Starting phenix.real_space_refine on Thu Mar 5 00:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b1c_11983/03_2026/7b1c_11983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b1c_11983/03_2026/7b1c_11983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b1c_11983/03_2026/7b1c_11983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b1c_11983/03_2026/7b1c_11983.map" model { file = "/net/cci-nas-00/data/ceres_data/7b1c_11983/03_2026/7b1c_11983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b1c_11983/03_2026/7b1c_11983.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 10788 2.51 5 N 2929 2.21 5 O 3394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17197 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 5064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5064 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PTRANS': 33, 'TRANS': 716} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 970 Unresolved non-hydrogen angles: 1228 Unresolved non-hydrogen dihedrals: 780 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLU:plan': 28, 'PHE:plan': 12, 'ASN:plan1': 22, 'ASP:plan': 27, 'ARG:plan': 20, 'HIS:plan': 11, 'TYR:plan': 3, 'GLN:plan1': 17, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 584 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 4943 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 318} Link IDs: {'PTRANS': 33, 'TRANS': 718} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1108 Unresolved non-hydrogen angles: 1393 Unresolved non-hydrogen dihedrals: 888 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 19, 'HIS:plan': 11, 'ARG:plan': 21, 'ASN:plan1': 30, 'GLN:plan1': 22, 'PHE:plan': 10, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 629 Chain: "D" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 675 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 513 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5530 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 488 Unresolved non-hydrogen angles: 611 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 19, 'PHE:plan': 3, 'ASN:plan1': 14, 'ARG:plan': 12, 'HIS:plan': 7, 'GLN:plan1': 15, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 339 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.74, per 1000 atoms: 0.28 Number of scatterers: 17197 At special positions: 0 Unit cell: (102.92, 138.61, 198.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 3394 8.00 N 2929 7.00 C 10788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 561 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 622 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 767 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 783 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 46 " distance=2.02 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 561 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 622 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 783 " distance=2.03 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 95 " distance=2.02 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS P 59 " distance=2.02 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS P 94 " distance=1.96 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 65 " distance=2.03 Simple disulfide: pdb=" SG CYS P 47 " - pdb=" SG CYS P 95 " distance=2.02 Simple disulfide: pdb=" SG CYS P 56 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 57 " distance=2.04 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 767 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 783 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 801 " - " ASN A 687 " " NAG B 801 " - " ASN B 525 " " NAG C 801 " - " ASN C 521 " " NAG E 1 " - " ASN C 151 " " NAG F 1 " - " ASN B 634 " " NAG G 1 " - " ASN C 194 " " NAG H 1 " - " ASN C 481 " " NAG I 1 " - " ASN A 521 " " NAG J 1 " - " ASN A 194 " " NAG K 1 " - " ASN A 151 " " NAG L 1 " - " ASN A 481 " " NAG M 1 " - " ASN A 634 " " NAG N 1 " - " ASN B 481 " " NAG O 1 " - " ASN B 521 " " NAG Q 1 " - " ASN B 194 " " NAG R 1 " - " ASN B 151 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 814.3 milliseconds 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 29 sheets defined 14.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 117 through 120 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.660A pdb=" N GLY C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.813A pdb=" N LEU C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 4.041A pdb=" N PHE C 237 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 238 " --> pdb=" O GLY C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.099A pdb=" N LYS C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 463 removed outlier: 3.624A pdb=" N ASP C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 463 " --> pdb=" O ILE C 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 463' Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.946A pdb=" N VAL C 470 " --> pdb=" O THR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'C' and resid 514 through 517 Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.740A pdb=" N GLY C 637 " --> pdb=" O ASN C 634 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C 638 " --> pdb=" O CYS C 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 716 through 723 Processing helix chain 'C' and resid 742 through 751 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.928A pdb=" N ARG C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 778 Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.283A pdb=" N SER A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.661A pdb=" N PHE A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 263 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 4.041A pdb=" N ASN A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.363A pdb=" N LEU A 334 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.546A pdb=" N LEU A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 4.070A pdb=" N PHE A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.515A pdb=" N VAL A 470 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 716 through 723 removed outlier: 4.212A pdb=" N LEU A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'P' and resid 49 through 52 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.582A pdb=" N TYR B 142 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.314A pdb=" N GLY B 168 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.186A pdb=" N PHE B 237 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.785A pdb=" N PHE B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 650 through 655 removed outlier: 3.538A pdb=" N ASP B 655 " --> pdb=" O GLN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 724 removed outlier: 3.925A pdb=" N GLN B 722 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 724 " --> pdb=" O ALA B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.835A pdb=" N PHE B 748 " --> pdb=" O PRO B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 759 Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 780 through 784 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 47 removed outlier: 