Starting phenix.real_space_refine on Sun Aug 24 08:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e92_27953/08_2025/8e92_27953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e92_27953/08_2025/8e92_27953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e92_27953/08_2025/8e92_27953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e92_27953/08_2025/8e92_27953.map" model { file = "/net/cci-nas-00/data/ceres_data/8e92_27953/08_2025/8e92_27953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e92_27953/08_2025/8e92_27953.cif" } resolution = 3.96 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= 0.008 sd= 0.472 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 72 5.16 5 C 11549 2.51 5 N 3025 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18011 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4526 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 29, 'TRANS': 624} Chain breaks: 1 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 818 Unresolved non-hydrogen dihedrals: 566 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 37, 'GLN:plan1': 11, 'PHE:plan': 4, 'ARG:plan': 21, 'TRP:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 16, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 451 Chain: "B" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4229 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 38, 'TRANS': 594} Chain breaks: 3 Unresolved non-hydrogen bonds: 706 Unresolved non-hydrogen angles: 866 Unresolved non-hydrogen dihedrals: 592 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 6, 'GLN:plan1': 21, 'ARG:plan': 28, 'ASP:plan': 17, 'GLU:plan': 24, 'ASN:plan1': 8, 'HIS:plan': 8, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 513 Chain: "C" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4468 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 886 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 23, 'HIS:plan': 5, 'GLU:plan': 38, 'GLN:plan1': 14, 'PHE:plan': 3, 'ASN:plan1': 16, 'ASP:plan': 18, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 489 Chain: "D" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4366 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 492 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 17, 'PHE:plan': 4, 'ARG:plan': 23, 'ASP:plan': 16, 'GLU:plan': 23, 'ASN:plan1': 5, 'HIS:plan': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 411 Chain: "E" 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: "F" 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: "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: 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: "I" 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: "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: 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: "D" 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: 3.68, per 1000 atoms: 0.20 Number of scatterers: 18011 At special positions: 0 Unit cell: (134.392, 145.52, 134.392, 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 72 16.00 O 3365 8.00 N 3025 7.00 C 11549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.08 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.02 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.04 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.04 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.04 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.04 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 901 " - " ASN A 61 " " NAG A 903 " - " ASN A 203 " " NAG C 901 " - " ASN C 203 " " NAG C 902 " - " ASN C 368 " " NAG D 901 " - " ASN D 685 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN A 771 " " NAG G 1 " - " ASN A 368 " " NAG H 1 " - " ASN B 337 " " NAG I 1 " - " ASN B 685 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 276 " " NAG L 1 " - " ASN C 771 " " NAG M 1 " - " ASN C 350 " " NAG N 1 " - " ASN D 337 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 718.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4780 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 28 sheets defined 37.3% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.884A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.898A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.361A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 4.068A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.531A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.837A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 277 through 296 removed outlier: 4.066A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.589A pdb=" N GLY A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 4.166A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 removed outlier: 3.604A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.783A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 723 removed outlier: 4.114A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.702A pdb=" N PHE B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.713A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 174 through 187 removed outlier: 4.073A pdb=" N PHE B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.933A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 284 through 303 removed outlier: 3.707A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.511A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 486 through 490 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.611A pdb=" N GLU B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.808A pdb=" N HIS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.629A pdb=" N LYS B 739 " --> pdb=" O TYR B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 Processing helix chain 'B' and resid 768 through 783 removed outlier: 3.936A pdb=" N ALA B 772 " --> pdb=" O HIS B 768 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 792 Processing helix chain 'C' and resid 35 through 53 Processing helix chain 'C' and resid 70 through 85 Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.287A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.841A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.826A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.731A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.612A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 278 through 296 Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.594A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 501 through 508 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.637A pdb=" N ALA C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.685A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 694 removed outlier: 3.565A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 708 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.072A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 782 removed outlier: 4.132A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.035A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 