Starting phenix.real_space_refine on Mon May 4 22:43:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unr_64361/05_2026/9unr_64361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unr_64361/05_2026/9unr_64361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9unr_64361/05_2026/9unr_64361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unr_64361/05_2026/9unr_64361.map" model { file = "/net/cci-nas-00/data/ceres_data/9unr_64361/05_2026/9unr_64361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unr_64361/05_2026/9unr_64361.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.035 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 144 5.16 5 Cl 1 4.86 5 C 15359 2.51 5 N 4009 2.21 5 O 4426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 23939 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 5939 Classifications: {'peptide': 794} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 35, 'TRANS': 758} Chain breaks: 1 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 22, 'HIS:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 260 Chain: "B" Number of atoms: 5725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5725 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 29, 'TRANS': 762} Chain breaks: 1 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 15, 'ARG:plan': 9, 'TRP:plan': 3, 'GLU:plan': 26, 'GLN:plan1': 9, 'PHE:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 389 Chain: "C" Number of atoms: 6085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6085 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 35, 'TRANS': 769} Chain breaks: 1 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 3, 'ASN:plan1': 6, 'ASP:plan': 8, 'HIS:plan': 1, 'GLU:plan': 17, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 202 Chain: "D" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5882 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 29, 'TRANS': 761} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 9, 'HIS:plan': 5, 'GLU:plan': 27, 'ASN:plan1': 6, 'GLN:plan1': 5, 'TYR:plan': 3, 'ARG:plan': 3, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.25 Number of scatterers: 23939 At special positions: 0 Unit cell: (107.61, 147.7, 186.735, 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 144 16.00 O 4426 8.00 N 4009 7.00 C 15359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 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 B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " 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 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 239 " " NAG A 903 " - " ASN A 276 " " NAG A 904 " - " ASN A 350 " " NAG A 905 " - " ASN A 368 " " NAG A 906 " - " ASN A 471 " " NAG A 907 " - " ASN A 771 " " NAG B 901 " - " ASN B 380 " " NAG B 902 " - " ASN B 687 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 239 " " NAG C 903 " - " ASN C 276 " " NAG C 904 " - " ASN C 350 " " NAG C 905 " - " ASN C 368 " " NAG C 906 " - " ASN C 471 " " NAG C 907 " - " ASN C 771 " " NAG D 901 " - " ASN D 341 " " NAG D 902 " - " ASN D 348 " " NAG D 903 " - " ASN D 688 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5954 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 29 sheets defined 45.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.402A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (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 158 removed outlier: 4.163A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.510A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.796A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.832A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.078A 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 525 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.621A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 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 696 Processing helix chain 'A' and resid 699 through 710 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 792 Processing helix chain 'A' and resid 792 through 797 removed outlier: 4.089A pdb=" N GLN A 796 " --> pdb=" O TRP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 839 removed outlier: 3.671A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.600A pdb=" N ARG B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASN B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 4.276A pdb=" N GLY B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 211 through 222 removed outlier: 4.003A pdb=" N THR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.684A pdb=" N SER B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.621A pdb=" N GLU B 427 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 428' Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 557 through 580 removed outlier: 3.647A pdb=" N MET B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 614 removed outlier: 4.590A pdb=" N ILE B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 655 removed outlier: 3.504A pdb=" N GLN B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 708 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 770 through 786 removed outlier: 4.349A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.606A pdb=" N GLU B 790 " --> pdb=" O GLY B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 841 Processing helix chain 'C' and resid 35 through 54 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: 4.536A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.516A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (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 157 removed outlier: 3.904A 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 238 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.523A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.604A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.613A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.991A 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 500 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 549 through 554 removed