5.969A pdb=" N VAL C 74 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL C 102 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 152 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 175 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 200 through 201 removed outlier: 6.988A pdb=" N LEU C 246 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR C 273 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU C 248 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 297 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 438 through 440 removed outlier: 7.585A pdb=" N ILE C 439 " --> pdb=" O HIS C 478 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU C 477 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 501 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 548 " --> pdb=" O GLN C 579 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN C 581 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 550 " --> pdb=" O ASN C 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 510 through 512 removed outlier: 6.764A pdb=" N LEU C 511 " --> pdb=" O LEU C 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 586 through 587 Processing sheet with id=AA6, first strand: chain 'C' and resid 766 through 767 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA8, first strand: chain 'A' and resid 64 through 68 removed outlier: 8.147A pdb=" N VAL A 102 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 101 " --> pdb=" O ASN A 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.502A pdb=" N ILE A 136 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 160 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.617A pdb=" N VAL A 201 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 246 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N THR A 273 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 248 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 297 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 343 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 368 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 367 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 438 through 439 removed outlier: 5.953A pdb=" N ILE A 439 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 502 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 501 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 551 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 548 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 447 through 448 removed outlier: 3.897A pdb=" N LEU A 448 " --> pdb=" O SER A 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.301A pdb=" N LEU A 511 " --> pdb=" O LEU A 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 623 through 625 removed outlier: 3.573A pdb=" N THR A 630 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 659 " --> pdb=" O GLN A 682 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 708 removed outlier: 3.744A pdb=" N SER A 735 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 17 Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 99 removed outlier: 5.244A pdb=" N LYS D 86 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA D 76 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN D 88 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU D 74 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU D 90 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG D 72 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS D 70 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 98 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 20.206A pdb=" N GLN D 67 " --> pdb=" O CYS P 47 " (cutoff:3.500A) removed outlier: 17.137A pdb=" N CYS P 47 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N PHE D 69 " --> pdb=" O GLU P 45 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLU P 45 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR D 71 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 66 through 73 removed outlier: 6.416A pdb=" N LYS P 66 " --> pdb=" O CYS P 95 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS P 95 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU P 68 " --> pdb=" O SER P 93 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER P 93 " --> pdb=" O LEU P 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.554A pdb=" N ASP B 67 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 74 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL B 102 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 128 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA B 155 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR B 129 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 176 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 198 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 246 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR B 273 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 248 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 94 through 95 removed outlier: 7.078A pdb=" N GLY B 94 " --> pdb=" O ALA B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AC5, first strand: chain 'B' and resid 390 through 392 removed outlier: 3.652A pdb=" N LEU B 391 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 415 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 500 through 502 Processing sheet with id=AC7, first strand: chain 'B' and resid 511 through 512 removed outlier: 7.155A pdb=" N LEU B 511 " --> pdb=" O LEU B 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 556 through 557 removed outlier: 6.429A pdb=" N ARG B 586 " --> pdb=" O LEU B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 623 through 625 Processing sheet with id=AD1, first strand: chain 'B' and resid 682 through 683 Processing sheet with id=AD2, first strand: chain 'B' and resid 738 through 739 278 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5251 1.34 - 1.47: 3697 1.47 - 1.60: 8406 1.60 - 1.72: 0 1.72 - 1.85: 103 Bond restraints: 17457 Sorted by residual: bond pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta sigma weight residual 1.461 1.495 -0.034 8.70e-03 1.32e+04 1.51e+01 bond pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta sigma weight residual 1.460 1.493 -0.033 8.60e-03 1.35e+04 1.48e+01 bond pdb=" N ILE B 698 " pdb=" CA ILE B 698 " ideal model delta sigma weight residual 1.461 1.496 -0.035 9.10e-03 1.21e+04 1.47e+01 bond pdb=" N ILE B 454 " pdb=" CA ILE B 454 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.04e-02 9.25e+03 1.43e+01 bond pdb=" N THR B 466 " pdb=" CA THR B 466 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.30e+01 ... (remaining 17452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 22059 2.28 - 4.57: 1744 4.57 - 6.85: 118 6.85 - 9.14: 16 9.14 - 11.42: 3 Bond angle restraints: 23940 Sorted by residual: angle pdb=" N LEU C 198 " pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 113.20 102.90 10.30 1.21e+00 6.83e-01 7.25e+01 angle pdb=" N ILE C 341 " pdb=" CA ILE C 341 " pdb=" C ILE C 341 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.52e+01 angle pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 