158 removed outlier: 3.515A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 Processing helix chain 'D' and resid 208 through 218 removed outlier: 3.678A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 4.050A pdb=" N VAL D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 457 through 470 removed outlier: 3.649A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.800A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 698 through 703 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.662A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 784 removed outlier: 3.952A pdb=" N ARG D 771 " --> pdb=" O SER D 767 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 784 " --> pdb=" O PHE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 removed outlier: 4.192A pdb=" N LYS D 788 " --> pdb=" O GLY D 784 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.755A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.630A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.178A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.561A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 66 removed outlier: 6.131A pdb=" N ILE B 93 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.880A pdb=" N TYR B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 170 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 358 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.919A pdb=" N TRP B 340 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 414 through 417 removed outlier: 4.460A pdb=" N LEU B 475 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 477 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 403 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR B 476 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 405 " --> pdb=" O TYR B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 527 through 528 removed outlier: 4.158A pdb=" N VAL B 527 " --> pdb=" O TYR B 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 531 through 534 Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 65 removed outlier: 11.720A pdb=" N ILE C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N ALA C 89 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASN C 28 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 138 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 195 through 197 removed outlier: 8.051A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 267 through 271 removed outlier: 7.024A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 478 removed outlier: 3.553A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AB9, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.638A pdb=" N THR C 486 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 499 " --> pdb=" O THR C 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.792A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.590A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 749 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.590A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.300A pdb=" N ALA D 33 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 201 removed outlier: 3.678A pdb=" N TYR D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER D 170 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE D 224 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.617A pdb=" N SER D 275 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU D 376 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 472 through 477 removed outlier: 7.314A pdb=" N LEU D 403 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N TYR D 476 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 405 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET D 505 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 762 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 521 " --> pdb=" O MET D 763 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 416 through 417 Processing sheet with id=AC9, first strand: chain 'D' and resid 726 through 729 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 729 removed outlier: 4.734A pdb=" N ILE D 531 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA D 755 " --> pdb=" O ILE D 531 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.31: 2870 1.31 - 1.62: 15445 1.62 - 1.93: 108 1.93 - 2.24: 1 2.24 - 2.55: 1 Bond restraints: 18425 Sorted by residual: bond pdb=" CB PRO D 677 " pdb=" CG PRO D 677 " ideal model delta sigma weight residual 1.492 2.552 -1.060 5.00e-02 4.00e+02 4.50e+02 bond pdb=" CG PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 1.503 1.005 0.498 3.40e-02 8.65e+02 2.15e+02 bond pdb=" CG PRO B 388 " pdb=" CD PRO B 388 " ideal model delta sigma weight residual 1.503 1.024 0.479 3.40e-02 8.65e+02 1.99e+02 bond pdb=" CA CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sigma weight residual 1.530 1.671 -0.141 1.48e-02 4.57e+03 9.10e+01 bond pdb=" CG1 ILE C 519 " pdb=" CD1 ILE C 519 " ideal model delta sigma weight residual 1.513 1.155 0.358 3.90e-02 6.57e+02 8.43e+01 ... (remaining 18420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 25394 21.21 - 42.43: 4 42.43 - 63.64: 0 63.64 - 84.86: 0 84.86 - 106.07: 1 Bond angle restraints: 25399 Sorted by residual: angle pdb=" CB PRO D 677 " pdb=" CG PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO B 388 " pdb=" CD PRO B 388 " pdb=" CG PRO B 388 " ideal model delta sigma weight residual 103.20 70.88 32.32 1.50e+00 4.44e-01 4.64e+02 angle pdb=" CA PRO D 677 " pdb=" N PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 112.00 83.47 28.53 1.40e+00 5.10e-01 4.15e+02 angle pdb=" CA PRO B 388 " pdb=" CB PRO B 388 " pdb=" CG PRO B 388 " ideal model delta sigma weight residual 104.50 73.72 30.78 1.90e+00 2.77e-01 2.62e+02 angle pdb=" N PRO D 677 " pdb=" CA PRO D 677 " pdb=" CB PRO D 677 " ideal model delta sigma weight residual 103.25 86.80 16.45 1.05e+00 9.07e-01 2.46e+02 ... (remaining 25394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 10218 24.90 - 49.81: 638 49.81 - 74.71: 95 74.71 - 99.61: 66 99.61 - 124.51: 46 Dihedral angle restraints: 11063 sinusoidal: 3646 harmonic: 7417 Sorted by residual: dihedral pdb=" CA GLY B 204 " pdb=" C GLY B 204 " pdb=" N PRO B 205 " pdb=" CA PRO B 205 " ideal model delta harmonic sigma weight residual -180.00 -137.31 -42.69 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" C TYR D 473 " pdb=" N TYR D 473 " pdb=" CA TYR D 473 " pdb=" CB TYR D 473 " ideal model delta harmonic sigma weight residual -122.60 -102.10 -20.50 0 2.50e+00 1.60e-01 6.72e+01 dihedral pdb=" CB CYS D 82 " pdb=" SG CYS D 82 " pdb=" SG CYS D 317 " pdb=" CB CYS D 317 " ideal model delta sinusoidal sigma weight residual 93.00 29.08 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 11060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3125 0.116 - 0.233: 89 0.233 - 0.349: 14 0.349 - 0.465: 4 0.465 - 0.582: 1 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA VAL D 468 " pdb=" N VAL D 468 " pdb=" C VAL D 468 " pdb=" CB VAL D 468 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.46e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.02e+00 chirality pdb=" CA ARG D 401 " pdb=" N ARG D 401 " pdb=" C ARG D 401 " pdb=" CB ARG D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 3230 not shown) Planarity restraints: 3217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 438 " 0.113 5.00e-02 4.00e+02 1.58e-01 3.99e+01 pdb=" N PRO A 439 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 676 " -0.110 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO D 677 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 677 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 677 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 463 " 0.023 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C LYS D 463 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS D 463 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS D 464 " 0.028 2.00e-02 2.50e+03 ... (remaining 3214 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 567 2.68 - 3.24: 18036 3.24 - 3.79: 26024 3.79 - 4.35: 30346 4.35 - 4.90: 50504 Nonbonded interactions: 125477 Sorted by model distance: nonbonded pdb=" O GLN D 779 " pdb=" OD1 ASP D 783 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR A 312 " pdb=" O THR B 72 " model vdw 2.170 3.040 nonbonded pdb=" O SER D 400 " pdb=" OG SER D 400 " model vdw 2.184 3.040 nonbonded pdb=" O6 NAG M 1 " pdb=" O7 NAG M 2 " model vdw 2.201 3.040 nonbonded pdb=" O4 NAG L 1 " pdb=" O7 NAG L 1 " model vdw 2.202 3.040 ... (remaining 125472 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 25 through 35 or (resid 36 through 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 46 or (resid 47 through \ 52 and (name N or name CA or name C or name O or name CB )) or resid 53 through \ 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or res \ id 81 through 100 or (resid 101 through 102 and (name N or name CA or name C or \ name O or name CB )) or resid 103 through 146 or (resid 147 and (name N or name \ CA or name C or name O or name CB )) or resid 148 through 155 or (resid 156 and \ (name N or name CA or name C or name O or name CB )) or resid 157 through 212 or \ (resid 213 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 4 through 225 or (resid 226 through 229 and (name N or name CA or name C or name \ O or name CB )) or resid 230 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 through 251 or (resid 252 through \ 253 and (name N or name CA or name C or name O or name CB )) or resid 254 throug \ h 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or \ resid 265 through 266 or (resid 267 and (name N or name CA or name C or name O o \ r name CB )) or resid 268 through 272 or (resid 273 and (name N or name CA or na \ me C or name O or name CB )) or resid 274 through 300 or (resid 301 and (name N \ or name CA or name C or name O or name CB )) or resid 302 or (resid 303 and (nam \ e N or name CA or name C or name O or name CB )) or resid 304 through 310 or (re \ sid 311 and (name N or name CA or name C or name O or name CB )) or resid 312 th \ rough 347 or (resid 348 through 349 and (name N or name CA or name C or name O o \ r name CB )) or resid 350 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 359 or (resid 360 and (name N \ or name CA or name C or name O or name CB )) or resid 361 through 376 or (resid \ 377 through 379 and (name N or name CA or name C or name O or name CB )) or resi \ d 380 through 391 or (resid 392 through 394 and (name N or name CA or name C or \ name O or name CB )) or resid 395 through 418 or (resid 419 and (name N or name \ CA or name C or name O or name CB )) or resid 420 through 424 or (resid 425 thro \ ugh 427 and (name N or name CA or name C or name O or name CB )) or resid 428 th \ rough 442 or (resid 443 and (name N or name CA or name C or name O or name CB )) \ or resid 444 through 445 or (resid 446 and (name N or name CA or name C or name \ O or name CB )) or resid 447 through 448 or (resid 449 and (name N or name CA o \ r name C or name O or name CB )) or resid 450 through 464 or (resid 465 and (nam \ e N or name CA or name C or name O or name CB )) or resid 466 through 467 or (re \ sid 468 and (name N or name CA or name C or name O or name CB )) or resid 469 or \ (resid 470 and (name N or name CA or name C or name O or name CB )) or resid 47 \ 1 through 498 or (resid 499 and (name N or name CA or name C or name O or name C \ B )) or resid 500 through 527 or (resid 528 and (name N or name CA or name C or \ name O or name CB )) or resid 529 through 530 or (resid 531 and (name N or name \ CA or name C or name O or name CB )) or resid 532 through 533 or (resid 534 and \ (name N or name CA or name C or name O or name CB )) or resid 535 through 544 or \ resid 664 through 684 or (resid 685 and (name N or name CA or name C or name O \ or name CB )) or resid 686 through 701 or (resid 702 through 704 and (name N or \ name CA or name C or name O or name CB )) or resid 705 through 708 or (resid 709 \ through 711 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 12 through 754 or (resid 755 and (name N or name CA or name C or name O or name \ CB )) or resid 756 through 764 or (resid 765 and (name N or name CA or name C or \ name O or name CB )) or resid 766 through 788 or (resid 789 through 790 and (na \ me N or name CA or name C or name O or name CB )) or resid 791 through 796 or re \ sid 903 through 904)) selection = (chain 'C' and (resid 25 through 55 or (resid 56 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 173 or \ (resid 174 through 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 214 or (resid 215 through 217 and (name N or name CA or nam \ e C or name O or name CB )) or resid 218 through 271 or (resid 272 through 273 a \ nd (name N or name CA or name C or name O or name CB )) or resid 274 through 340 \ or (resid 341 through 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 366 or (resid 367 and (name N or name CA or name C or n \ ame O or name CB )) or resid 368 through 378 or (resid 379 and (name N or name C \ A or name C or name O or name CB )) or resid 380 through 398 or (resid 399 and ( \ name N or name CA or name C or name O or name CB )) or resid 400 through 423 or \ (resid 424 through 427 and (name N or name CA or name C or name O or name CB )) \ or resid 428 through 474 or (resid 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 480 or (resid 481 and (name N or name CA or \ name C or name O or name CB )) or resid 482 through 510 or (resid 511 and (name \ N or name CA or name C or name O or name CB )) or resid 512 through 519 or (res \ id 520 and (name N or name CA or name C or name O or name CB )) or resid 521 thr \ ough 540 or (resid 541 and (name N or name CA or name C or name O or name CB )) \ or resid 542 through 544 or (resid 664 through 665 and (name N or name CA or nam \ e C or name O or name CB )) or resid 666 through 667 or (resid 668 