Starting phenix.real_space_refine on Sat Jul 4 04:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_27953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_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_27953/07_2026/8e92_27953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_27953.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_27953.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_27953.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_27953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e92_27953/07_2026/8e92_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.18, per 1000 atoms: 0.23 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: 1.66 Conformation dependent library (CDL) restraints added in 980.4 milliseconds 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: 0.56 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: 3.46 Time building geometry restraints manager: 2.16 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 - 23.06: 9726 23.06 - 46.11: 626 46.11 - 69.17: 59 69.17 - 92.23: 8 92.23 - 115.28: 1 Dihedral angle restraints: 10420 sinusoidal: 3003 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 10417 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.830 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 14.651 115.282 5598 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 are 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/Z covalent geometry : bond 0.01161 / 0.38 (18425) covalent geometry : angle 1.20083 / 0.62 (25399) SS BOND : bond 0.01533 / 0.84 ( 14) SS BOND : angle 4.36437 / 2.42 ( 28) hydrogen bonds : bond 0.18769 / 13.38 ( 710) hydrogen bonds : angle 7.62342 / 5.60 ( 2043) Misc. bond : bond 0.00172 / 0.09 ( 1) link_BETA1-4 : bond 0.00821 / 0.66 ( 14) link_BETA1-4 : angle 3.08174 / 2.39 ( 42) link_NAG-ASN : bond 0.00805 / 0.69 ( 15) link_NAG-ASN : angle 4.52300 / 3.20 ( 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 : 0.722 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: 0.1064 time to fit residues: 41.8030 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 : 0.752 ------------------------------------------------------------------------------- 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... B 175 HIS B 218 GLN D 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.112639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095469 restraints weight = 64242.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.097592 restraints weight = 37725.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099055 restraints weight = 25918.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100055 restraints weight = 19967.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100642 restraints weight = 16648.618| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18469 Z= 0.139 Angle : 0.721 12.698 25514 Z= 0.359 Chirality : 0.047 0.297 3233 Planarity : 0.005 0.099 3202 Dihedral : 6.240 58.155 2707 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.03 % Favored : 90.93 % Rotamer: Outliers : 4.04 % Allowed : 25.42 % Favored : 70.54 % 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 are not related in a simple way. whole: -2.37 (0.16), residues: 2558 helix: 0.22 (0.18), residues: 854 sheet: -1.83 (0.26), residues: 385 loop : -2.83 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 389 TYR 0.013 0.001 TYR A 392 PHE 0.012 0.001 PHE A 458 TRP 0.020 0.001 TRP A 151 HIS 0.008 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (18425) covalent geometry : angle 0.69441 / 0.35 (25399) SS BOND : bond 0.00488 / 0.40 ( 14) SS BOND : angle 1.44428 / 1.01 ( 28) hydrogen bonds : bond 0.04372 / 3.04 ( 710) hydrogen bonds : angle 5.90357 / 4.29 ( 2043) Misc. bond : bond 0.00090 / 0.05 ( 1) link_BETA1-4 : bond 0.00696 / 0.57 ( 14) link_BETA1-4 : angle 2.63327 / 2.04 ( 42) link_NAG-ASN : bond 0.00616 / 0.53 ( 15) link_NAG-ASN : angle 3.89678 / 2.88 ( 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 299 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 236 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 752 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8314 (mt) REVERT: B 228 CYS cc_start: 0.7262 (p) cc_final: 0.6850 (p) REVERT: C 237 MET cc_start: 0.8658 (tmm) cc_final: 0.8344 (tmm) REVERT: C 525 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7806 (mp10) REVERT: D 401 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8124 (mtt90) outliers start: 63 outliers final: 33 residues processed: 281 average time/residue: 0.0958 time to fit residues: 45.5694 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 : 0.647 ------------------------------------------------------------------------------- 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: 3.9990 chunk 208 optimal weight: 0.9990 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: 2.9990 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 HIS A 405 GLN A 449 HIS B 218 GLN B 702 HIS C 94 HIS D 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091565 restraints weight = 64861.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093721 restraints weight = 37567.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095203 restraints weight = 25643.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096098 restraints weight = 19665.