outlier: 4.079A pdb=" N SER C 553 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.514A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 Processing helix chain 'C' and resid 627 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 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 783 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 843 removed outlier: 4.082A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.558A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.881A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.719A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.613A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.742A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 546 through 551 Processing helix chain 'D' and resid 561 through 581 Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 625 through 652 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 706 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.296A 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 815 through 817 No H-bonds generated for 'chain 'D' and resid 815 through 817' Processing helix chain 'D' and resid 818 through 841 removed outlier: 4.049A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 7.126A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.974A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP A 247 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU A 269 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A 266 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 473 through 477 removed outlier: 3.541A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ILE A 513 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ARG A 763 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.362A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 73 removed outlier: 7.022A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 97 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 37 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.869A pdb=" N PHE B 170 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN B 202 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 172 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 479 removed outlier: 5.773A pdb=" N LEU B 406 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B 478 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE B 408 " --> pdb=" O TYR B 478 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 523 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 421 removed outlier: 3.848A pdb=" N VAL B 434 " --> pdb=" O CYS B 456 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.449A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.449A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 529 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 66 removed outlier: 8.282A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.908A 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: 8.293A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 193 through 197 removed outlier: 4.007A 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: 6.514A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 474 through 477 removed outlier: 7.199A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (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 486 through 489 removed outlier: 3.776A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.718A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N LYS C 534 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N ARG C 755 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N GLN C 536 " --> pdb=" O PHE C 753 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE C 753 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.592A pdb=" N ILE D 37 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA D 100 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE D 40 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.650A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC6, first strand: chain 'D' and resid 475 through 480 Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 419 Processing sheet with id=AC8, first strand: chain 'D' and resid 438 through 440 Processing sheet with id=AC9, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD1, first strand: chain 'D' and resid 683 through 685 removed outlier: 6.709A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 683 through 685 removed outlier: 6.709A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3390 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: 5.23 Time building geometry restraints manager: 2.80 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: 5508 1.33 - 1.45: 5105 1.45 - 1.57: 13598 1.57 - 1.70: 0 1.70 - 1.82: 249 Bond restraints: 24460 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C10 JC9 D 905 " pdb=" N1 JC9 D 905 " ideal model delta sigma weight residual 1.493 1.463 0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG C 906 " pdb=" O5 NAG C 906 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 24455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 32861 1.73 - 3.46: 420 3.46 - 5.19: 38 5.19 - 6.92: 11 6.92 - 8.65: 3 Bond angle restraints: 33333 Sorted by residual: angle pdb=" CB MET D 394 " pdb=" CG MET D 394 " pdb=" SD MET D 394 " ideal model delta sigma weight residual 112.70 121.35 -8.65 3.00e+00 1.11e-01 8.31e+00 angle pdb=" CA ARG C 630 " pdb=" CB ARG C 630 " pdb=" CG ARG C 630 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" C2 JC9 D 905 " pdb=" C1 JC9 D 905 " pdb=" C7 JC9 D 905 " ideal model delta sigma weight residual 115.56 108.13 7.43 3.00e+00 1.11e-01 6.14e+00 angle pdb=" C SER D 617 " pdb=" N VAL D 618 " pdb=" CA VAL D 618 " ideal model delta sigma weight residual 122.13 126.44 -4.31 1.85e+00 2.92e-01 5.42e+00 angle pdb=" CB MET B 828 " pdb=" CG MET B 828 " pdb=" SD MET B 828 " ideal model delta sigma weight residual 112.70 119.66 -6.96 3.00e+00 1.11e-01 5.38e+00 ... (remaining 33328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 13947 22.84 - 45.69: 652 45.69 - 68.53: 107 68.53 - 91.37: 17 91.37 - 114.22: 2 Dihedral angle restraints: 14725 sinusoidal: 5502 harmonic: 9223 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual 93.00 10.02 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 25.41 67.59 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 27.07 65.93 1 1.00e+01 1.00e-02 5.69e+01 ... (remaining 14722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3311 0.056 - 0.113: 589 0.113 - 0.169: 53 0.169 - 0.225: 2 0.225 - 0.281: 1 Chirality restraints: 3956 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG C 905 " pdb=" ND2 ASN C 368 " pdb=" C2 NAG C 905 " pdb=" O5 NAG C 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 471 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 3953 not shown) Planarity restraints: 4228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 77 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO D 78 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 78 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 78 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO A 319 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 104 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.032 5.00e-02 4.00e+02 ... (remaining 4225 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 551 2.71 - 3.25: 24292 3.25 - 3.80: 39614 3.80 - 4.35: 48829 4.35 - 4.90: 82783 Nonbonded interactions: 196069 Sorted by model distance: nonbonded pdb=" O ILE B 116 " pdb=" OG1 THR B 120 " model vdw 2.157 3.040 nonbonded pdb=" O VAL B 339 " pdb=" OG SER B 349 " model vdw 2.210 3.040 nonbonded pdb=" OD2 ASP B 731 " pdb=" OH TYR B 761 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR C 114 " pdb=" O CYS C 308 " model vdw 2.222 3.040 nonbonded pdb=" O GLY A 567 " pdb=" ND1 HIS A 571 " model vdw 2.237 3.120 ... (remaining 196064 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 33 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 130 or (re \ sid 131 and (name N or name CA or name C or name O or name CB )) or resid 132 th \ rough 189 or (resid 190 through 193 and (name N or name CA or name C or name O o \ r name CB )) or resid 194 through 225 or (resid 226 and (name N or name CA or na \ me C or name O or name CB )) or resid 227 through 358 or (resid 359 through 360 \ and (name N or name CA or name C or name O or name CB )) or resid 361 through 42 \ 5 or (resid 426 through 427 and (name N or name CA or name C or name O or name C \ B )) or resid 428 through 440 or (resid 441 and (name N or name CA or name C or \ name O or name CB )) or resid 442 through 474 or (resid 475 and (name N or name \ CA or name C or name O or name CB )) or resid 476 through 487 or (resid 488 thro \ ugh 489 and (name N or name CA or name C or name O or name CB )) or resid 490 th \ rough 496 or (resid 497 and (name N or name CA or name C or name O or name CB )) \ or resid 498 through 550 or (resid 551 through 552 and (name N or name CA or na \ me C or name O or name CB )) or resid 553 through 554 or (resid 555 and (name N \ or name CA or name C or name O or name CB )) or resid 556 through 586 or resid 6 \ 01 through 620 or (resid 621 and (name N or name CA or name C or name O or name \ CB )) or resid 622 through 624 or (resid 625 and (name N or name CA or name C or \ name O or name CB )) or resid 626 through 656 or (resid 657 and (name N or name \ CA or name C or name O or name CB )) or resid 658 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 723 o \ r (resid 724 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 25 through 769 or (resid 770 and (name N or name CA or name C or name O or name \ CB )) or resid 771 through 809 or (resid 810 and (name N or name CA or name C or \ name O or name CB )) or resid 811 through 816 or (resid 817 and (name N or name \ CA or name C or name O or name CB )) or resid 818 through 908)) selection = (chain 'C' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 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 43 or (resid 44 through 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 through 51 or (re \ sid 52 through 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 through 55 or (resid 56 through 58 and (name N or name CA or name C or na \ me O or name CB )) or resid 59 through 72 or (resid 73 and (name N or name CA or \ name C or name O or name CB )) or resid 74 through 96 or (resid 97 and (name N \ or name CA or name C or name O or name CB )) or resid 98 through 101 or (resid 1 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 103 through \ 197 or (resid 198 and (name N or name CA or name C or name O or name CB )) or r \ esid 199 through 201 or (resid 202 and (name N or name CA or name C or name O or \ name CB )) or resid 203 through 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 through 296 or (resid 297 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 302 through 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 through 315 or (resid 316 and (name N or name CA or name C or name O or nam \ e CB )) or resid 317 through 321 or (resid 322 through 323 and (name N or name C \ A or name C or name O or name CB )) or resid 324 through 328 or (resid 329 and ( \ name N or name CA or name C or name O or name CB )) or resid 330 through 338 or \ (resid 339 and (name N or name CA or name C or name O or name CB )) or resid 340 \ through 377 or (resid 378 and (name N or name CA or name C or name O or name CB \ )) or resid 379 through 384 or (resid 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 414 or (resid 415 and (name N or name C \ A or name C or name O or name CB )) or resid 416 through 490 or (resid 491 throu \ gh 492 and (name N or name CA or name C or name O or name CB )) or resid 493 or \ (resid 494 and (name N or name CA or name C or name O or name CB )) or resid 495 \ through 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 673 or (resid 674 and (name N or name CA or name C or n \ ame O or name CB )) or resid 675 through 676 or (resid 677 through 678 and (name \ N or name CA or name C or name O or