through 669 a \ nd (name N or name CA or name C or name O or name CB )) or resid 670 through 693 \ or (resid 694 through 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 706 or (resid 707 through 711 and (name N or name CA or \ name C or name O or name CB )) or resid 712 through 721 or (resid 722 through 7 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 727 through \ 796 or resid 901 through 902)) } ncs_group { reference = (chain 'B' and (resid 31 through 53 or (resid 54 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 88 or (resid 89 through \ 91 and (name N or name CA or name C or name O or name CB )) or resid 92 through \ 96 or (resid 97 through 103 and (name N or name CA or name C or name O or name \ CB )) or resid 104 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 through 133 or (resid 134 and (name N or name \ CA or name C or name O or name CB )) or resid 135 through 179 or (resid 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 182 o \ r (resid 183 through 184 and (name N or name CA or name C or name O or name CB ) \ ) or resid 185 through 186 or (resid 187 through 188 and (name N or name CA or n \ ame C or name O or name CB )) or resid 189 through 216 or (resid 217 and (name N \ or name CA or name C or name O or name CB )) or resid 218 through 231 or (resid \ 232 through 234 and (name N or name CA or name C or name O or name CB )) or res \ id 235 through 258 or (resid 259 and (name N or name CA or name C or name O or n \ ame CB )) or resid 260 through 284 or (resid 285 through 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 through 302 or (resid 303 and \ (name N or name CA or name C or name O or name CB )) or resid 304 through 335 o \ r (resid 336 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 37 through 343 or (resid 344 and (name N or name CA or name C or name O or name \ CB )) or resid 345 through 363 or (resid 364 through 365 and (name N or name CA \ or name C or name O or name CB )) or resid 366 through 434 or (resid 435 through \ 436 and (name N or name CA or name C or name O or name CB )) or resid 437 or (r \ esid 448 through 449 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 459 or (resid 460 and (name N or name CA or name C or name O \ or name CB )) or resid 461 through 500 or (resid 501 and (name N or name CA or n \ ame C or name O or name CB )) or resid 502 through 701 or (resid 702 through 703 \ and (name N or name CA or name C or name O or name CB )) or resid 704 through 7 \ 05 or (resid 706 through 709 and (name N or name CA or name C or name O or name \ CB )) or resid 710 through 767 or (resid 768 and (name N or name CA or name C or \ name O or name CB )) or resid 769 through 786 or (resid 787 through 788 and (na \ me N or name CA or name C or name O or name CB )) or resid 789 through 798)) selection = (chain 'D' and (resid 31 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 89 or (resid 90 throu \ gh 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throu \ gh 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or \ resid 115 through 147 or (resid 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 through 158 or (resid 159 through 161 and (name N or \ name CA or name C or name O or name CB )) or resid 162 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 173 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB )) or res \ id 195 through 208 or (resid 209 through 211 and (name N or name CA or name C or \ name O or name CB )) or resid 212 or (resid 213 through 214 and (name N or name \ CA or name C or name O or name CB )) or resid 215 through 238 or (resid 239 thr \ ough 243 and (name N or name CA or name C or name O or name CB )) or resid 244 o \ r (resid 245 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 46 through 270 or (resid 271 and (name N or name CA or name C or name O or name \ CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or \ name O or name CB )) or resid 280 through 285 or (resid 286 through 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 or (resid 290 thr \ ough 291 and (name N or name CA or name C or name O or name CB )) or resid 292 t \ hrough 306 or (resid 307 and (name N or name CA or name C or name O or name CB ) \ ) or resid 308 through 333 or (resid 334 and (name N or name CA or name C or nam \ e O or name CB )) or resid 335 through 347 or (resid 348 and (name N or name CA \ or name C or name O or name CB )) or resid 349 through 382 or (resid 383 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 throu \ gh 389 or (resid 390 and (name N or name CA or name C or name O or name CB )) or \ resid 391 or resid 398 or (resid 399 and (name N or name CA or name C or name O \ or name CB )) or resid 400 through 401 or (resid 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 437 or (resid 448 through 44 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 450 through \ 470 or (resid 471 and (name N or name CA or name C or name O or name CB )) or re \ sid 472 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 484 or (resid 485 through 486 and (name N or nam \ e CA or name C or name O or name CB )) or resid 487 through 514 or (resid 515 an \ d (name N or name CA or name C or name O or name CB )) or resid 516 through 527 \ or (resid 528 and (name N or name CA or name C or name O or name CB )) or resid \ 529 through 664 or (resid 665 through 670 and (name N or name CA or name C or na \ me O or name CB )) or resid 671 through 672 or (resid 673 through 675 and (name \ N or name CA or name C or name O or name CB )) or resid 676 through 679 or (resi \ d 680 and (name N or name CA or name C or name O or name CB )) or resid 681 thro \ ugh 692 or (resid 693 and (name N or name CA or name C or name O or name CB )) o \ r resid 694 or (resid 695 through 697 and (name N or name CA or name C or name O \ or name CB )) or resid 698 through 728 or (resid 729 through 731 and (name N or \ name CA or name C or name O or name CB )) or resid 732 through 733 or (resid 73 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 735 through \ 763 or (resid 764 through 766 and (name N or name CA or name C or name O or name \ CB )) or resid 767 through 770 or (resid 771 through 772 and (name N or name CA \ or name C or name O or name CB )) or resid 773 through 782 or (resid 783 and (n \ ame N or name CA or name C or name O or name CB )) or resid 784 through 798)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.870 Find NCS groups from input model: 0.440 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.012 1.060 18469 Z= 0.377 Angle : 1.228 106.070 25514 Z= 0.626 Chirality : 0.055 0.582 3233 Planarity : 0.007 0.158 3202 Dihedral : 20.025 124.514 6241 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.81 % Favored : 90.07 % Rotamer: Outliers : 1.03 % Allowed : 28.24 % Favored : 70.73 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.71 (0.16), residues: 2558 helix: -0.14 (0.18), residues: 814 sheet: -1.95 (0.26), residues: 370 