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096838 restraints weight = 16555.234| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18469 Z= 0.170 Angle : 0.719 12.766 25514 Z= 0.360 Chirality : 0.047 0.283 3233 Planarity : 0.005 0.099 3202 Dihedral : 5.992 59.956 2699 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 6.23 % Allowed : 25.48 % Favored : 68.29 % 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 are not related in a simple way. whole: -2.26 (0.17), residues: 2558 helix: 0.35 (0.18), residues: 864 sheet: -1.81 (0.26), residues: 393 loop : -2.81 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.011 0.001 TYR A 392 PHE 0.018 0.001 PHE A 458 TRP 0.014 0.001 TRP C 247 HIS 0.019 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (18425) covalent geometry : angle 0.69326 / 0.35 (25399) SS BOND : bond 0.00446 / 0.34 ( 14) SS BOND : angle 1.55317 / 1.09 ( 28) hydrogen bonds : bond 0.04380 / 3.07 ( 710) hydrogen bonds : angle 5.71178 / 4.12 ( 2043) Misc. bond : bond 0.00038 / 0.02 ( 1) link_BETA1-4 : bond 0.00601 / 0.49 ( 14) link_BETA1-4 : angle 2.45493 / 1.89 ( 42) link_NAG-ASN : bond 0.00651 / 0.55 ( 15) link_NAG-ASN : angle 3.84028 / 2.88 ( 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 317 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 220 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8329 (m-40) cc_final: 0.7745 (p0) REVERT: A 74 MET cc_start: 0.7836 (tmm) cc_final: 0.7617 (tmm) REVERT: A 232 TYR cc_start: 0.7444 (m-80) cc_final: 0.7179 (m-80) REVERT: A 512 MET cc_start: 0.9052 (ttp) cc_final: 0.8699 (ttm) REVERT: A 752 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8324 (mt) REVERT: B 332 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7045 (t80) REVERT: C 237 MET cc_start: 0.8707 (tmm) cc_final: 0.8488 (tmm) REVERT: C 405 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7626 (mm-40) REVERT: C 525 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7814 (mp10) REVERT: C 762 MET cc_start: 0.8916 (ptp) cc_final: 0.8301 (pmm) REVERT: D 269 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6338 (m-10) outliers start: 97 outliers final: 65 residues processed: 294 average time/residue: 0.0939 time to fit residues: 47.5795 Evaluate side-chains 279 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 184 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 317 THR 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 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 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 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 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 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: 0.0170 chunk 40 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 247 optimal weight: 0.0980 chunk 217 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 overall best weight: 0.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3755 r_free = 0.3755 target = 0.112878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095605 restraints weight = 63961.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.097784 restraints weight = 37278.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099292 restraints weight = 25578.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100202 restraints weight = 19604.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100937 restraints weight = 16520.262| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18469 Z= 0.114 Angle : 0.679 11.991 25514 Z= 0.335 Chirality : 0.046 0.297 3233 Planarity : 0.005 0.098 3202 Dihedral : 5.591 56.942 2695 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.30 % Allowed : 27.92 % Favored : 67.78 % 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 are not related in a simple way. whole: -2.07 (0.17), residues: 2558 helix: 0.54 (0.18), residues: 867 sheet: -1.69 (0.26), residues: 401 loop : -2.73 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.014 0.001 TYR A 392 PHE 0.014 0.001 PHE D 754 TRP 0.011 0.001 TRP D 304 HIS 0.024 0.001 HIS B 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18425) covalent geometry : angle 0.65723 / 0.33 (25399) SS BOND : bond 0.00422 / 0.34 ( 14) SS BOND : angle 1.59876 / 1.16 ( 28) hydrogen bonds : bond 0.03547 / 2.51 ( 710) hydrogen bonds : angle 5.39185 / 3.91 ( 2043) Misc. bond : bond 0.00083 / 0.04 ( 1) link_BETA1-4 : bond 0.00648 / 0.52 ( 14) link_BETA1-4 : angle 2.32935 / 1.81 ( 42) link_NAG-ASN : bond 0.00577 / 0.50 ( 15) link_NAG-ASN : angle 3.32153 / 2.56 ( 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 305 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8347 (m-40) cc_final: 0.7860 (p0) REVERT: A 74 MET cc_start: 0.7777 (tmm) cc_final: 0.7526 (tmm) REVERT: A 184 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 232 TYR cc_start: 0.7320 (m-80) cc_final: 0.6838 (m-10) REVERT: A 512 MET cc_start: 0.8991 (ttp) cc_final: 0.8738 (ttm) REVERT: A 752 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8307 (mt) REVERT: B 219 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6828 (pt) REVERT: B 702 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8041 (p-80) REVERT: B 787 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8904 (mp10) REVERT: C 398 LEU