108.35 99.91 8.44 1.32e+00 5.74e-01 4.09e+01 angle pdb=" N GLN A 472 " pdb=" CA GLN A 472 " pdb=" C GLN A 472 " ideal model delta sigma weight residual 114.56 106.60 7.96 1.27e+00 6.20e-01 3.93e+01 angle pdb=" N PHE C 60 " pdb=" CA PHE C 60 " pdb=" C PHE C 60 " ideal model delta sigma weight residual 113.18 105.33 7.85 1.33e+00 5.65e-01 3.48e+01 ... (remaining 23935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 10433 21.92 - 43.84: 477 43.84 - 65.76: 108 65.76 - 87.68: 49 87.68 - 109.60: 25 Dihedral angle restraints: 11092 sinusoidal: 3882 harmonic: 7210 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 104 " pdb=" CB CYS A 104 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 783 " pdb=" CB CYS B 783 " ideal model delta sinusoidal sigma weight residual -86.00 -171.28 85.28 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS C 561 " pdb=" SG CYS C 561 " pdb=" SG CYS C 608 " pdb=" CB CYS C 608 " ideal model delta sinusoidal sigma weight residual -86.00 -171.10 85.10 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 11089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2644 0.110 - 0.220: 372 0.220 - 0.330: 44 0.330 - 0.440: 1 0.440 - 0.551: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-02 2.50e+03 7.58e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.25e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.69e+00 ... (remaining 3059 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.283 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG N 1 " -0.061 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.010 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.415 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.071 2.00e-02 2.50e+03 5.90e-02 4.34e+01 pdb=" C7 NAG N 2 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.048 2.00e-02 2.50e+03 3.92e-02 1.93e+01 pdb=" C7 NAG L 1 " 0.014 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.062 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.008 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 701 2.69 - 3.24: 18665 3.24 - 3.80: 27183 3.80 - 4.35: 35673 4.35 - 4.90: 55971 Nonbonded interactions: 138193 Sorted by model distance: nonbonded pdb=" OD1 ASP B 75 " pdb=" N PHE B 76 " model vdw 2.139 3.120 nonbonded pdb=" OD1 ASP A 109 " pdb=" NH1 ARG A 110 " model vdw 2.149 3.120 nonbonded pdb=" OG SER B 726 " pdb=" O HIS B 728 " model vdw 2.218 3.040 nonbonded pdb=" O ASP A 716 " pdb=" OG1 THR A 719 " model vdw 2.219 3.040 nonbonded pdb=" O THR C 597 " pdb=" N LEU C 601 " model vdw 2.233 3.120 ... (remaining 138188 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 35 through 36 or (resid 37 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 50 or (resid 51 through 53 and (name N or name CA or name C or name O or name C \ B )) or resid 54 through 58 or (resid 59 through 61 and (name N or name CA or na \ me C or name O or name CB )) or resid 62 through 68 or (resid 69 through 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 79 or ( \ resid 80 through 81 and (name N or name CA or name C or name O or name CB )) or \ resid 82 through 83 or (resid 84 and (name N or name CA or name C or name O or n \ ame CB )) or resid 85 through 86 or (resid 87 through 88 and (name N or name CA \ or name C or name O or name CB )) or resid 89 through 94 or (resid 95 through 98 \ and (name N or name CA or name C or name O or name CB )) or resid 99 through 10 \ 2 or (resid 103 and (name N or name CA or name C or name O or name CB )) or resi \ d 104 through 118 or (resid 119 through 123 and (name N or name CA or name C or \ name O or name CB )) or resid 124 through 131 or (resid 132 through 134 and (nam \ e N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) \ or resid 142 or (resid 143 through 144 and (name N or name CA or name C or name \ O or name CB )) or (resid 145 through 147 and (name N or name CA or name C or n \ ame O or name CB )) or resid 148 through 158 or (resid 159 and (name N or name C \ A or name C or name O or name CB )) or resid 160 or (resid 161 through 166 and ( \ name N or name CA or name C or name O or name CB )) or resid 167 through 168 or \ (resid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 \ through 181 or (resid 182 and (name N or name CA or name C or name O or name CB \ )) or resid 183 through 184 or (resid 185 and (name N or name CA or name C or n \ ame O or name CB )) or resid 186 through 187 or (resid 188 and (name N or name C \ A or name C or name O or name CB )) or resid 189 through 191 or (resid 192 and ( \ name N or name CA or name C or name O or name CB )) or resid 193 through 194 or \ (resid 195 through 198 and (name N or name CA or name C or name O or name CB )) \ or resid 199 through 201 or (resid 202 through 203 and (name N or name CA or nam \ e C or name O or name CB )) or resid 204 through 223 or (resid 224 and (name N o \ r name CA or name C or name O or name CB )) or resid 225 through 250 or (resid 2 \ 51 through 252 and (name N or name CA or name C or name O or name CB )) or resid \ 253 through 272 or (resid 273 and (name N or name CA or name C or name O or nam \ e CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or nam \ e C or name O or name CB )) or resid 294 or (resid 295 through 324 and (name N o \ r name CA or name C or name O or name CB )) or resid 325 through 448 or (resid 4 \ 49 through 480 and (name N or name CA or name C or name O or name CB )) or resid \ 481 through 489 or (resid 490 and (name N or name CA or name C or name O or nam \ e CB )) or resid 491 through 495 or (resid 496 through 497 and (name N or name C \ A or name C or name O or name CB )) or resid 498 through 507 or (resid 508 and ( \ name N or name CA or name C or name O or name CB )) or resid 509 through 537 or \ (resid 538 through 539 and (name N or name CA or name C or name O or name CB )) \ or resid 540 or (resid 541 through 543 and (name N or name CA or name C or name \ O or name CB )) or resid 544 through 561 or (resid 562 through 563 and (name N o \ r name CA or name C or name O or name CB )) or resid 564 or (resid 565 and (name \ N or name CA or name C or name O or name CB )) or resid 566 or (resid 567 throu \ gh 569 and (name N or name CA or name C or name O or name CB )) or resid 570 or \ (resid 571 through 576 and (name N or name CA or name C or name O or name CB )) \ or resid 577 through 580 or (resid 581 and (name N or name CA or name C or name \ O or name CB )) or resid 582 or (resid 583 through 584 and (name N or name CA or \ name C or name O or name CB )) or resid 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 or (resid 588 and (name N or na \ me CA or name C or name O or name CB )) or resid 589 through 591 or (resid 592 t \ hrough 594 and (name N or name CA or name C or name O or name CB )) or resid 595 \ through 596 or (resid 597 and (name N or name CA or name C or name O or name CB \ )) or resid 598 or (resid 599 through 606 and (name N or name CA or name C or n \ ame O or name CB )) or resid 607 through 608 or (resid 609 through 615 and (name \ N or name CA or name C or name O or name CB )) or resid 616 through 618 or (res \ id 619 and (name N or name CA or name