loop : -2.91 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG D 389 TYR 0.028 0.001 TYR A 232 PHE 0.027 0.001 PHE D 471 TRP 0.026 0.001 TRP C 731 HIS 0.026 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.01161 (18425) covalent geometry : angle 1.20083 (25399) SS BOND : bond 0.01533 ( 14) SS BOND : angle 4.36437 ( 28) hydrogen bonds : bond 0.18769 ( 710) hydrogen bonds : angle 7.62342 ( 2043) Misc. bond : bond 0.00172 ( 1) link_BETA1-4 : bond 0.00821 ( 14) link_BETA1-4 : angle 3.08174 ( 42) link_NAG-ASN : bond 0.00805 ( 15) link_NAG-ASN : angle 4.52300 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 CYS cc_start: 0.7386 (p) cc_final: 0.7058 (p) outliers start: 16 outliers final: 10 residues processed: 232 average time/residue: 0.0909 time to fit residues: 35.6672 Evaluate side-chains 221 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 387 TRP Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 472 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS D 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.111615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094196 restraints weight = 64202.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096397 restraints weight = 37176.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.097899 restraints weight = 25407.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098899 restraints weight = 19505.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099496 restraints weight = 16257.695| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18469 Z= 0.131 Angle : 0.747 12.994 25514 Z= 0.365 Chirality : 0.048 0.272 3233 Planarity : 0.005 0.093 3202 Dihedral : 16.517 108.262 3350 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.03 % Favored : 90.93 % Rotamer: Outliers : 3.92 % Allowed : 25.48 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -2.39 (0.16), residues: 2558 helix: 0.21 (0.18), residues: 855 sheet: -1.78 (0.27), residues: 380 loop : -2.86 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.013 0.001 TYR A 392 PHE 0.012 0.001 PHE A 458 TRP 0.019 0.001 TRP D 304 HIS 0.008 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00290 (18425) covalent geometry : angle 0.71628 (25399) SS BOND : bond 0.00500 ( 14) SS BOND : angle 1.45571 ( 28) hydrogen bonds : bond 0.04563 ( 710) hydrogen bonds : angle 5.95296 ( 2043) Misc. bond : bond 0.00071 ( 1) link_BETA1-4 : bond 0.00809 ( 14) link_BETA1-4 : angle 3.11966 ( 42) link_NAG-ASN : bond 0.00601 ( 15) link_NAG-ASN : angle 4.01162 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 752 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 228 CYS cc_start: 0.7292 (p) cc_final: 0.6908 (p) REVERT: C 237 MET cc_start: 0.8654 (tmm) cc_final: 0.8354 (tmm) REVERT: D 401 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: D 677 PRO cc_start: 0.4643 (OUTLIER) cc_final: 0.4226 (Cg_exo) outliers start: 61 outliers final: 32 residues processed: 280 average time/residue: 0.0927 time to fit residues: 44.0952 Evaluate side-chains 249 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 780 PHE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 778 LEU Chi-restraints excluded: chain D residue 780 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 240 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 249 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 405 GLN A 449 HIS A 477 HIS B 218 GLN B 702 HIS C 94 HIS D 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090588 restraints weight = 65653.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092723 restraints weight = 38144.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094198 restraints weight = 26160.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094901 restraints weight = 20077.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095738 restraints weight = 17287.731| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18469 Z= 0.197 Angle : 0.775 13.925 25514 Z= 0.381 Chirality : 0.049 0.259 3233 Planarity : 0.005 0.097 3202 Dihedral : 14.209 106.667 3342 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 6.87 % Allowed : 25.03 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -2.30 (0.17), residues: 2558 helix: 0.32 (0.18), residues: 861 sheet: -1.90 (0.26), residues: 389 loop : -2.79 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.013 0.002 TYR A 144 PHE 0.020 0.002 PHE A 458 TRP 0.016 0.001 TRP C 247 HIS 0.017 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00441 (18425) covalent geometry : angle 0.74557 (25399) SS BOND : bond 0.00591 ( 14) SS BOND : angle 1.57502 ( 28) hydrogen bonds : bond 0.04603 ( 710) hydrogen bonds : angle 5.80328 ( 2043) Misc. bond : bond 0.00005 ( 1) link_BETA1-4 : bond 0.00768 ( 14) link_BETA1-4 : angle 2.92907 ( 42) link_NAG-ASN : bond 0.00737 ( 15) link_NAG-ASN : angle 4.10119 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 220 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8340 (m-40) cc_final: 0.7748 (p0) REVERT: A 74 MET cc_start: 0.7852 (tmm) cc_final: 0.7651 (tmm) REVERT: A 125 MET cc_start: 0.7822 (mmm) cc_final: 0.7556 (mmm) REVERT: A 752 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8334 (mt) REVERT: B 332 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7055 (t80) REVERT: C 237 MET cc_start: 0.8697 (tmm) cc_final: 0.8479 (tmm) REVERT: C 525 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7840 (mp10) REVERT: D 269 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6450 (m-10) outliers start: 107 outliers final: 68 residues processed: 303 average time/residue: 0.0869 time to fit residues: 45.0843 Evaluate side-chains 279 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 208 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 780 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 402 HIS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 766 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 3 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN B 218 GLN ** B 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 134 HIS D 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089177 restraints weight = 64832.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091060 restraints weight = 38897.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.092324 restraints weight = 27596.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092935 restraints weight = 21907.