cc_start: 0.8595 (mp) cc_final: 0.8373 (tt) REVERT: C 405 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7681 (mm-40) REVERT: C 525 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7886 (mt0) REVERT: C 762 MET cc_start: 0.8806 (ptp) cc_final: 0.8512 (pmm) REVERT: D 304 TRP cc_start: 0.8037 (OUTLIER) cc_final: 0.6766 (t-100) outliers start: 67 outliers final: 40 residues processed: 284 average time/residue: 0.0974 time to fit residues: 47.2813 Evaluate side-chains 271 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 455 CYS 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 219 LEU 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 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 702 HIS 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 241 THR 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 C residue 780 HIS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 416 VAL 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 780 PHE 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: 0.9990 chunk 211 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 197 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN D 114 GLN D 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.111494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094053 restraints weight = 64235.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096254 restraints weight = 37191.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097748 restraints weight = 25470.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098752 restraints weight = 19602.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099202 restraints weight = 16338.190| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18469 Z= 0.121 Angle : 0.681 11.961 25514 Z= 0.334 Chirality : 0.046 0.287 3233 Planarity : 0.005 0.099 3202 Dihedral : 5.436 56.507 2693 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.84 % Allowed : 27.09 % Favored : 67.07 % 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 are not related in a simple way. whole: -1.96 (0.17), residues: 2558 helix: 0.63 (0.18), residues: 866 sheet: -1.66 (0.25), residues: 412 loop : -2.65 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.013 0.001 TYR A 392 PHE 0.023 0.001 PHE D 110 TRP 0.010 0.001 TRP D 304 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (18425) covalent geometry : angle 0.66046 / 0.33 (25399) SS BOND : bond 0.00547 / 0.45 ( 14) SS BOND : angle 1.67320 / 1.22 ( 28) hydrogen bonds : bond 0.03552 / 2.50 ( 710) hydrogen bonds : angle 5.28733 / 3.84 ( 2043) Misc. bond : bond 0.00067 / 0.04 ( 1) link_BETA1-4 : bond 0.00607 / 0.49 ( 14) link_BETA1-4 : angle 2.25694 / 1.75 ( 42) link_NAG-ASN : bond 0.00547 / 0.47 ( 15) link_NAG-ASN : angle 3.22172 / 2.52 ( 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 326 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 235 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8300 (m-40) cc_final: 0.7881 (p0) REVERT: A 74 MET cc_start: 0.7877 (tmm) cc_final: 0.7600 (tmm) REVERT: A 184 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 259 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8333 (pt) REVERT: A 512 MET cc_start: 0.9034 (ttp) cc_final: 0.8751 (ttm) REVERT: A 752 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8333 (mt) REVERT: B 371 MET cc_start: 0.8641 (tmm) cc_final: 0.8317 (tmm) REVERT: B 702 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7913 (p90) REVERT: B 787 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8942 (mp10) REVERT: C 293 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6996 (t-90) REVERT: C 381 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: C 525 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7895 (mt0) REVERT: C 762 MET cc_start: 0.8880 (ptp) cc_final: 0.8455 (pmm) REVERT: D 269 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6402 (m-10) REVERT: D 304 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.6714 (t-100) REVERT: D 401 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8140 (mtt90) REVERT: D 763 MET cc_start: 0.7958 (ptm) cc_final: 0.7585 (ptm) outliers start: 91 outliers final: 55 residues processed: 307 average time/residue: 0.0959 time to fit residues: 50.3842 Evaluate side-chains 287 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 131 THR 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 433 CYS Chi-restraints excluded: chain B residue 453 CYS 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 747 THR 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 157 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 241 THR 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 354 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 TRP 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 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 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 304 TRP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 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 791 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 198 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 217 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 GLN B 218 GLN D 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093705 restraints weight = 63977.