C or name O or name CB )) or resid 620 thr \ ough 625 or (resid 626 through 636 and (name N or name CA or name C or name O or \ name CB )) or (resid 637 through 740 and (name N or name CA or name C or name O \ or name CB )) or resid 741 through 774 or (resid 775 through 776 and (name N or \ name CA or name C or name O or name CB )) or resid 777 or (resid 778 through 78 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 783 through \ 801)) selection = (chain 'B' and (resid 35 through 50 or (resid 51 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 62 or (resid 63 and (na \ me N or name CA or name C or name O or name CB )) or resid 64 through 72 or (res \ id 73 and (name N or name CA or name C or name O or name CB )) or resid 74 or (r \ esid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 or \ (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 78 t \ hrough 86 or (resid 87 through 88 and (name N or name CA or name C or name O or \ name CB )) or resid 89 through 94 or (resid 95 through 98 and (name N or name CA \ or name C or name O or name CB )) or resid 99 through 102 or (resid 103 and (na \ me N or name CA or name C or name O or name CB )) or resid 104 through 118 or (r \ esid 119 through 123 and (name N or name CA or name C or name O or name CB )) or \ resid 124 through 131 or (resid 132 through 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 or (resid 136 through 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 140 or (resid 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 or (resid \ 143 through 144 and (name N or name CA or name C or name O or name CB )) or res \ id 145 or (resid 146 through 147 and (name N or name CA or name C or name O or n \ ame CB )) or resid 148 through 158 or (resid 159 and (name N or name CA or name \ C or name O or name CB )) or resid 160 or (resid 161 through 166 and (name N or \ name CA or name C or name O or name CB )) or resid 167 through 168 or (resid 169 \ and (name N or name CA or name C or name O or name CB )) or resid 170 or (resid \ 171 through 173 and (name N or name CA or name C or name O or name CB )) or res \ id 174 through 177 or (resid 178 and (name N or name CA or name C or name O or n \ ame CB )) or resid 179 through 180 or (resid 181 through 182 and (name N or name \ CA or name C or name O or name CB )) or resid 183 through 187 or (resid 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 191 o \ r (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 93 through 194 or (resid 195 through 198 and (name N or name CA or name C or nam \ e O or name CB )) or resid 199 through 205 or (resid 206 through 209 and (name N \ or name CA or name C or name O or name CB )) or resid 210 through 211 or (resid \ 212 through 214 and (name N or name CA or name C or name O or name CB )) or res \ id 215 through 216 or (resid 217 through 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 or (resid 220 through 221 and (name N or name \ CA or name C or name O or name CB )) or resid 222 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 or (resid 230 \ and (name N or name CA or name C or name O or name CB )) or resid 231 through 2 \ 32 or (resid 233 through 234 and (name N or name CA or name C or name O or name \ CB )) or resid 235 or (resid 236 and (name N or name CA or name C or name O or n \ ame CB )) or resid 237 or (resid 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 or (resid 240 through 245 and (name N or name CA or n \ ame C or name O or name CB )) or resid 246 through 248 or (resid 249 and (name N \ or name CA or name C or name O or name CB )) or resid 250 or (resid 251 through \ 252 and (name N or name CA or name C or name O or name CB )) or resid 253 or (r \ esid 254 through 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 or (resid 257 through 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 264 or (resid 265 through 266 and (name N or \ name CA or name C or name O or name CB )) or resid 267 through 268 or (resid 269 \ and (name N or name CA or name C or name O or name CB )) or resid 270 through 2 \ 72 or (resid 273 and (name N or name CA or name C or name O or name CB )) or res \ id 274 through 278 or (resid 279 and (name N or name CA or name C or name O or n \ ame CB )) or resid 280 through 281 or (resid 282 and (name N or name CA or name \ C or name O or name CB )) or resid 283 through 285 or (resid 286 through 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 or (resid 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 2 \ 92 or (resid 293 and (name N or name CA or name C or name O or name CB )) or res \ id 294 through 295 or (resid 296 through 324 and (name N or name CA or name C or \ name O or name CB )) or resid 325 or (resid 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 or (resid 328 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 or (resid 337 through 338 \ and (name N or name CA or name C or name O or name CB )) or resid 339 or (resid \ 340 through 345 and (name N or name CA or name C or name O or name CB )) or res \ id 346 or (resid 347 through 431 and (name N or name CA or name C or name O or n \ ame CB )) or resid 432 or (resid 433 and (name N or name CA or name C or name O \ or name CB )) or resid 434 or (resid 435 and (name N or name CA or name C or nam \ e O or name CB )) or resid 436 or (resid 437 and (name N or name CA or name C or \ name O or name CB )) or resid 438 through 448 or (resid 449 through 480 and (na \ me N or name CA or name C or name O or name CB )) or resid 481 or (resid 482 thr \ ough 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 489 or (resid 490 and (name N or name CA or name C or name O or name CB ) \ ) or resid 491 through 496 or (resid 497 and (name N or name CA or name C or nam \ e O or name CB )) or resid 498 through 541 or (resid 542 through 543 and (name N \ or name CA or name C or name O or name CB )) or resid 544 through 567 or (resid \ 568 through 569 and (name N or name CA or name C or name O or name CB )) or res \ id 570 through 598 or (resid 599 through 606 and (name N or name CA or name C or \ name O or name CB )) or resid 607 through 609 or (resid 610 through 615 and (na \ me N or name CA or name C or name O or name CB )) or resid 616 through 624 or (r \ esid 625 through 636 and (name N or name CA or name C or name O or name CB )) or \ (resid 637 through 740 and (name N or name CA or name C or name O or name CB )) \ or resid 741 or (resid 742 and (name N or name CA or name C or name O or name C \ B )) or resid 743 through 745 or (resid 746 through 766 and (name N or name CA o \ r name C or name O or name CB )) or resid 767 through 769 or (resid 770 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 771 through 776 and ( \ name N or name CA or name C or name O or name CB )) or resid 777 or (resid 778 t \ hrough 782 and (name N or name CA or name C or name O or name CB )) or resid 783 \ or resid 801)) selection = (chain 'C' and (resid 35 through 37 or (resid 38 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 52 or (resid 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 58 or (resid 59 through 61 and (name N or name CA or name C or