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093547 restraints weight = 19253.145| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 18469 Z= 0.249 Angle : 0.830 14.869 25514 Z= 0.413 Chirality : 0.050 0.268 3233 Planarity : 0.006 0.096 3202 Dihedral : 13.312 100.968 3338 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.67 % Favored : 87.29 % Rotamer: Outliers : 8.34 % Allowed : 25.29 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.24 % 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 aren not related in a simple way. whole: -2.42 (0.16), residues: 2558 helix: 0.22 (0.18), residues: 858 sheet: -1.79 (0.26), residues: 367 loop : -2.91 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.020 0.002 TYR C 88 PHE 0.023 0.002 PHE A 458 TRP 0.030 0.002 TRP C 381 HIS 0.029 0.002 HIS B 702 Details of bonding type rmsd covalent geometry : bond 0.00554 (18425) covalent geometry : angle 0.80151 (25399) SS BOND : bond 0.00866 ( 14) SS BOND : angle 1.81355 ( 28) hydrogen bonds : bond 0.04964 ( 710) hydrogen bonds : angle 5.97809 ( 2043) Misc. bond : bond 0.00014 ( 1) link_BETA1-4 : bond 0.00856 ( 14) link_BETA1-4 : angle 3.00282 ( 42) link_NAG-ASN : bond 0.00882 ( 15) link_NAG-ASN : angle 4.19475 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 208 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8367 (m-40) cc_final: 0.7760 (p0) REVERT: A 74 MET cc_start: 0.7920 (tmm) cc_final: 0.7704 (tmm) REVERT: A 125 MET cc_start: 0.7786 (mmm) cc_final: 0.7573 (mmm) REVERT: A 259 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8268 (pt) REVERT: A 536 GLN cc_start: 0.8451 (pp30) cc_final: 0.7864 (pp30) REVERT: A 752 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 332 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7081 (t80) REVERT: B 516 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8255 (mtt90) REVERT: B 787 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8921 (mp10) REVERT: D 269 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6500 (m-10) REVERT: D 401 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8205 (mtt90) outliers start: 130 outliers final: 93 residues processed: 307 average time/residue: 0.0917 time to fit residues: 47.4683 Evaluate side-chains 298 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 199 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 458 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 518 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 780 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 402 HIS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 763 MET Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 246 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 197 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN D 148 GLN 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 = 0.109725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092331 restraints weight = 64887.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094465 restraints weight = 38239.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095916 restraints weight = 26449.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.096777 restraints weight = 20475.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097517 restraints weight = 17388.181| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18469 Z= 0.131 Angle : 0.738 13.897 25514 Z= 0.357 Chirality : 0.048 0.260 3233 Planarity : 0.005 0.092 3202 Dihedral : 12.108 100.284 3337 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.35 % Allowed : 27.79 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -2.14 (0.17), residues: 2558 helix: 0.56 (0.18), residues: 858 sheet: -1.88 (0.25), residues: 412 loop : -2.76 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.012 0.001 TYR A 392 PHE 0.015 0.001 PHE A 458 TRP 0.037 0.001 TRP C 381 HIS 0.008 0.001 HIS B 702 Details of bonding type rmsd covalent geometry : bond 0.00294 (18425) covalent geometry : angle 0.71226 (25399) SS BOND : bond 0.00565 ( 14) SS BOND : angle 1.46311 ( 28) hydrogen bonds : bond 0.03714 ( 710) hydrogen bonds : angle 5.48515 ( 2043) Misc. bond : bond 0.00054 ( 1) link_BETA1-4 : bond 0.00810 ( 14) link_BETA1-4 : angle 2.93745 ( 42) link_NAG-ASN : bond 0.00638 ( 15) link_NAG-ASN : angle 3.57001 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 226 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8330 (m-40) cc_final: 0.7791 (p0) REVERT: A 74 MET cc_start: 0.7825 (tmm) cc_final: 0.7604 (tmm) REVERT: A 512 MET cc_start: 0.8966 (ttp) cc_final: 0.8755 (ttm) REVERT: A 536 GLN cc_start: 0.8446 (pp30) cc_final: 0.7875 (pp30) REVERT: A 752 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 332 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6964 (t80) REVERT: B 787 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8888 (mp10) REVERT: C 293 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.6896 (t-90) REVERT: C 762 MET cc_start: 0.8801 (ptp) cc_final: 0.8350 (pmm) REVERT: D 130 LEU cc_start: 0.8350 (pp) cc_final: 0.7855 (mt) REVERT: D 304 TRP cc_start: 0.8112 (OUTLIER) cc_final: 0.6870 (t-100) REVERT: D 401 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8114 (mtt90) outliers start: 99 outliers final: 56 residues processed: 304 average time/residue: 0.0887 time to fit residues: 45.7826 Evaluate side-chains 279 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 198 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 702 HIS D 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090843 restraints weight = 65016.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092877 restraints weight = 38057.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094288 restraints weight = 26518.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095255 restraints weight = 20626.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095803 restraints weight = 17329.649| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18469 Z= 0.165 Angle : 0.754 14.589 25514 Z= 0.367 Chirality : 0.048 0.263 3233 Planarity : 0.005 0.093 3202 Dihedral : 11.674 99.322 3337 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 7.45 % Allowed : 27.73 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -2.11 (0.17), residues: 2558 helix: 0.55 (0.18), residues: 858 sheet: -1.80 (0.25), residues: 418 loop : -2.74 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.015 0.001 TYR C 88 PHE 0.020 0.001 PHE A 458 TRP 0.019 0.001 TRP C 381 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00373 (18425) covalent geometry : angle 0.72741 (25399) SS BOND : bond 0.00713 ( 14) SS BOND : angle 2.01444 ( 28) hydrogen bonds : bond 0.04081 ( 710) hydrogen bonds : angle 5.52034 ( 2043) Misc. bond : bond 0.00023 ( 1) link_BETA1-4 : bond 0.00816 ( 14) link_BETA1-4 : angle 2.90029 ( 42) link_NAG-ASN : bond 0.00693 ( 15) link_NAG-ASN : angle 3.63348 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 212 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8332 (m-40) cc_final: 0.7836 (p0) REVERT: A 74 MET cc_start: 0.7928 (tmm) cc_final: 0.7674 (tmm) REVERT: A 259 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8289 (pt) REVERT: A 512 MET cc_start: 0.9041 (ttp) cc_final: 0.8808 (ttm) REVERT: A 752 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 787 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8951 (mp10) REVERT: C 237 MET cc_start: 0.8675 (tmm) cc_final: 0.8264 (tmm) REVERT: C 293 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.6942 (t-90) REVERT: D 130 LEU cc_start: 0.8387 (pp) cc_final: 0.7861 (mt) REVERT: D 269 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6427 (m-10) REVERT: D 401 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8139 (mtt90) REVERT: D 781 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8281 (tt) outliers start: 116 outliers final: 85 residues processed: 308 average time/residue: 0.0891 time to fit residues: 46.3881 Evaluate side-chains 299 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 207 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 702 HIS Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 753 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 402 HIS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 170 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN D 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092607 restraints weight = 64576.