name CB )) or resid 679 through 706 or (res \ id 707 and (name N or name CA or name C or name O or name CB )) or resid 708 thr \ ough 738 or (resid 739 through 740 and (name N or name CA or name C or name O or \ name CB )) or resid 741 through 742 or (resid 743 and (name N or name CA or nam \ e C or name O or name CB )) or resid 744 through 750 or (resid 751 and (name N o \ r name CA or name C or name O or name CB )) or resid 752 through 763 or (resid 7 \ 64 through 765 and (name N or name CA or name C or name O or name CB )) or resid \ 766 through 785 or (resid 786 and (name N or name CA or name C or name O or nam \ e CB )) or resid 787 through 793 or (resid 794 through 797 and (name N or name C \ A or name C or name O or name CB )) or resid 798 or (resid 799 through 801 and ( \ name N or name CA or name C or name O or name CB )) or resid 802 through 838 or \ (resid 839 and (name N or name CA or name C or name O or name CB )) or resid 901 \ through 908)) } 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: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.400 Find NCS groups from input model: 0.530 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:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.002 0.041 24492 Z= 0.117 Angle : 0.481 8.646 33416 Z= 0.239 Chirality : 0.042 0.281 3956 Planarity : 0.003 0.067 4209 Dihedral : 13.159 114.215 8732 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 3166 helix: 2.23 (0.14), residues: 1337 sheet: -0.36 (0.29), residues: 384 loop : -0.50 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 704 TYR 0.024 0.001 TYR B 286 PHE 0.023 0.001 PHE D 313 TRP 0.031 0.001 TRP A 315 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00241 (24460) covalent geometry : angle 0.47571 (33333) SS BOND : bond 0.00271 ( 13) SS BOND : angle 0.82510 ( 26) hydrogen bonds : bond 0.15049 ( 1160) hydrogen bonds : angle 5.90540 ( 3390) link_NAG-ASN : bond 0.00426 ( 19) link_NAG-ASN : angle 1.74642 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8926 (mm) cc_final: 0.8618 (mt) REVERT: A 233 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7628 (ptp-110) REVERT: A 429 ASP cc_start: 0.7570 (m-30) cc_final: 0.7252 (m-30) REVERT: B 165 TYR cc_start: 0.6564 (m-10) cc_final: 0.6176 (m-80) REVERT: B 200 MET cc_start: 0.4072 (mmm) cc_final: 0.3847 (mmm) REVERT: B 450 MET cc_start: 0.6739 (pmm) cc_final: 0.6453 (pmm) REVERT: B 840 LEU cc_start: 0.7628 (pp) cc_final: 0.7041 (mm) REVERT: C 238 LEU cc_start: 0.8303 (tp) cc_final: 0.7982 (tp) REVERT: C 492 ASN cc_start: 0.8361 (m110) cc_final: 0.7928 (t0) REVERT: C 571 HIS cc_start: 0.7573 (m-70) cc_final: 0.7156 (m-70) REVERT: C 627 PHE cc_start: 0.6145 (m-80) cc_final: 0.5893 (m-80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.6372 time to fit residues: 205.5309 Evaluate side-chains 245 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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: 0.2980 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 616 ASN B 387 HIS B 432 ASN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS C 487 GLN C 521 ASN D 615 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.134687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.109578 restraints weight = 60762.633| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.88 r_work: 0.3537 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24492 Z= 0.129 Angle : 0.523 10.981 33416 Z= 0.265 Chirality : 0.043 0.322 3956 Planarity : 0.004 0.068 4209 Dihedral : 5.146 81.796 3793 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.01 % Allowed : 7.87 % Favored : 91.12 % 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: 0.97 (0.15), residues: 3166 helix: 2.24 (0.14), residues: 1325 sheet: -0.49 (0.27), residues: 417 loop : -0.52 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 337 TYR 0.020 0.001 TYR B 286 PHE 0.028 0.001 PHE A 554 TRP 0.019 0.001 TRP A 315 HIS 0.008 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00299 (24460) covalent geometry : angle 0.51699 (33333) SS BOND : bond 0.00323 ( 13) SS BOND : angle 0.89372 ( 26) hydrogen bonds : bond 0.03618 ( 1160) hydrogen bonds : angle 4.72259 ( 3390) link_NAG-ASN : bond 0.00433 ( 19) link_NAG-ASN : angle 1.90365 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7734 (ttt) cc_final: 0.7513 (ttm) REVERT: A 74 MET cc_start: 0.5020 (tpp) cc_final: 0.4699 (tpp) REVERT: A 183 LEU cc_start: 0.9005 (mm) cc_final: 0.8662 (mt) REVERT: A 209 MET cc_start: 0.8066 (mmm) cc_final: 0.7827 (mmm) REVERT: A 233 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7724 (ptp-110) REVERT: A 429 ASP cc_start: 0.7757 (m-30) cc_final: 0.7428 (m-30) REVERT: A 706 MET cc_start: 0.8106 (mtt) cc_final: 0.7689 (mtm) REVERT: B 54 LEU cc_start: 0.6297 (pp) cc_final: 0.5993 (mp) REVERT: B 165 TYR cc_start: 0.6404 (m-10) cc_final: 0.6053 (m-80) REVERT: B 200 MET cc_start: 0.4561 (mmm) cc_final: 0.4174 (mmm) REVERT: B 255 TRP cc_start: 0.6071 (m100) cc_final: 0.5435 (m100) REVERT: B 338 MET cc_start: 0.6799 (mmt) cc_final: 0.6564 (mmp) REVERT: B 450 MET cc_start: 0.6909 (pmm) cc_final: 0.6641 (pmm) REVERT: B 840 LEU cc_start: 0.7663 (pp) cc_final: 0.7230 (mm) REVERT: C 209 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (mpp) REVERT: C 492 ASN cc_start: 0.8462 (m110) cc_final: 0.8047 (t0) REVERT: C 512 MET cc_start: 0.9040 (ttm) cc_final: 0.8669 (ttm) REVERT: C 627 PHE cc_start: 0.6434 (m-80) cc_final: 0.5886 (m-80) REVERT: C 631 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7014 (mp) REVERT: D 394 MET cc_start: 0.3559 (ppp) cc_final: 0.3326 (ppp) REVERT: D 452 TYR cc_start: 0.7964 (m-80) cc_final: 0.7722 (m-80) REVERT: D 463 ASP cc_start: 0.8118 (m-30) cc_final: 0.7910 (m-30) REVERT: D 562 MET cc_start: 0.4058 (ptt) cc_final: 0.3426 (mtm) REVERT: D 677 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5971 (t80) outliers start: 24 outliers final: 6 residues processed: 271 average time/residue: 0.6363 time to fit residues: 198.3155 Evaluate side-chains 253 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 