nam \ e O or name CB )) or resid 62 or (resid 63 and (name N or name CA or name C or n \ ame O or name CB )) or resid 64 through 74 or (resid 75 and (name N or name CA o \ r name C or name O or name CB )) or resid 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 95 or (resid 96 through 9 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 99 through 1 \ 70 or (resid 171 through 173 and (name N or name CA or name C or name O or name \ CB )) or resid 174 through 177 or (resid 178 and (name N or name CA or name C or \ name O or name CB )) or resid 179 through 184 or (resid 185 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 201 or (resid 202 thr \ ough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 t \ hrough 205 or (resid 206 through 209 and (name N or name CA or name C or name O \ or name CB )) or resid 210 through 211 or (resid 212 through 214 and (name N or \ name CA or name C or name O or name CB )) or resid 215 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 or (resid \ 220 through 221 and (name N or name CA or name C or name O or name CB )) or res \ id 222 through 232 or (resid 233 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 and (name N or name CA or name \ C or name O or name CB )) or resid 237 or (resid 238 and (name N or name CA or n \ ame C or name O or name CB )) or resid 239 or (resid 240 through 245 and (name N \ or name CA or name C or name O or name CB )) or resid 246 through 248 or (resid \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 throu \ gh 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 or (resid 257 through 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 264 or (resid 265 through 266 and (name N or \ name CA or name C or name O or name CB )) or resid 267 through 268 or (resid 269 \ and (name N or name CA or name C or name O or name CB )) or resid 270 through 2 \ 74 or (resid 275 and (name N or name CA or name C or name O or name CB )) or res \ id 276 through 278 or (resid 279 and (name N or name CA or name C or name O or n \ ame CB )) or resid 280 through 285 or (resid 286 through 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 or (resid 290 and (name N or \ name CA or name C or name O or name CB )) or resid 291 through 294 or (resid 295 \ through 324 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 25 or (resid 326 and (name N or name CA or name C or name O or name CB )) or res \ id 327 or (resid 328 through 335 and (name N or name CA or name C or name O or n \ ame CB )) or resid 336 or (resid 337 through 338 and (name N or name CA or name \ C or name O or name CB )) or resid 339 or (resid 340 through 345 and (name N or \ name CA or name C or name O or name CB )) or resid 346 or (resid 347 through 431 \ and (name N or name CA or name C or name O or name CB )) or resid 432 or (resid \ 433 and (name N or name CA or name C or name O or name CB )) or resid 434 or (r \ esid 435 and (name N or name CA or name C or name O or name CB )) or resid 436 o \ r (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 38 through 464 or (resid 465 through 480 and (name N or name CA or name C or nam \ e O or name CB )) or resid 481 or (resid 482 through 486 and (name N or name CA \ or name C or name O or name CB )) or resid 487 through 495 or (resid 496 through \ 497 and (name N or name CA or name C or name O or name CB )) or resid 498 throu \ gh 507 or (resid 508 and (name N or name CA or name C or name O or name CB )) or \ resid 509 through 561 or (resid 562 through 563 and (name N or name CA or name \ C or name O or name CB )) or resid 564 or (resid 565 and (name N or name CA or n \ ame C or name O or name CB )) or resid 566 or (resid 567 through 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 or (resid 571 through \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 throu \ gh 580 or (resid 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 or (resid 583 through 584 and (name N or name CA or name C or name O \ or name CB )) or resid 585 or (resid 586 and (name N or name CA or name C or nam \ e O or name CB )) or resid 587 or (resid 588 and (name N or name CA or name C or \ name O or name CB )) or resid 589 through 591 or (resid 592 through 594 and (na \ me N or name CA or name C or name O or name CB )) or resid 595 through 596 or (r \ esid 597 and (name N or name CA or name C or name O or name CB )) or resid 598 t \ hrough 600 or (resid 601 through 606 and (name N or name CA or name C or name O \ or name CB )) or resid 607 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB )) or resid 620 through 783 or resid 801)) } ncs_group { reference = (chain 'D' and (resid 7 through 19 or (resid 20 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 or (resid 42 through 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 54 or (resi \ d 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or re \ sid 59 through 62 or (resid 63 through 64 and (name N or name CA or name C or na \ me O or name CB )) or resid 65 or (resid 66 through 83 and (name N or name CA or \ name C or name O or name CB )) or resid 84 or (resid 85 through 89 and (name N \ or name CA or name C or name O or name CB )) or resid 90 through 92 or (resid 93 \ and (name N or name CA or name C or name O or name CB )) or resid 94 through 97 \ )) selection = (chain 'P' and (resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 97)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.810 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.010 0.100 17526 Z= 0.664 Angle : 1.270 25.332 24113 Z= 0.839 Chirality : 0.076 0.551 3062 Planarity : 0.007 0.244 3139 Dihedral : 15.531 109.601 6262 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.17 % Allowed : 4.01 % Favored : 93.82 % 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: -2.29 (0.16), residues: 2430 helix: -1.34 (0.35), residues: 202 sheet: -2.26 (0.25), residues: 415 loop : -1.43 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.015 0.002 TYR C 440 PHE 0.016 0.002 PHE A 143 TRP 0.018 0.002 TRP A 491 HIS 0.006 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00971 (17457) covalent geometry : angle 1.23310 (23940) SS BOND : bond 0.01271 ( 34) SS BOND : angle 3.70385 ( 68) hydrogen bonds : bond 0.26658 ( 278) hydrogen bonds : angle 10.14710 ( 657) link_BETA1-4 : bond 0.02456 ( 19) link_BETA1-4 : angle 3.95092 ( 57) link_NAG-ASN : bond 0.00807 ( 16) link_NAG-ASN : angle 3.67011 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 189 PHE cc_start: 0.8216 (m-80) cc_final: 0.7852 (m-10) REVERT: C 294 LEU cc_start: 0.9167 (tp) cc_final: 0.8787 (tp) REVERT: B 245 MET cc_start: 0.7914 (tmm) cc_final: 0.6446 (tmm) outliers start: 32 outliers final: 8 residues processed: 102 average time/residue: 0.1146 time to fit residues: 19.3688 Evaluate side-chains 46 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 551 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 444 ASN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 348 ASN B 372 ASN B 385 ASN B 427 GLN B 444 ASN ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.052886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.040621 restraints weight = 147923.