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094690 restraints weight = 37988.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096133 restraints weight = 26143.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097123 restraints weight = 20283.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097701 restraints weight = 16942.083| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18469 Z= 0.125 Angle : 0.727 14.127 25514 Z= 0.351 Chirality : 0.047 0.264 3233 Planarity : 0.005 0.092 3202 Dihedral : 11.111 96.492 3336 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.03 % Allowed : 28.95 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -1.98 (0.17), residues: 2558 helix: 0.70 (0.18), residues: 852 sheet: -1.76 (0.25), residues: 419 loop : -2.66 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 183 TYR 0.012 0.001 TYR A 392 PHE 0.015 0.001 PHE A 458 TRP 0.032 0.001 TRP C 381 HIS 0.013 0.001 HIS B 702 Details of bonding type rmsd covalent geometry : bond 0.00284 (18425) covalent geometry : angle 0.70179 (25399) SS BOND : bond 0.00597 ( 14) SS BOND : angle 1.85561 ( 28) hydrogen bonds : bond 0.03636 ( 710) hydrogen bonds : angle 5.35984 ( 2043) Misc. bond : bond 0.00073 ( 1) link_BETA1-4 : bond 0.00841 ( 14) link_BETA1-4 : angle 2.92677 ( 42) link_NAG-ASN : bond 0.00618 ( 15) link_NAG-ASN : angle 3.37840 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 225 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8357 (m-40) cc_final: 0.7924 (p0) REVERT: A 74 MET cc_start: 0.7991 (tmm) cc_final: 0.7726 (tmm) REVERT: A 512 MET cc_start: 0.8995 (ttp) cc_final: 0.8748 (ttm) REVERT: A 536 GLN cc_start: 0.8501 (pp30) cc_final: 0.7814 (pp30) REVERT: A 752 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 371 MET cc_start: 0.8627 (tmm) cc_final: 0.8305 (tmm) REVERT: B 787 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8945 (mp10) REVERT: C 237 MET cc_start: 0.8706 (tmm) cc_final: 0.8272 (tmm) REVERT: C 293 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6872 (t-90) REVERT: C 484 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: C 762 MET cc_start: 0.8929 (ptp) cc_final: 0.8330 (pmm) REVERT: D 304 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.6853 (t-100) REVERT: D 401 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8091 (mtt90) outliers start: 94 outliers final: 71 residues processed: 302 average time/residue: 0.0918 time to fit residues: 46.8297 Evaluate side-chains 286 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 484 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 753 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 780 PHE Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089876 restraints weight = 64602.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091936 restraints weight = 37731.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093353 restraints weight = 26037.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094312 restraints weight = 20186.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094852 restraints weight = 16905.062| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18469 Z= 0.197 Angle : 0.773 14.736 25514 Z= 0.380 Chirality : 0.048 0.264 3233 Planarity : 0.005 0.092 3202 Dihedral : 11.030 95.034 3336 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 7.32 % Allowed : 28.18 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -2.06 (0.17), residues: 2558 helix: 0.60 (0.18), residues: 852 sheet: -1.64 (0.26), residues: 385 loop : -2.73 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 183 TYR 0.021 0.001 TYR C 88 PHE 0.022 0.001 PHE A 458 TRP 0.028 0.001 TRP C 381 HIS 0.006 0.001 HIS B 702 Details of bonding type rmsd covalent geometry : bond 0.00441 (18425) covalent geometry : angle 0.74828 (25399) SS BOND : bond 0.00672 ( 14) SS BOND : angle 1.78943 ( 28) hydrogen bonds : bond 0.04254 ( 710) hydrogen bonds : angle 5.55973 ( 2043) Misc. bond : bond 0.00029 ( 1) link_BETA1-4 : bond 0.00808 ( 14) link_BETA1-4 : angle 2.86387 ( 42) link_NAG-ASN : bond 0.00740 ( 15) link_NAG-ASN : angle 3.58217 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 205 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8391 (m-40) cc_final: 0.7947 (p0) REVERT: A 74 MET cc_start: 0.8075 (tmm) cc_final: 0.7779 (tmm) REVERT: A 259 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8297 (pt) REVERT: A 752 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 703 MET cc_start: 0.7451 (mmm) cc_final: 0.7202 (mmm) REVERT: B 787 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (mp10) REVERT: C 237 MET cc_start: 0.8754 (tmm) cc_final: 0.8374 (tmm) REVERT: D 130 LEU cc_start: 0.8427 (pp) cc_final: 0.7865 (mt) REVERT: D 269 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: D 401 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: D 781 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8294 (tt) outliers start: 114 outliers final: 88 residues processed: 297 average time/residue: 0.0882 time to fit residues: 45.0847 Evaluate side-chains 294 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 200 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 753 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 402 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 114 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 104 optimal weight: 0.0070 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.107081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089843 restraints weight = 64790.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091908 restraints weight = 38315.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093284 restraints weight = 26584.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094200 restraints weight = 20725.