76 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN B 387 HIS B 693 ASN B 702 HIS B 736 ASN C 70 ASN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 371 HIS C 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106142 restraints weight = 60115.382| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.60 r_work: 0.3424 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 24492 Z= 0.247 Angle : 0.613 11.340 33416 Z= 0.314 Chirality : 0.047 0.329 3956 Planarity : 0.005 0.070 4209 Dihedral : 4.969 68.255 3793 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.56 % Allowed : 11.53 % Favored : 86.92 % 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: 0.35 (0.15), residues: 3166 helix: 1.67 (0.14), residues: 1330 sheet: -0.99 (0.26), residues: 412 loop : -0.73 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 630 TYR 0.024 0.002 TYR D 338 PHE 0.035 0.002 PHE D 313 TRP 0.018 0.002 TRP C 768 HIS 0.009 0.002 HIS C 709 Details of bonding type rmsd covalent geometry : bond 0.00600 (24460) covalent geometry : angle 0.60622 (33333) SS BOND : bond 0.00414 ( 13) SS BOND : angle 1.30747 ( 26) hydrogen bonds : bond 0.04216 ( 1160) hydrogen bonds : angle 4.86106 ( 3390) link_NAG-ASN : bond 0.00425 ( 19) link_NAG-ASN : angle 2.19331 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8329 (mmm) cc_final: 0.7947 (mmt) REVERT: A 233 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7781 (ptp-110) REVERT: A 429 ASP cc_start: 0.7990 (m-30) cc_final: 0.7672 (m-30) REVERT: A 706 MET cc_start: 0.8577 (mtt) cc_final: 0.8152 (mtm) REVERT: B 200 MET cc_start: 0.5088 (mmm) cc_final: 0.4804 (mmm) REVERT: B 255 TRP cc_start: 0.5772 (m100) cc_final: 0.5154 (m100) REVERT: B 288 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.5039 (mm) REVERT: B 338 MET cc_start: 0.6883 (mmt) cc_final: 0.6660 (mmp) REVERT: B 789 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8017 (mp0) REVERT: B 840 LEU cc_start: 0.7768 (pp) cc_final: 0.7456 (mm) REVERT: C 179 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7552 (ttt180) REVERT: C 492 ASN cc_start: 0.8558 (m110) cc_final: 0.8304 (t0) REVERT: C 512 MET cc_start: 0.9095 (ttm) cc_final: 0.8700 (ttm) REVERT: C 627 PHE cc_start: 0.6447 (m-80) cc_final: 0.5956 (m-80) REVERT: C 631 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7495 (mp) REVERT: C 677 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8058 (p0) REVERT: D 191 GLU cc_start: 0.8478 (pp20) cc_final: 0.8216 (mm-30) REVERT: D 239 TYR cc_start: 0.8250 (t80) cc_final: 0.8037 (t80) REVERT: D 269 VAL cc_start: 0.8670 (t) cc_final: 0.8341 (p) REVERT: D 322 TYR cc_start: 0.7086 (m-10) cc_final: 0.6845 (m-10) REVERT: D 557 ASP cc_start: 0.6370 (t0) cc_final: 0.6047 (t0) REVERT: D 562 MET cc_start: 0.4294 (OUTLIER) cc_final: 0.2930 (mtm) REVERT: D 650 LEU cc_start: 0.8039 (mt) cc_final: 0.7769 (mm) REVERT: D 706 MET cc_start: 0.7474 (mtt) cc_final: 0.7211 (mtt) outliers start: 37 outliers final: 12 residues processed: 288 average time/residue: 0.6413 time to fit residues: 213.3600 Evaluate side-chains 271 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 618 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 291 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 267 optimal weight: 0.2980 chunk 264 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 218 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 615 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 = 0.4151 r_free = 0.4151 target = 0.132138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107271 restraints weight = 60444.452| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.85 r_work: 0.3450 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24492 Z= 0.131 Angle : 0.533 11.332 33416 Z= 0.271 Chirality : 0.043 0.330 3956 Planarity : 0.004 0.069 4209 Dihedral : 4.787 82.318 3793 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.81 % Allowed : 14.05 % Favored : 84.14 % 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: 0.50 (0.15), residues: 3166 helix: 1.85 (0.14), residues: 1329 sheet: -1.06 (0.26), residues: 405 loop : -0.67 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 360 TYR 0.020 0.001 TYR D 579 PHE 0.029 0.001 PHE D 671 TRP 0.010 0.001 TRP D 635 HIS 0.016 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00306 (24460) covalent geometry : angle 0.52712 (33333) SS BOND : bond 0.00299 ( 13) SS BOND : angle 0.94571 ( 26) hydrogen bonds : bond 0.03496 ( 1160) hydrogen bonds : angle 4.57789 ( 3390) link_NAG-ASN : bond 0.00404 ( 19) link_NAG-ASN : angle 1.93519 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4700 (tpp) cc_final: 0.4214 (tpp) REVERT: A 183 LEU cc_start: 0.9048 (mm) cc_final: 0.8419 (mp) REVERT: A 233 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7694 (ptp-110) REVERT: A 429 ASP cc_start: 0.7582 (m-30) cc_final: 0.7304 (m-30) REVERT: A 706 MET cc_start: 0.8330 (mtt) cc_final: 0.7806 (mtm) REVERT: B 200 MET cc_start: 0.5087 (mmm) cc_final: 0.4664 (mmm) REVERT: B 255 TRP cc_start: 0.5836 (m100) cc_final: 0.5221 (m100) REVERT: B 338 MET cc_start: 0.6970 (mmt) cc_final: 0.6760 (mmp) REVERT: B 840 LEU cc_start: 0.7753 (pp) cc_final: 0.7443 (mm) REVERT: C 512 MET cc_start: 0.9013 (ttm) cc_final: 0.8739 (ttm) REVERT: C 627 PHE cc_start: 0.6276 (m-80) cc_final: 0.5809 (m-80) REVERT: C 631 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7342 (mp) REVERT: C 785 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8197 (mmt) REVERT: D 239 TYR cc_start: 0.8245 (t80) cc_final: 0.8031 (t80) REVERT: D 557 ASP cc_start: 0.6274 (t0) cc_final: 0.5906 (t0) REVERT: D 562 MET cc_start: 0.4005 (OUTLIER) cc_final: 0.3494 (mtm) REVERT: D 677 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.5662 (t80) REVERT: D 706 MET cc_start: 0.6906 (mtt) cc_final: 0.6681 (mtt) outliers start: 43 outliers final: 15 residues processed: 283 average time/residue: 0.6406 time to fit residues: 209.1492 Evaluate side-chains 270 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 240 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN C 371 HIS D 672 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.130511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105947 restraints weight = 60103.368| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.97 r_work: 0.3410 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24492 Z= 0.226 Angle : 0.592 11.933 33416 Z= 0.301 Chirality : 0.045 0.328 3956 Planarity : 0.004 0.069 4209 Dihedral : 4.906 74.001 3793 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.15 % Allowed : 15.94 % Favored : 81.91 % 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: 0.25 (0.15), residues: 3166 helix: 1.60 (0.14), residues: 1337 sheet: -1.18 (0.27), residues: 363 loop : -0.79 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 360 TYR 0.021 0.002 TYR D 579 PHE 0.036 0.002 PHE D 313 TRP 0.013 0.001 TRP C 768 HIS 0.006 0.002 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00549 (24460) covalent geometry : angle 0.58497 (33333) SS BOND : bond 0.00488 ( 13) SS BOND : angle 1.28625 ( 26) hydrogen bonds : bond 0.03885 ( 1160) hydrogen bonds : angle 4.72093 ( 3390) link_NAG-ASN : bond 0.00390 ( 19) link_NAG-ASN : angle 2.10368 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8956 (mm) cc_final: 0.8384 (mp) REVERT: A 233 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7711 (ptp-110) REVERT: A 326 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7278 (mtt) REVERT: A 429 ASP cc_start: 0.7880 (m-30) cc_final: 0.7546 (m-30) REVERT: A 706 MET cc_start: 0.8543 (mtt) cc_final: 0.8036 (mtm) REVERT: B 54 LEU cc_start: 0.6674 (pp) cc_final: 0.6411 (mp) REVERT: B 200 MET cc_start: 0.5198 (mmm) cc_final: 0.4962 (mmm) REVERT: B 255 TRP cc_start: 0.5575 (m100) cc_final: 0.4981 (m100) REVERT: B 288 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5171 (mm) REVERT: B 840 LEU cc_start: 0.7825 (pp) cc_final: 0.7489 (mm) REVERT: C 87 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8452 (t) REVERT: C 627 PHE cc_start: 0.6395 (m-80) cc_final: 0.5890 (m-80) REVERT: C 631 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7440 (mp) REVERT: C 635 VAL cc_start: 0.8541 (t) cc_final: 0.8169 (m) REVERT: C 785 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8145 (mmt) REVERT: D 239 TYR cc_start: 0.8294 (t80) cc_final: 0.8058 (t80) REVERT: D 269 VAL cc_start: 0.8883 (t) cc_final: 0.8588 (p) REVERT: D 534 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8222 (mt) REVERT: D 557 ASP cc_start: 0.6644 (t0) cc_final: 0.6262 (t0) REVERT: D 562 MET cc_start: 0.4331 (OUTLIER) cc_final: 0.3622 (mtm) outliers start: 51 outliers final: 19 residues processed: 294 average time/residue: 0.6100 time to fit residues: 207.9758 Evaluate side-chains 284 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 785 MET Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 618 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 288 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 27 optimal weight: 0.0010 chunk 3 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS B 223 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS ** D 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.130912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106511 restraints weight = 60200.104| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.00 r_work: 0.3427 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24492 Z= 0.152 Angle : 0.559 14.249 33416 Z= 0.282 Chirality : 0.044 0.328 3956 Planarity : 0.004 0.068 4209 Dihedral : 4.445 48.730 3793 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.10 % Allowed : 17.04 % Favored : 80.86 % 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: 0.40 (0.15), residues: 3166 helix: 1.75 (0.14), residues: 1335 sheet: -1.16 (0.27), residues: 373 loop : -0.72 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 156 TYR 0.019 0.001 TYR D 579 PHE 0.030 0.002 PHE D 671 TRP 0.012 0.001 TRP D 635 HIS 0.012 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00361 (24460) covalent geometry : angle 0.55351 (33333) SS BOND : bond 0.00279 ( 13) SS BOND : angle 1.03896 ( 26) hydrogen bonds : bond 0.03577 ( 1160) hydrogen bonds : angle 4.57955 ( 3390) link_NAG-ASN : bond 0.00392 ( 19) link_NAG-ASN : angle 1.96082 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4807 (tpp) cc_final: 0.4310 (tpp) REVERT: A 183 LEU cc_start: 0.8946 (mm) cc_final: 0.8380 (mp) REVERT: A 233 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7731 (ptp-110) REVERT: A 326 MET cc_start: 0.7562 (mtp) cc_final: 0.7328 (mtt) REVERT: A 429 ASP cc_start: 0.7856 (m-30) cc_final: 0.7531 (m-30) REVERT: B 200 MET cc_start: 0.5282 (mmm) cc_final: 0.4911 (mmm) REVERT: B 255 TRP cc_start: 0.5717 (m100) cc_final: 0.5102 (m100) REVERT: B 288 LEU cc_start: 0.5401 (mm) cc_final: 0.4963 (mm) REVERT: B 840 LEU cc_start: 0.7981 (pp) cc_final: 0.7665 (mm) REVERT: C 87 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8448 (t) REVERT: C 627 PHE cc_start: 0.6409 (m-80) cc_final: 0.6114 (m-80) REVERT: C 635 VAL cc_start: 0.8504 (t) cc_final: 0.8136 (m) REVERT: D 191 GLU cc_start: 0.8473 (pp20) cc_final: 0.8239 (mm-30) REVERT: D 239 TYR cc_start: 0.8299 (t80) cc_final: 0.8068 (t80) REVERT: D 557 ASP cc_start: 0.6623 (t0) cc_final: 0.6279 (t0) REVERT: D 562 MET cc_start: 0.4268 (OUTLIER) cc_final: 0.2999 (mtm) REVERT: D 677 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6541 (t80) outliers start: 50 outliers final: 23 residues processed: 290 average time/residue: 0.6168 time to fit residues: 207.8191 Evaluate side-chains 283 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 264 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 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 293 HIS A 449 HIS A 616 ASN B 223 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105176 restraints weight = 59409.237| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.75 r_work: 0.3447 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24492 Z= 0.135 Angle : 0.550 16.064 33416 Z= 0.278 Chirality : 0.043 0.326 3956 Planarity : 0.004 0.068 4209 Dihedral : 4.100 