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.041605 restraints weight = 77820.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.042323 restraints weight = 50418.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.042828 restraints weight = 37106.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.043164 restraints weight = 29833.797| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17526 Z= 0.119 Angle : 0.690 8.870 24113 Z= 0.338 Chirality : 0.045 0.315 3062 Planarity : 0.003 0.039 3139 Dihedral : 10.722 69.308 3258 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.02 % Allowed : 7.74 % Favored : 91.24 % 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: -1.91 (0.17), residues: 2430 helix: -0.93 (0.35), residues: 210 sheet: -2.12 (0.23), residues: 456 loop : -1.09 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 586 TYR 0.011 0.001 TYR C 440 PHE 0.016 0.001 PHE B 76 TRP 0.019 0.002 TRP B 491 HIS 0.004 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00245 (17457) covalent geometry : angle 0.66413 (23940) SS BOND : bond 0.00325 ( 34) SS BOND : angle 1.14917 ( 68) hydrogen bonds : bond 0.04683 ( 278) hydrogen bonds : angle 7.52483 ( 657) link_BETA1-4 : bond 0.00875 ( 19) link_BETA1-4 : angle 3.01033 ( 57) link_NAG-ASN : bond 0.00637 ( 16) link_NAG-ASN : angle 2.50583 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: C 189 PHE cc_start: 0.7365 (m-80) cc_final: 0.7045 (m-10) REVERT: C 212 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7201 (pp) REVERT: C 245 MET cc_start: 0.7531 (tpp) cc_final: 0.7045 (tpp) REVERT: C 285 PHE cc_start: 0.8516 (m-80) cc_final: 0.8114 (m-10) REVERT: A 442 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8643 (mp10) outliers start: 15 outliers final: 3 residues processed: 56 average time/residue: 0.1063 time to fit residues: 10.2589 Evaluate side-chains 43 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 442 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 20 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 192 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 50.0000 overall best weight: 3.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN C 482 ASN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN B 54 HIS ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.050831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.038028 restraints weight = 148941.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.039006 restraints weight = 81441.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.039668 restraints weight = 53772.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.040072 restraints weight = 40419.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.040406 restraints weight = 33429.609| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 17526 Z= 0.209 Angle : 0.709 9.049 24113 Z= 0.343 Chirality : 0.046 0.311 3062 Planarity : 0.004 0.036 3139 Dihedral : 7.741 59.736 3248 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.15 % Allowed : 10.94 % Favored : 87.91 % 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: -1.91 (0.17), residues: 2430 helix: -0.89 (0.35), residues: 218 sheet: -2.10 (0.23), residues: 439 loop : -1.13 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 249 TYR 0.022 0.002 TYR A 79 PHE 0.012 0.002 PHE C 55 TRP 0.005 0.001 TRP A 491 HIS 0.004 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00453 (17457) covalent geometry : angle 0.68608 (23940) SS BOND : bond 0.00384 ( 34) SS BOND : angle 1.05066 ( 68) hydrogen bonds : bond 0.04107 ( 278) hydrogen bonds : angle 6.60576 ( 657) link_BETA1-4 : bond 0.00741 ( 19) link_BETA1-4 : angle 2.81883 ( 57) link_NAG-ASN : bond 0.00671 ( 16) link_NAG-ASN : angle 2.62043 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.717 Fit side-chains REVERT: A 441 MET cc_start: 0.8239 (ptt) cc_final: 0.7990 (ptt) REVERT: B 146 MET cc_start: 0.8462 (mmm) cc_final: 0.7722 (tmm) REVERT: B 245 MET cc_start: 0.7609 (tmm) cc_final: 0.7254 (tmm) REVERT: B 762 MET cc_start: 0.6563 (mmt) cc_final: 0.6028 (mmt) outliers start: 17 outliers final: 7 residues processed: 54 average time/residue: 0.0963 time to fit residues: 9.4670 Evaluate side-chains 42 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 55 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 76 optimal weight: 0.0010 chunk 221 optimal weight: 8.9990 chunk 70 optimal weight: 0.0040 chunk 194 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 174 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 132 optimal weight: 50.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.051168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.039022 restraints weight = 148529.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.040149 restraints weight = 87024.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.040268 restraints weight = 51470.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.040454 restraints weight = 47940.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.040504 restraints weight = 41048.356| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17526 Z= 0.133 Angle : 0.618 8.984 24113 Z= 0.301 Chirality : 0.044 0.315 3062 Planarity : 0.003 0.039 3139 Dihedral : 6.955 59.571 3246 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.15 % Allowed : 12.23 % Favored : 86.62 % 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: -1.74 (0.17), residues: 2430 helix: -0.59 (0.36), residues: 212 sheet: -1.97 (0.23), residues: 438 loop : -1.03 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.010 0.001 TYR A 79 PHE 0.010 0.001 PHE A 285 TRP 0.004 0.001 TRP B 491 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00288 (17457) covalent geometry : angle 0.59514 (23940) SS BOND : bond 0.00329 ( 34) SS BOND : angle 0.95047 ( 68) hydrogen bonds : bond 0.03249 ( 278) hydrogen bonds : angle 6.19351 ( 657) link_BETA1-4 : bond 0.00779 ( 19) link_BETA1-4 : angle 2.65932 ( 57) link_NAG-ASN : bond 0.00501 ( 16) link_NAG-ASN : angle 2.37344 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.444 Fit side-chains REVERT: C 498 MET cc_start: 0.8973 (tmm) cc_final: 0.8638 (tmm) REVERT: A 441 MET cc_start: 0.8225 (ptt) cc_final: 0.7917 (mpp) REVERT: B 146 MET cc_start: 0.8339 (mmm) cc_final: 0.7677 (mmm) REVERT: B 245 MET cc_start: 0.7583 (tmm) cc_final: 0.7301 (tmm) REVERT: B 762 MET cc_start: 0.6562 (mmt) cc_final: 0.6152 (mmt) outliers start: 17 outliers final: 9 residues processed: 53 average time/residue: 0.0818 time to fit residues: 8.1279 Evaluate side-chains 45 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.0980 chunk 212 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 103 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.050876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.037359 restraints weight = 147423.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.038388 restraints weight = 78417.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.039090 restraints weight = 52108.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.039522 restraints weight = 39415.