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095870 restraints weight = 37048.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097248 restraints weight = 25322.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098328 restraints weight = 19694.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098927 restraints weight = 16360.876| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18469 Z= 0.129 Angle : 0.687 12.212 25514 Z= 0.337 Chirality : 0.047 0.316 3233 Planarity : 0.005 0.097 3202 Dihedral : 5.396 56.048 2693 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.46 % Allowed : 27.54 % Favored : 67.01 % 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 are not related in a simple way. whole: -1.87 (0.17), residues: 2558 helix: 0.74 (0.18), residues: 860 sheet: -1.60 (0.25), residues: 412 loop : -2.62 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.013 0.001 TYR A 392 PHE 0.015 0.001 PHE A 458 TRP 0.011 0.001 TRP C 381 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (18425) covalent geometry : angle 0.66714 / 0.33 (25399) SS BOND : bond 0.00513 / 0.42 ( 14) SS BOND : angle 1.44941 / 1.03 ( 28) hydrogen bonds : bond 0.03557 / 2.49 ( 710) hydrogen bonds : angle 5.25793 / 3.82 ( 2043) Misc. bond : bond 0.00058 / 0.03 ( 1) link_BETA1-4 : bond 0.00604 / 0.49 ( 14) link_BETA1-4 : angle 2.28653 / 1.76 ( 42) link_NAG-ASN : bond 0.00558 / 0.48 ( 15) link_NAG-ASN : angle 3.15896 / 2.51 ( 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 317 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 232 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8252 (m-40) cc_final: 0.7865 (p0) REVERT: A 74 MET cc_start: 0.7899 (tmm) cc_final: 0.7613 (tmm) REVERT: A 259 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8309 (pt) REVERT: A 512 MET cc_start: 0.9059 (ttp) cc_final: 0.8806 (ttm) REVERT: A 752 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 787 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8915 (mp10) REVERT: C 125 MET cc_start: 0.8283 (mmm) cc_final: 0.8078 (mmm) REVERT: C 293 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7014 (t-90) REVERT: C 381 TRP cc_start: 0.8674 (OUTLIER) cc_final: 0.8462 (m-10) REVERT: C 525 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7908 (mt0) REVERT: C 762 MET cc_start: 0.8902 (ptp) cc_final: 0.8336 (pmm) REVERT: D 269 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6363 (m-10) REVERT: D 304 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.6776 (t-100) REVERT: D 401 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8109 (mtt90) REVERT: D 763 MET cc_start: 0.8117 (ptm) cc_final: 0.7781 (ptm) REVERT: D 783 ASP cc_start: 0.8662 (t70) cc_final: 0.8421 (p0) outliers start: 85 outliers final: 63 residues processed: 296 average time/residue: 0.1013 time to fit residues: 50.9437 Evaluate side-chains 296 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 131 THR 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 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 747 THR 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 238 LEU 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 381 TRP 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 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 169 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 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 170 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 109 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093913 restraints weight = 64359.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096126 restraints weight = 36973.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097614 restraints weight = 25319.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098554 restraints weight = 19437.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099182 restraints weight = 16375.610| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18469 Z= 0.120 Angle : 0.676 11.943 25514 Z= 0.331 Chirality : 0.046 0.301 3233 Planarity : 0.005 0.097 3202 Dihedral : 5.311 55.956 2693 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 6.10 % Allowed : 26.77 % Favored : 67.14 % 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 are not related in a simple way. whole: -1.75 (0.17), residues: 2558 helix: 0.87 (0.18), residues: 855 sheet: -1.52 (0.26), residues: 407 loop : -2.56 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 183 TYR 0.013 0.001 TYR A 392 PHE 0.015 0.001 PHE A 458 TRP 0.011 0.001 TRP C 381 HIS 0.007 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (18425) covalent geometry : angle 0.65802 / 0.33 (25399) SS BOND : bond 0.00537 / 0.44 ( 14) SS BOND : angle 1.35008 / 0.95 ( 28) hydrogen bonds : bond 0.03370 / 2.37 ( 710) hydrogen bonds : angle 5.16122 / 3.75 ( 2043) Misc. bond : bond 0.00063 / 0.03 ( 1) link_BETA1-4 : bond 0.00596 / 0.48 ( 14) link_BETA1-4 : angle 2.21008 / 1.70 ( 42) link_NAG-ASN : bond 0.00525 / 0.46 ( 15) link_NAG-ASN : angle 3.00413 / 2.41 ( 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 327 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 232 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8269 (m-40) cc_final: 0.7935 (p0) REVERT: A 74 MET cc_start: 0.7927 (tmm) cc_final: 0.7649 (tmm) REVERT: A 184 