35.533 3793 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.81 % Allowed : 18.09 % Favored : 80.10 % 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: 0.45 (0.15), residues: 3166 helix: 1.81 (0.14), residues: 1336 sheet: -1.12 (0.27), residues: 365 loop : -0.73 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 360 TYR 0.018 0.001 TYR D 579 PHE 0.034 0.002 PHE B 652 TRP 0.015 0.001 TRP D 635 HIS 0.012 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00321 (24460) covalent geometry : angle 0.54437 (33333) SS BOND : bond 0.00242 ( 13) SS BOND : angle 0.99230 ( 26) hydrogen bonds : bond 0.03436 ( 1160) hydrogen bonds : angle 4.49531 ( 3390) link_NAG-ASN : bond 0.00401 ( 19) link_NAG-ASN : angle 1.91715 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4781 (tpp) cc_final: 0.4305 (tpp) REVERT: A 183 LEU cc_start: 0.8925 (mm) cc_final: 0.8363 (mt) REVERT: A 233 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7700 (ptp-110) REVERT: A 326 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7301 (mtt) REVERT: A 429 ASP cc_start: 0.7848 (m-30) cc_final: 0.7518 (m-30) REVERT: A 501 MET cc_start: 0.9116 (mtm) cc_final: 0.8912 (mtm) REVERT: B 255 TRP cc_start: 0.5689 (m100) cc_final: 0.5086 (m100) REVERT: B 288 LEU cc_start: 0.5440 (mm) cc_final: 0.5011 (mm) REVERT: B 358 HIS cc_start: 0.7968 (m90) cc_final: 0.7730 (m170) REVERT: B 561 MET cc_start: 0.5194 (tmm) cc_final: 0.4670 (tmt) REVERT: B 840 LEU cc_start: 0.7963 (pp) cc_final: 0.7699 (mm) REVERT: C 87 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8415 (t) REVERT: C 237 MET cc_start: 0.8437 (ttp) cc_final: 0.8112 (ptt) REVERT: C 512 MET cc_start: 0.9101 (ttm) cc_final: 0.8789 (ttm) REVERT: C 627 PHE cc_start: 0.6238 (m-80) cc_final: 0.6014 (m-80) REVERT: C 635 VAL cc_start: 0.8495 (t) cc_final: 0.8133 (m) REVERT: D 191 GLU cc_start: 0.8473 (pp20) cc_final: 0.8120 (mm-30) REVERT: D 239 TYR cc_start: 0.8299 (t80) cc_final: 0.8064 (t80) REVERT: D 565 MET cc_start: 0.7106 (pp-130) cc_final: 0.6860 (pp-130) REVERT: D 677 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6430 (t80) outliers start: 43 outliers final: 23 residues processed: 291 average time/residue: 0.6271 time to fit residues: 211.1071 Evaluate side-chains 283 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 181 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 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 293 HIS A 449 HIS ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.131284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.105725 restraints weight = 59065.830| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.03 r_work: 0.3433 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24492 Z= 0.143 Angle : 0.573 19.146 33416 Z= 0.288 Chirality : 0.043 0.324 3956 Planarity : 0.004 0.067 4209 Dihedral : 4.035 35.158 3793 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.85 % Allowed : 18.26 % Favored : 79.89 % 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: 0.41 (0.15), residues: 3166 helix: 1.77 (0.14), residues: 1331 sheet: -1.13 (0.27), residues: 367 loop : -0.74 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 360 TYR 0.017 0.001 TYR D 579 PHE 0.031 0.002 PHE A 654 TRP 0.015 0.001 TRP D 635 HIS 0.012 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00340 (24460) covalent geometry : angle 0.56795 (33333) SS BOND : bond 0.00261 ( 13) SS BOND : angle 1.00987 ( 26) hydrogen bonds : bond 0.03510 ( 1160) hydrogen bonds : angle 4.49113 ( 3390) link_NAG-ASN : bond 0.00399 ( 19) link_NAG-ASN : angle 1.91395 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4850 (tpp) cc_final: 0.4410 (tpp) REVERT: A 183 LEU cc_start: 0.9024 (mm) cc_final: 0.8452 (mt) REVERT: A 233 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7704 (ptp-110) REVERT: A 326 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7219 (mtt) REVERT: A 429 ASP cc_start: 0.7638 (m-30) cc_final: 0.7347 (m-30) REVERT: A 501 MET cc_start: 0.9067 (mtm) cc_final: 0.8861 (mtm) REVERT: B 54 LEU cc_start: 0.6964 (pp) cc_final: 0.6712 (mp) REVERT: B 255 TRP cc_start: 0.5813 (m100) cc_final: 0.5187 (m100) REVERT: B 288 LEU cc_start: 0.5265 (mm) cc_final: 0.4914 (mm) REVERT: B 358 HIS cc_start: 0.7947 (m90) cc_final: 0.7735 (m90) REVERT: B 561 MET cc_start: 0.5069 (tmm) cc_final: 0.4617 (tmt) REVERT: B 840 LEU cc_start: 0.7961 (pp) cc_final: 0.7711 (mm) REVERT: C 87 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8297 (t) REVERT: C 627 PHE cc_start: 0.6208 (m-80) cc_final: 0.5941 (m-80) REVERT: C 635 VAL cc_start: 0.8458 (t) cc_final: 0.8120 (m) REVERT: D 239 TYR cc_start: 0.8294 (t80) cc_final: 0.8066 (t80) REVERT: D 565 MET cc_start: 0.7026 (pp-130) cc_final: 0.6797 (pp-130) REVERT: D 677 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5614 (t80) outliers start: 44 outliers final: 25 residues processed: 284 average time/residue: 0.6159 time to fit residues: 202.7928 Evaluate side-chains 279 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 57 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 34 optimal weight: 0.0020 chunk 300 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 449 HIS ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105841 restraints weight = 60033.585| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.73 r_work: 0.3444 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24492 Z= 0.120 Angle : 0.574 20.972 33416 Z= 0.286 Chirality : 0.043 0.323 3956 Planarity : 0.004 0.067 4209 Dihedral : 3.907 34.328 3793 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.77 % Allowed : 18.72 % Favored : 79.51 % 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: 0.48 (0.15), residues: 3166 helix: 1.82 (0.14), residues: 1331 sheet: -1.08 (0.28), residues: 367 loop : -0.69 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 360 TYR 0.017 0.001 TYR D 579 PHE 0.036 0.001 PHE B 652 TRP 0.019 0.001 TRP D 635 HIS 0.012 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00279 (24460) covalent geometry : angle 0.56906 (33333) SS BOND : bond 0.00214 ( 13) SS