtt) REVERT: C 392 TYR cc_start: 0.8201 (t80) cc_final: 0.7879 (t80) REVERT: C 563 TRP cc_start: 0.8429 (m100) cc_final: 0.8146 (m100) REVERT: C 632 LEU cc_start: 0.8383 (pp) cc_final: 0.8073 (tt) REVERT: C 641 MET cc_start: 0.8912 (tmm) cc_final: 0.8317 (tmm) REVERT: C 762 MET cc_start: 0.8121 (mtp) cc_final: 0.7843 (mtm) REVERT: C 818 MET cc_start: 0.6050 (mmp) cc_final: 0.3047 (tmm) REVERT: D 89 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7252 (mpp) REVERT: D 207 MET cc_start: 0.7170 (tpp) cc_final: 0.6691 (mmm) REVERT: D 386 MET cc_start: 0.8328 (mmm) cc_final: 0.8078 (mmm) REVERT: D 430 MET cc_start: 0.7367 (tmm) cc_final: 0.6923 (tmm) REVERT: D 562 MET cc_start: 0.7970 (ttt) cc_final: 0.7732 (tmm) REVERT: D 565 MET cc_start: 0.3670 (ttt) cc_final: 0.3399 (tmm) REVERT: D 566 LEU cc_start: 0.7707 (pp) cc_final: 0.7258 (mp) REVERT: D 643 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8356 (mm) REVERT: D 670 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7993 (mmtp) REVERT: D 671 PHE cc_start: 0.7346 (m-80) cc_final: 0.6973 (m-10) outliers start: 27 outliers final: 22 residues processed: 225 average time/residue: 0.1407 time to fit residues: 52.0339 Evaluate side-chains 223 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 129 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 115 optimal weight: 0.0970 chunk 130 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 257 optimal weight: 0.0370 chunk 286 optimal weight: 0.9980 chunk 232 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.098895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079930 restraints weight = 84212.960| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.00 r_work: 0.3372 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23998 Z= 0.102 Angle : 0.535 13.269 32855 Z= 0.259 Chirality : 0.042 0.305 3980 Planarity : 0.003 0.059 4123 Dihedral : 5.263 113.934 4063 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.15 % Allowed : 16.42 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3175 helix: 1.82 (0.14), residues: 1362 sheet: -1.07 (0.28), residues: 378 loop : -0.58 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 233 TYR 0.022 0.001 TYR D 579 PHE 0.038 0.001 PHE C 639 TRP 0.014 0.001 TRP B 610 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00228 (23952) covalent geometry : angle 0.51630 (32731) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.83100 ( 28) hydrogen bonds : bond 0.03107 ( 1158) hydrogen bonds : angle 4.32944 ( 3372) link_NAG-ASN : bond 0.00519 ( 32) link_NAG-ASN : angle 2.64622 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6350 Ramachandran restraints generated. 3175 Oldfield, 0 Emsley, 3175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8348 (tpp) cc_final: 0.7907 (tpp) REVERT: A 354 MET cc_start: 0.8087 (mmm) cc_final: 0.7876 (mmp) REVERT: A 818 MET cc_start: 0.3826 (ttm) cc_final: 0.3522 (ttm) REVERT: B 89 MET cc_start: 0.8124 (mmm) cc_final: 0.7873 (mmm) REVERT: B 430 MET cc_start: 0.6891 (pmm) cc_final: 0.6157 (tmm) REVERT: B 503 MET cc_start: 0.7807 (ppp) cc_final: 0.7220 (ptp) REVERT: B 561 MET cc_start: 0.8123 (ppp) cc_final: 0.7843 (mtt) REVERT: C 392 TYR cc_start: 0.8228 (t80) cc_final: 0.7898 (t80) REVERT: C 563 TRP cc_start: 0.8447 (m100) cc_final: 0.8103 (m100) REVERT: C 632 LEU cc_start: 0.8407 (pp) cc_final: 0.8075 (tt) REVERT: C 641 MET cc_start: 0.8926 (tmm) cc_final: 0.8333 (tmm) REVERT: C 762 MET cc_start: 0.8136 (mtp) cc_final: 0.7867 (mtm) REVERT: C 818 MET cc_start: 0.6044 (mmp) cc_final: 0.3049 (tmm) REVERT: D 89 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7254 (mpp) REVERT: D 207 MET cc_start: 0.7199 (tpp) cc_final: 0.6717 (mmm) REVERT: D 386 MET cc_start: 0.8349 (mmm) cc_final: 0.8088 (mmm) REVERT: D 430 MET cc_start: 0.7361 (tmm) cc_final: 0.6973 (tmm) REVERT: D 562 MET cc_start: 0.7971 (ttt) cc_final: 0.7746 (tmm) REVERT: D 565 MET cc_start: 0.3671 (ttt) cc_final: 0.3380 (tmm) REVERT: D 566 LEU cc_start: 0.7708 (pp) cc_final: 0.7247 (mp) REVERT: D 643 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (mm) REVERT: D 670 LYS cc_start: 0.8319 (mmtp) cc_final: 0.8025 (mmtp) REVERT: D 671 PHE cc_start: 0.7443 (m-80) cc_final: 0.7060 (m-10) outliers start: 25 outliers final: 23 residues processed: 221 average time/residue: 0.1368 time to fit residues: 49.8150 Evaluate side-chains 225 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 840 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 714 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 171 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 306 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 266 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.098285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081480 restraints weight = 81766.664| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.71 r_work: 0.3379 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23998 Z= 0.114 Angle : 0.541 12.658 32855 Z= 0.263 Chirality : 0.042 0.306 3980 Planarity : 0.004 0.058 4123 Dihedral : 5.204 112.470 4063 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.34 % Allowed : 16.14 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3175 helix: 1.77 (0.14), residues: 1369 sheet: -1.08 (0.28), residues: 379 loop : -0.62 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 233 TYR 0.022 0.001 TYR D 579 PHE 0.038 0.001 PHE C 639 TRP 0.016 0.001 TRP B 610 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00261 (23952) covalent geometry : angle 0.52253 (32731) SS BOND : bond 0.00168 ( 14) SS BOND : angle 0.80598 ( 28) hydrogen bonds : bond 0.03151 ( 1158) hydrogen bonds : angle 4.33103 ( 3372) link_NAG-ASN : bond 0.00503 ( 32) link_NAG-ASN : angle 2.63017 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5166.79 seconds wall clock time: 89 minutes 18.31 seconds (5358.31 seconds total)