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 259 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8318 (pt) REVERT: A 512 MET cc_start: 0.9044 (ttp) cc_final: 0.8810 (ttm) REVERT: A 752 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8326 (mt) REVERT: B 371 MET cc_start: 0.8533 (tmm) cc_final: 0.8205 (tmm) REVERT: C 293 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.7007 (t-90) REVERT: C 501 MET cc_start: 0.9193 (pmm) cc_final: 0.8922 (pmm) REVERT: C 525 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7874 (mt0) REVERT: C 762 MET cc_start: 0.8842 (ptp) cc_final: 0.8392 (pmm) REVERT: D 269 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: D 304 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.6845 (t-100) REVERT: D 401 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8106 (mtt90) REVERT: D 783 ASP cc_start: 0.8710 (t70) cc_final: 0.8404 (p0) outliers start: 95 outliers final: 68 residues processed: 306 average time/residue: 0.1042 time to fit residues: 54.1537 Evaluate side-chains 298 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 184 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 288 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 752 LEU 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 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 433 CYS Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain B residue 468 VAL 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 747 THR 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 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 238 LEU 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 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN 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 128 VAL 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 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 296 LEU Chi-restraints excluded: chain D residue 304 TRP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 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 692 ILE 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: 5.9990 chunk 196 optimal weight: 0.0570 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 247 optimal weight: 20.0000 overall best weight: 3.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3698 r_free = 0.3698 target = 0.109133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091814 restraints weight = 65417.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093932 restraints weight = 38434.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095357 restraints weight = 26593.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096297 restraints weight = 20671.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096820 restraints weight = 17380.724| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18469 Z= 0.175 Angle : 0.723 12.352 25514 Z= 0.360 Chirality : 0.047 0.302 3233 Planarity : 0.005 0.095 3202 Dihedral : 5.554 56.126 2693 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 6.10 % Allowed : 27.28 % Favored : 66.62 % 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 are not related in a simple way. whole: -1.83 (0.17), residues: 2558 helix: 0.80 (0.18), residues: 856 sheet: -1.65 (0.25), residues: 407 loop : -2.57 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 183 TYR 0.015 0.001 TYR C 88 PHE 0.020 0.001 PHE A 458 TRP 0.035 0.001 TRP C 381 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (18425) covalent geometry : angle 0.70312 / 0.36 (25399) SS BOND : bond 0.00735 / 0.55 ( 14) SS BOND : angle 1.92496 / 1.45 ( 28) hydrogen bonds : bond 0.04045 / 2.86 ( 710) hydrogen bonds : angle 5.33485 / 3.87 ( 2043) Misc. bond : bond 0.00043 / 0.02 ( 1) link_BETA1-4 : bond 0.00533 / 0.44 ( 14) link_BETA1-4 : angle 2.23472 / 1.72 ( 42) link_NAG-ASN : bond 0.00613 / 0.52 ( 15) link_NAG-ASN : angle 3.20700 / 2.55 ( 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 310 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 215 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8287 (m-40) cc_final: 0.7971 (p0) REVERT: A 74 MET cc_start: 0.7924 (tmm) cc_final: 0.7534 (tmm) REVERT: A 184 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 259 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8302 (pt) REVERT: A 512 MET cc_start: 0.9120 (ttp) cc_final: 0.8896 (ttm) REVERT: A 752 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 703 MET cc_start: 0.7507 (mmm) cc_final: 0.7264 (mmm) REVERT: C 237 MET cc_start: 0.8687 (tmm) cc_final: 0.8314 (tmm) REVERT: C 293 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: C 525 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7930 (mt0) REVERT: D 269 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6448 (m-10) REVERT: D 304 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.6731 (t-100) REVERT: D 401 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8192 (mtp85) REVERT: D 781 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8348 (tt) outliers start: 95 outliers final: 72 residues processed: 292 average time/residue: 0.1020 time to fit residues: 50.9449 Evaluate side-chains 290 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 210 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL 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 184 