BOND : angle 0.93738 ( 26) hydrogen bonds : bond 0.03354 ( 1160) hydrogen bonds : angle 4.44110 ( 3390) link_NAG-ASN : bond 0.00422 ( 19) link_NAG-ASN : angle 1.85443 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5088 (tpp) cc_final: 0.4739 (tpp) REVERT: A 181 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 183 LEU cc_start: 0.9001 (mm) cc_final: 0.8434 (mt) REVERT: A 233 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7704 (ptp-110) REVERT: A 326 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7224 (mtt) REVERT: A 429 ASP cc_start: 0.7653 (m-30) cc_final: 0.7358 (m-30) REVERT: A 501 MET cc_start: 0.9074 (mtm) cc_final: 0.8839 (mtm) REVERT: A 621 GLU cc_start: 0.7422 (pp20) cc_final: 0.6222 (pp20) REVERT: B 255 TRP cc_start: 0.5649 (m100) cc_final: 0.5020 (m100) REVERT: B 288 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4919 (mm) REVERT: B 338 MET cc_start: 0.7095 (mmt) cc_final: 0.6869 (mmp) REVERT: B 840 LEU cc_start: 0.8005 (pp) cc_final: 0.7768 (mm) REVERT: C 87 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8284 (t) REVERT: C 512 MET cc_start: 0.9111 (ttm) cc_final: 0.8581 (ttm) REVERT: C 635 VAL cc_start: 0.8438 (t) cc_final: 0.8081 (m) REVERT: C 655 LEU cc_start: 0.4958 (pp) cc_final: 0.4690 (pp) REVERT: C 744 CYS cc_start: 0.6005 (p) cc_final: 0.5455 (p) REVERT: D 239 TYR cc_start: 0.8270 (t80) cc_final: 0.8014 (t80) REVERT: D 562 MET cc_start: 0.4705 (mtm) cc_final: 0.4047 (mtm) REVERT: D 677 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.5517 (t80) outliers start: 42 outliers final: 21 residues processed: 281 average time/residue: 0.5770 time to fit residues: 188.9371 Evaluate side-chains 275 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 209 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 187 optimal weight: 0.0770 chunk 129 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 449 HIS ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.131647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106059 restraints weight = 59931.789| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.75 r_work: 0.3468 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24492 Z= 0.133 Angle : 0.592 21.834 33416 Z= 0.295 Chirality : 0.044 0.321 3956 Planarity : 0.004 0.067 4209 Dihedral : 3.895 34.533 3793 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.26 % Allowed : 19.35 % Favored : 79.39 % 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: 0.48 (0.15), residues: 3166 helix: 1.83 (0.14), residues: 1331 sheet: -1.12 (0.27), residues: 392 loop : -0.67 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 360 TYR 0.016 0.001 TYR D 579 PHE 0.037 0.002 PHE A 654 TRP 0.019 0.001 TRP D 635 HIS 0.014 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00314 (24460) covalent geometry : angle 0.58685 (33333) SS BOND : bond 0.00321 ( 13) SS BOND : angle 0.94313 ( 26) hydrogen bonds : bond 0.03408 ( 1160) hydrogen bonds : angle 4.46901 ( 3390) link_NAG-ASN : bond 0.00398 ( 19) link_NAG-ASN : angle 1.88780 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5033 (tpp) cc_final: 0.4714 (tpp) REVERT: A 183 LEU cc_start: 0.8949 (mm) cc_final: 0.8409 (mt) REVERT: A 233 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7716 (ptp-110) REVERT: A 326 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7309 (mtt) REVERT: A 429 ASP cc_start: 0.7815 (m-30) cc_final: 0.7478 (m-30) REVERT: A 501 MET cc_start: 0.9112 (mtm) cc_final: 0.8879 (mtm) REVERT: A 621 GLU cc_start: 0.7545 (pp20) cc_final: 0.6303 (pp20) REVERT: A 706 MET cc_start: 0.8554 (mtp) cc_final: 0.8262 (mtm) REVERT: B 255 TRP cc_start: 0.5642 (m100) cc_final: 0.5023 (m100) REVERT: B 288 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.4967 (mm) REVERT: B 296 LEU cc_start: 0.8045 (mm) cc_final: 0.7766 (mp) REVERT: B 561 MET cc_start: 0.5033 (tmm) cc_final: 0.4671 (tmt) REVERT: B 623 LYS cc_start: 0.8067 (mppt) cc_final: 0.7689 (mmtm) REVERT: C 87 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (t) REVERT: C 472 PHE cc_start: 0.7644 (t80) cc_final: 0.7341 (t80) REVERT: C 635 VAL cc_start: 0.8541 (t) cc_final: 0.8184 (m) REVERT: C 655 LEU cc_start: 0.4954 (pp) cc_final: 0.4686 (pp) REVERT: D 239 TYR cc_start: 0.8349 (t80) cc_final: 0.8097 (t80) REVERT: D 562 MET cc_start: 0.4703 (mtm) cc_final: 0.4014 (mtm) REVERT: D 677 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6088 (t80) outliers start: 30 outliers final: 23 residues processed: 272 average time/residue: 0.6285 time to fit residues: 197.5549 Evaluate side-chains 273 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 677 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 134 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 288 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 449 HIS ** A 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 387 HIS ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.130984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105380 restraints weight = 59548.366| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.08 r_work: 0.3438 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24492 Z= 0.148 Angle : 0.600 14.655 33416 Z= 0.300 Chirality : 0.044 0.321 3956 Planarity : 0.004 0.067 4209 Dihedral : 3.942 35.012 3793 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.43 % Allowed : 19.10 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3166 helix: 1.74 (0.14), residues: 1338 sheet: -1.10 (0.27), residues: 378 loop : -0.71 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 156 TYR 0.016 0.001 TYR D 579 PHE 0.052 0.002 PHE A 654 TRP 0.018 0.001 TRP D 635 HIS 0.014 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00356 (24460) covalent geometry : angle 0.59492 (33333) SS BOND : bond 0.00296 ( 13) SS BOND : angle 0.98805 ( 26) hydrogen bonds : bond 0.03471 ( 1160) hydrogen bonds : angle 4.49294 ( 3390) link_NAG-ASN : bond 0.00389 ( 19) link_NAG-ASN : angle 1.90900 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9298.60 seconds wall clock time: 158 minutes 57.49 seconds (9537.49 seconds total)