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.094837 restraints weight = 17509.513| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18469 Z= 0.193 Angle : 0.790 14.693 25514 Z= 0.386 Chirality : 0.048 0.263 3233 Planarity : 0.005 0.091 3202 Dihedral : 10.880 92.867 3336 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 7.06 % Allowed : 28.31 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -2.14 (0.17), residues: 2558 helix: 0.56 (0.18), residues: 849 sheet: -1.76 (0.26), residues: 381 loop : -2.78 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.020 0.001 TYR C 88 PHE 0.022 0.002 PHE A 458 TRP 0.030 0.001 TRP C 381 HIS 0.006 0.001 HIS B 702 Details of bonding type rmsd covalent geometry : bond 0.00435 (18425) covalent geometry : angle 0.76514 (25399) SS BOND : bond 0.00858 ( 14) SS BOND : angle 2.12480 ( 28) hydrogen bonds : bond 0.04329 ( 710) hydrogen bonds : angle 5.61432 ( 2043) Misc. bond : bond 0.00058 ( 1) link_BETA1-4 : bond 0.00798 ( 14) link_BETA1-4 : angle 2.83228 ( 42) link_NAG-ASN : bond 0.00735 ( 15) link_NAG-ASN : angle 3.60444 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 205 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8414 (m-40) cc_final: 0.7998 (p0) REVERT: A 74 MET cc_start: 0.8024 (tmm) cc_final: 0.7733 (tmm) REVERT: A 259 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8255 (pt) REVERT: A 512 MET cc_start: 0.8985 (ttp) cc_final: 0.8685 (ttt) REVERT: A 752 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 187 ASP cc_start: 0.8025 (t70) cc_final: 0.7807 (m-30) REVERT: B 332 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7028 (t80) REVERT: B 787 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8926 (mp10) REVERT: C 237 MET cc_start: 0.8760 (tmm) cc_final: 0.8393 (tmm) REVERT: D 130 LEU cc_start: 0.8447 (pp) cc_final: 0.7895 (mt) REVERT: D 269 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: D 304 TRP cc_start: 0.8127 (OUTLIER) cc_final: 0.6758 (t-100) REVERT: D 401 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8260 (mtp85) REVERT: D 781 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8339 (tt) outliers start: 110 outliers final: 95 residues processed: 293 average time/residue: 0.0813 time to fit residues: 40.7414 Evaluate side-chains 301 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 198 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 753 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 402 HIS Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 245 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 198 optimal weight: 0.4980 chunk 244 optimal weight: 4.9990 chunk 201 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092990 restraints weight = 63387.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095133 restraints weight = 36922.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096616 restraints weight = 25353.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097597 restraints weight = 19499.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.098265 restraints weight = 16323.335| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18469 Z= 0.124 Angle : 0.738 13.918 25514 Z= 0.355 Chirality : 0.047 0.263 3233 Planarity : 0.005 0.090 3202 Dihedral : 10.137 90.076 3336 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.65 % Allowed : 29.91 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.90 (0.17), residues: 2558 helix: 0.79 (0.18), residues: 855 sheet: -1.69 (0.26), residues: 407 loop : -2.64 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 183 TYR 0.012 0.001 TYR A 392 PHE 0.015 0.001 PHE B 95 TRP 0.026 0.001 TRP C 381 HIS 0.004 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00279 (18425) covalent geometry : angle 0.71419 (25399) SS BOND : bond 0.00590 ( 14) SS BOND : angle 2.13030 ( 28) hydrogen bonds : bond 0.03491 ( 710) hydrogen bonds : angle 5.30711 ( 2043) Misc. bond : bond 0.00141 ( 1) link_BETA1-4 : bond 0.00838 ( 14) link_BETA1-4 : angle 2.88479 ( 42) link_NAG-ASN : bond 0.00603 ( 15) link_NAG-ASN : angle 3.26634 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5116 Ramachandran restraints generated. 2558 Oldfield, 0 Emsley, 2558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 220 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7998 (tmm) cc_final: 0.7711 (tmm) REVERT: A 502 MET cc_start: 0.8592 (tpp) cc_final: 0.8195 (tpp) REVERT: A 752 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 187 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: B 332 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 371 MET cc_start: 0.8657 (tmm) cc_final: 0.8361 (tmm) REVERT: B 516 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8281 (mtt90) REVERT: C 237 MET cc_start: 0.8733 (tmm) cc_final: 0.8373 (tmm) REVERT: C 762 MET cc_start: 0.8840 (ptp) cc_final: 0.8415 (pmm) REVERT: D 304 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.6753 (t-100) REVERT: D 401 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: D 781 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8242 (tt) outliers start: 88 outliers final: 72 residues processed: 287 average time/residue: 0.0924 time to fit residues: 44.8674 Evaluate side-chains 289 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 162 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 753 PHE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 116 HIS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain D residue 677 PRO Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 27 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 244 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 42 optimal weight: 0.0270 chunk 4 optimal weight: 9.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN D 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093982 restraints weight = 63709.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096209 restraints weight = 37057.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097715 restraints weight = 25221.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098720 restraints weight = 19300.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099325 restraints weight = 16022.594| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18469 Z= 0.120 Angle : 0.723 13.844 25514 Z= 0.346 Chirality : 0.047 0.271 3233 Planarity : 0.005 0.091 3202 Dihedral : 9.594 89.096 3336 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.75 % Allowed : 30.68 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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 aren not related in a simple way. whole: -1.81 (0.17), residues: 2558 helix: 0.85 (0.18), residues: 859 sheet: -1.64 (0.26), residues: 399 loop : -2.58 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.012 0.001 TYR A 392 PHE 0.016 0.001 PHE B 95 TRP 0.023 0.001 TRP C 381 HIS 0.004 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00269 (18425) covalent geometry : angle 0.69993 (25399) SS BOND : bond 0.00736 ( 14) SS BOND : angle 1.90505 ( 28) hydrogen bonds : bond 0.03352 ( 710) hydrogen bonds : angle 5.14773 ( 2043) Misc. bond : bond 0.00133 ( 1) link_BETA1-4 : bond 0.00773 ( 14) link_BETA1-4 : angle 2.86001 ( 42) link_NAG-ASN : bond 0.00587 ( 15) link_NAG-ASN : angle 3.19151 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.89 seconds wall clock time: 44 minutes 44.64 seconds (2684.64 seconds total)