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 455 CYS Chi-restraints excluded: chain A residue 464 ILE 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 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 380 LEU 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 468 VAL 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 747 THR 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 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 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 520 ASN 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 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 128 VAL 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 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 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 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 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 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: 20.0000 chunk 65 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 164 optimal weight: 0.0050 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN B 702 HIS C 67 HIS ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090844 restraints weight = 65149.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092895 restraints weight = 38637.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094322 restraints weight = 26840.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095268 restraints weight = 20846.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095779 restraints weight = 17518.885| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18469 Z= 0.184 Angle : 0.751 12.435 25514 Z= 0.374 Chirality : 0.048 0.307 3233 Planarity : 0.005 0.092 3202 Dihedral : 5.771 56.521 2693 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.03 % Allowed : 27.34 % Favored : 66.62 % Cbeta Deviations : 0.04 % 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 are not related in a simple way. whole: -1.89 (0.17), residues: 2558 helix: 0.77 (0.18), residues: 854 sheet: -1.57 (0.26), residues: 387 loop : -2.66 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.016 0.001 TYR C 88 PHE 0.023 0.001 PHE A 458 TRP 0.026 0.001 TRP C 381 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (18425) covalent geometry : angle 0.73197 / 0.37 (25399) SS BOND : bond 0.00678 / 0.54 ( 14) SS BOND : angle 1.91596 / 1.44 ( 28) hydrogen bonds : bond 0.04123 / 2.91 ( 710) hydrogen bonds : angle 5.44844 / 3.94 ( 2043) Misc. bond : bond 0.00051 / 0.03 ( 1) link_BETA1-4 : bond 0.00583 / 0.47 ( 14) link_BETA1-4 : angle 2.21916 / 1.69 ( 42) link_NAG-ASN : bond 0.00631 / 0.54 ( 15) link_NAG-ASN : angle 3.27335 / 2.59 ( 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 299 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 205 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8391 (m-40) cc_final: 0.7995 (p0) REVERT: A 184 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 259 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8281 (pt) REVERT: A 512 MET cc_start: 0.9118 (ttp) cc_final: 0.8907 (ttm) REVERT: A 752 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 187 ASP cc_start: 0.8530 (m-30) cc_final: 0.8258 (m-30) REVERT: B 371 MET cc_start: 0.8660 (tmm) cc_final: 0.8342 (tmm) REVERT: B 703 MET cc_start: 0.7719 (mmm) cc_final: 0.7446 (mmm) REVERT: C 88 TYR cc_start: 0.7519 (m-80) cc_final: 0.7151 (m-80) REVERT: C 237 MET cc_start: 0.8712 (tmm) cc_final: 0.8382 (tmm) REVERT: D 269 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6429 (m-10) REVERT: D 304 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.6730 (t-100) REVERT: D 401 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8111 (mtt90) REVERT: D 781 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8326 (tt) outliers start: 94 outliers final: 77 residues processed: 280 average time/residue: 0.0989 time to fit residues: 47.3379 Evaluate side-chains 283 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 199 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL 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 184 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 455 CYS Chi-restraints excluded: chain A residue 464 ILE 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 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 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 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 747 THR 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 C residue 35 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 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 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 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 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 128 VAL 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 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 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 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 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: 0.9990 chunk 73 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 201 optimal weight: 0.0670 chunk 47 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092037 restraints weight = 64128.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094216 restraints weight = 37081.