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.039857 restraints weight = 32799.173| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17526 Z= 0.116 Angle : 0.594 8.840 24113 Z= 0.288 Chirality : 0.043 0.329 3062 Planarity : 0.003 0.032 3139 Dihedral : 6.532 58.392 3246 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.09 % Allowed : 13.32 % Favored : 85.60 % 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: -1.63 (0.17), residues: 2430 helix: -0.42 (0.37), residues: 212 sheet: -1.88 (0.24), residues: 441 loop : -0.97 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 586 TYR 0.010 0.001 TYR A 79 PHE 0.012 0.001 PHE A 285 TRP 0.004 0.001 TRP B 739 HIS 0.002 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00251 (17457) covalent geometry : angle 0.57225 (23940) SS BOND : bond 0.00281 ( 34) SS BOND : angle 0.87037 ( 68) hydrogen bonds : bond 0.02988 ( 278) hydrogen bonds : angle 5.82455 ( 657) link_BETA1-4 : bond 0.00742 ( 19) link_BETA1-4 : angle 2.46490 ( 57) link_NAG-ASN : bond 0.00505 ( 16) link_NAG-ASN : angle 2.35927 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.655 Fit side-chains REVERT: C 270 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8435 (tt) REVERT: A 441 MET cc_start: 0.8607 (ptt) cc_final: 0.8191 (mpp) REVERT: B 146 MET cc_start: 0.8674 (mmm) cc_final: 0.7872 (mmm) REVERT: B 245 MET cc_start: 0.7692 (tmm) cc_final: 0.7166 (tmm) REVERT: B 762 MET cc_start: 0.6439 (mmt) cc_final: 0.6030 (mmt) outliers start: 16 outliers final: 10 residues processed: 53 average time/residue: 0.0949 time to fit residues: 9.2911 Evaluate side-chains 47 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 548 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 211 optimal weight: 0.8980 chunk 226 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 240 optimal weight: 30.0000 chunk 221 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 139 optimal weight: 40.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.050245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.038247 restraints weight = 146070.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.039270 restraints weight = 86128.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.039353 restraints weight = 54263.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.039521 restraints weight = 46203.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.039532 restraints weight = 41436.881| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17526 Z= 0.243 Angle : 0.699 10.351 24113 Z= 0.339 Chirality : 0.045 0.321 3062 Planarity : 0.003 0.037 3139 Dihedral : 6.847 59.862 3246 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.56 % Allowed : 13.59 % Favored : 84.85 % 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: -1.86 (0.17), residues: 2430 helix: -0.74 (0.35), residues: 219 sheet: -1.99 (0.24), residues: 430 loop : -1.14 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 625 TYR 0.019 0.002 TYR A 79 PHE 0.012 0.002 PHE A 261 TRP 0.008 0.001 TRP D 31 HIS 0.004 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00521 (17457) covalent geometry : angle 0.67948 (23940) SS BOND : bond 0.00384 ( 34) SS BOND : angle 1.00400 ( 68) hydrogen bonds : bond 0.03522 ( 278) hydrogen bonds : angle 5.98784 ( 657) link_BETA1-4 : bond 0.00724 ( 19) link_BETA1-4 : angle 2.43547 ( 57) link_NAG-ASN : bond 0.00651 ( 16) link_NAG-ASN : angle 2.57850 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.661 Fit side-chains REVERT: C 219 LEU cc_start: 0.8468 (mt) cc_final: 0.8182 (mt) REVERT: C 245 MET cc_start: 0.7967 (tpp) cc_final: 0.7669 (tpp) REVERT: C 270 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8581 (tt) REVERT: C 498 MET cc_start: 0.9053 (tmm) cc_final: 0.8764 (tmm) REVERT: B 146 MET cc_start: 0.8462 (mmm) cc_final: 0.7683 (mmm) REVERT: B 245 MET cc_start: 0.7734 (tmm) cc_final: 0.7386 (tmm) REVERT: B 762 MET cc_start: 0.6479 (mmt) cc_final: 0.6071 (mmt) outliers start: 23 outliers final: 14 residues processed: 58 average time/residue: 0.0870 time to fit residues: 9.5323 Evaluate side-chains 49 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 152 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.050503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.038550 restraints weight = 143863.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.039827 restraints weight = 83382.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.039774 restraints weight = 48309.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.039922 restraints weight = 48378.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.039914 restraints weight = 39475.061| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17526 Z= 0.161 Angle : 0.625 9.721 24113 Z= 0.303 Chirality : 0.043 0.321 3062 Planarity : 0.003 0.037 3139 Dihedral : 6.630 59.622 3246 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.29 % Allowed : 13.93 % Favored : 84.78 % 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: -1.73 (0.17), residues: 2430 helix: -0.42 (0.37), residues: 214 sheet: -1.97 (0.24), residues: 426 loop : -1.07 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 475 TYR 0.013 0.001 TYR A 79 PHE 0.013 0.001 PHE B 656 TRP 0.004 0.001 TRP A 491 HIS 0.002 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00350 (17457) covalent geometry : angle 0.60491 (23940) SS BOND : bond 0.00345 ( 34) SS BOND : angle 0.94804 ( 68) hydrogen bonds : bond 0.03096 ( 278) hydrogen bonds : angle 5.78272 ( 657) link_BETA1-4 : bond 0.00728 ( 19) link_BETA1-4 : angle 2.41630 ( 57) link_NAG-ASN : bond 0.00521 ( 16) link_NAG-ASN : angle 2.37567 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8377 (mt) cc_final: 0.8091 (mt) REVERT: C 498 MET cc_start: 0.9101 (tmm) cc_final: 0.8799 (tmm) REVERT: B 146 MET cc_start: 0.8246 (mmm) cc_final: 0.7473 (mmm) REVERT: B 245 MET cc_start: 0.7643 (tmm) cc_final: 0.7342 (tmm) REVERT: B 762 MET cc_start: 0.6375 (mmt) cc_final: 0.6009 (mmt) outliers start: 19 outliers final: 12 residues processed: 54 average time/residue: 0.0887 time to fit residues: 9.0361 Evaluate side-chains 47 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 548 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 111 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 0.0010 chunk 61 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 151 optimal weight: 8.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.050638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.038900 restraints weight = 143898.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.039760 restraints weight = 83749.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.039863 restraints weight = 56138.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.040071 restraints weight = 49443.