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095687 restraints weight = 25432.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096622 restraints weight = 19570.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097150 restraints weight = 16414.570| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18469 Z= 0.141 Angle : 0.724 12.057 25514 Z= 0.357 Chirality : 0.047 0.312 3233 Planarity : 0.005 0.090 3202 Dihedral : 5.629 57.730 2693 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 5.58 % Allowed : 27.54 % Favored : 66.88 % 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 are not related in a simple way. whole: -1.82 (0.17), residues: 2558 helix: 0.84 (0.18), residues: 856 sheet: -1.64 (0.25), residues: 411 loop : -2.59 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.012 0.001 TYR C 88 PHE 0.018 0.001 PHE A 458 TRP 0.040 0.001 TRP C 381 HIS 0.007 0.001 HIS B 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18425) covalent geometry : angle 0.70611 / 0.35 (25399) SS BOND : bond 0.00602 / 0.48 ( 14) SS BOND : angle 1.64755 / 1.21 ( 28) hydrogen bonds : bond 0.03783 / 2.68 ( 710) hydrogen bonds : angle 5.33271 / 3.85 ( 2043) Misc. bond : bond 0.00067 / 0.04 ( 1) link_BETA1-4 : bond 0.00573 / 0.46 ( 14) link_BETA1-4 : angle 2.18211 / 1.68 ( 42) link_NAG-ASN : bond 0.00546 / 0.47 ( 15) link_NAG-ASN : angle 3.09180 / 2.46 ( 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 292 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 205 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 259 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8277 (pt) REVERT: A 512 MET cc_start: 0.9072 (ttp) cc_final: 0.8870 (ttm) REVERT: A 752 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 187 ASP cc_start: 0.8500 (m-30) cc_final: 0.8219 (m-30) REVERT: B 371 MET cc_start: 0.8669 (tmm) cc_final: 0.8335 (tmm) REVERT: B 702 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.8100 (p90) REVERT: C 88 TYR cc_start: 0.7577 (m-80) cc_final: 0.7240 (m-80) REVERT: C 237 MET cc_start: 0.8720 (tmm) cc_final: 0.8353 (tmm) REVERT: C 762 MET cc_start: 0.8918 (ptp) cc_final: 0.8249 (pmm) REVERT: D 269 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6348 (m-10) REVERT: D 304 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.6755 (t-100) REVERT: D 401 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: D 781 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8278 (tt) outliers start: 87 outliers final: 75 residues processed: 277 average time/residue: 0.1018 time to fit residues: 48.0080 Evaluate side-chains 284 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 201 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 184 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 455 CYS Chi-restraints excluded: chain A residue 464 ILE 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 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 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 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 747 THR 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 C residue 35 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 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 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 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 116 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 128 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 27 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 244 optimal weight: 0.0170 chunk 132 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.0060 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095160 restraints weight = 64007.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097397 restraints weight = 36834.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098910 restraints weight = 25101.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099876 restraints weight = 19212.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100564 restraints weight = 16102.987| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18469 Z= 0.116 Angle : 0.698 12.526 25514 Z= 0.339 Chirality : 0.046 0.310 3233 Planarity : 0.005 0.093 3202 Dihedral : 5.269 59.578 2693 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.17 % Allowed : 29.08 % Favored : 66.75 % 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 are not related in a simple way. whole: -1.63 (0.17), residues: 2558 helix: 0.99 (0.18), residues: 856 sheet: -1.51 (0.26), residues: 396 loop : -2.47 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 183 TYR 0.013 0.001 TYR A 392 PHE 0.015 0.001 PHE C 753 TRP 0.028 0.001 TRP C 381 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (18425) covalent geometry : angle 0.68276 / 0.34 (25399) SS BOND : bond 0.00643 / 0.44 ( 14) SS BOND : angle 1.52638 / 1.12 ( 28) hydrogen bonds : bond 0.03119 / 2.22 ( 710) hydrogen bonds : angle 5.09194 / 3.70 ( 2043) Misc. bond : bond 0.00101 / 0.05 ( 1) link_BETA1-4 : bond 0.00611 / 0.49 ( 14) link_BETA1-4 : angle 2.13024 / 1.64 ( 42) link_NAG-ASN : bond 0.00526 / 0.45 ( 15) link_NAG-ASN : angle 2.70463 / 2.19 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2907.05 seconds wall clock time: 50 minutes 58.93 seconds (3058.93 seconds total)