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.040073 restraints weight = 42871.843| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17526 Z= 0.130 Angle : 0.608 9.714 24113 Z= 0.294 Chirality : 0.043 0.326 3062 Planarity : 0.003 0.034 3139 Dihedral : 6.428 58.550 3246 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.29 % Allowed : 14.20 % Favored : 84.51 % 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: -1.64 (0.17), residues: 2430 helix: -0.17 (0.37), residues: 208 sheet: -1.88 (0.24), residues: 430 loop : -1.03 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 475 TYR 0.012 0.001 TYR A 79 PHE 0.011 0.001 PHE B 656 TRP 0.005 0.001 TRP B 739 HIS 0.002 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00283 (17457) covalent geometry : angle 0.58716 (23940) SS BOND : bond 0.00327 ( 34) SS BOND : angle 1.05997 ( 68) hydrogen bonds : bond 0.02925 ( 278) hydrogen bonds : angle 5.60892 ( 657) link_BETA1-4 : bond 0.00737 ( 19) link_BETA1-4 : angle 2.40504 ( 57) link_NAG-ASN : bond 0.00509 ( 16) link_NAG-ASN : angle 2.34620 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8391 (mt) cc_final: 0.8108 (mt) REVERT: C 498 MET cc_start: 0.9073 (tmm) cc_final: 0.8763 (tmm) REVERT: B 146 MET cc_start: 0.8216 (mmm) cc_final: 0.7514 (mmm) REVERT: B 245 MET cc_start: 0.7572 (tmm) cc_final: 0.7294 (tmm) REVERT: B 762 MET cc_start: 0.6239 (mmt) cc_final: 0.5897 (mmt) outliers start: 19 outliers final: 15 residues processed: 54 average time/residue: 0.0917 time to fit residues: 9.3193 Evaluate side-chains 50 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 548 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 2 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 67 optimal weight: 50.0000 chunk 175 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 165 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.049773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.037657 restraints weight = 146744.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.038977 restraints weight = 84489.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.038853 restraints weight = 49143.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.038990 restraints weight = 47624.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.039003 restraints weight = 40301.044| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17526 Z= 0.266 Angle : 0.728 11.668 24113 Z= 0.351 Chirality : 0.045 0.316 3062 Planarity : 0.004 0.035 3139 Dihedral : 6.837 59.322 3246 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.49 % Allowed : 14.20 % Favored : 84.31 % 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: -1.94 (0.17), residues: 2430 helix: -0.57 (0.36), residues: 216 sheet: -2.11 (0.24), residues: 423 loop : -1.22 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 475 TYR 0.019 0.002 TYR A 79 PHE 0.016 0.002 PHE B 656 TRP 0.009 0.001 TRP D 31 HIS 0.005 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00574 (17457) covalent geometry : angle 0.70924 (23940) SS BOND : bond 0.00428 ( 34) SS BOND : angle 1.13781 ( 68) hydrogen bonds : bond 0.03537 ( 278) hydrogen bonds : angle 5.90543 ( 657) link_BETA1-4 : bond 0.00698 ( 19) link_BETA1-4 : angle 2.37108 ( 57) link_NAG-ASN : bond 0.00728 ( 16) link_NAG-ASN : angle 2.57449 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8589 (mt) cc_final: 0.8286 (mt) REVERT: B 146 MET cc_start: 0.8384 (mmm) cc_final: 0.7507 (mmm) REVERT: B 245 MET cc_start: 0.7661 (tmm) cc_final: 0.7288 (tmm) REVERT: B 762 MET cc_start: 0.6404 (mmt) cc_final: 0.6041 (mmt) outliers start: 22 outliers final: 19 residues processed: 54 average time/residue: 0.0911 time to fit residues: 9.1103 Evaluate side-chains 51 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 184 optimal weight: 0.0570 chunk 84 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 219 optimal weight: 0.5980 chunk 138 optimal weight: 40.0000 chunk 71 optimal weight: 50.0000 chunk 2 optimal weight: 0.8980 chunk 208 optimal weight: 0.5980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.050707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.038872 restraints weight = 142655.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.039821 restraints weight = 82139.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.039987 restraints weight = 52575.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.040145 restraints weight = 45392.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.040145 restraints weight = 39580.959| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17526 Z= 0.101 Angle : 0.615 12.583 24113 Z= 0.294 Chirality : 0.043 0.326 3062 Planarity : 0.003 0.034 3139 Dihedral : 6.392 58.235 3246 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.82 % Allowed : 14.88 % Favored : 84.31 % 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: -1.63 (0.17), residues: 2430 helix: -0.16 (0.38), residues: 210 sheet: -1.91 (0.24), residues: 447 loop : -0.99 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.009 0.001 TYR C 440 PHE 0.011 0.001 PHE D 58 TRP 0.006 0.001 TRP C 491 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00220 (17457) covalent geometry : angle 0.59548 (23940) SS BOND : bond 0.00290 ( 34) SS BOND : angle 0.97932 ( 68) hydrogen bonds : bond 0.02740 ( 278) hydrogen bonds : angle 5.52075 ( 657) link_BETA1-4 : bond 0.00751 ( 19) link_BETA1-4 : angle 2.38818 ( 57) link_NAG-ASN : bond 0.00512 ( 16) link_NAG-ASN : angle 2.27399 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8401 (mt) cc_final: 0.8115 (mt) REVERT: C 498 MET cc_start: 0.9176 (tmm) cc_final: 0.8940 (tmm) REVERT: B 146 MET cc_start: 0.8195 (mmm) cc_final: 0.7499 (mmm) REVERT: B 245 MET cc_start: 0.7616 (tmm) cc_final: 0.7332 (tmm) REVERT: B 762 MET cc_start: 0.6386 (mmt) cc_final: 0.6071 (mmt) outliers start: 12 outliers final: 11 residues processed: 48 average time/residue: 0.1012 time to fit residues: 8.9961 Evaluate side-chains 45 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 147 optimal weight: 40.0000 chunk 69 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.050263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.038380 restraints weight = 144336.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.039149 restraints weight = 84570.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.039416 restraints weight = 56689.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.039541 restraints weight = 48767.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.039543 restraints weight = 42456.588| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17526 Z= 0.167 Angle : 0.630 11.632 24113 Z= 0.303 Chirality : 0.043 0.320 3062 Planarity : 0.003 0.033 3139 Dihedral : 6.438 59.055 3246 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.15 % Allowed : 14.67 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.17), residues: 2430 helix: -0.22 (0.37), residues: 210 sheet: -1.96 (0.24), residues: 438 loop : -1.05 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 475 TYR 0.015 0.001 TYR A 79 PHE 0.012 0.001 PHE B 656 TRP 0.004 0.001 TRP D 31 HIS 0.002 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00363 (17457) covalent geometry : angle 0.61050 (23940) SS BOND : bond 0.00320 ( 34) SS BOND : angle 0.95465 ( 68) hydrogen bonds : bond 0.02973 ( 278) hydrogen bonds : angle 5.53353 ( 657) link_BETA1-4 : bond 0.00715 ( 19) link_BETA1-4 : angle 2.33962 ( 57) link_NAG-ASN : bond 0.00555 ( 16) link_NAG-ASN : angle 2.38140 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.65 seconds wall clock time: 51 minutes 5.00 seconds (3065.00 seconds total)