Starting phenix.real_space_refine on Mon Aug 25 04:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vj7_43276/08_2025/8vj7_43276.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vj7_43276/08_2025/8vj7_43276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vj7_43276/08_2025/8vj7_43276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vj7_43276/08_2025/8vj7_43276.map" model { file = "/net/cci-nas-00/data/ceres_data/8vj7_43276/08_2025/8vj7_43276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vj7_43276/08_2025/8vj7_43276.cif" } resolution = 4.85 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= 0.002 sd= 0.015 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 119 5.16 5 C 16153 2.51 5 N 4167 2.21 5 O 4736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.10s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25175 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6269 Classifications: {'peptide': 796} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 772} Chain breaks: 2 Chain: "B" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6257 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6268 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 6253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6253 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'A1AB5': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'A1AB5': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'A1AB5': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'A1AB5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.22 Number of scatterers: 25175 At special positions: 0 Unit cell: (121.83, 161.82, 190.65, 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 119 16.00 O 4736 8.00 N 4167 7.00 C 16153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 956.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 48.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 116 through 128 removed outlier: 4.616A pdb=" N ALA A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 removed outlier: 3.808A pdb=" N GLY A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.747A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.634A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.555A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 390 through 390 No H-bonds generated for 'chain 'A' and resid 390 through 390' Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.537A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.485A pdb=" N GLU A 413 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.773A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 628 removed outlier: 3.532A pdb=" N ARG A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 removed outlier: 3.716A pdb=" N SER A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.896A pdb=" N GLY A 771 " --> pdb=" O TYR A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 818 removed outlier: 3.831A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.532A pdb=" N GLU B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.847A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.682A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.690A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.540A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.754A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.631A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 625 removed outlier: 3.703A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.671A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 817 removed outlier: 3.832A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 174 through 187 removed outlier: 3.876A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 231 through 236 removed outlier: 4.127A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 236 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.642A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 303 Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.327A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.816A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.704A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 627 Processing helix chain 'C' and resid 636 through 642 removed outlier: 3.931A pdb=" N SER C 640 " --> pdb=" O ALA C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.556A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.554A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.806A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.683A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.949A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.270A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.963A pdb=" N GLU D 413 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.893A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.704A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.717A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.594A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 792 through 817 removed outlier: 3.782A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 50 removed outlier: 7.136A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.558A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS A 132 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.549A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 340 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.453A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.114A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.541A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 721 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 50 removed outlier: 6.215A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N ALA B 72 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN B 13 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.084A pdb=" N TYR B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.433A pdb=" N VAL B 396 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.827A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 704 through 705 removed outlier: 4.128A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 721 " --> pdb=" O ILE B 504 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.445A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 50 removed outlier: 10.250A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.467A pdb=" N PHE C 133 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE C 163 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 135 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS C 132 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 359 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS C 364 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 373 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC3, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.523A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AC6, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.013A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.442A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 42 through 50 removed outlier: 6.103A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ALA D 72 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN D 13 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N PHE D 74 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.619A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AD2, first strand: chain 'D' and resid 441 through 444 Processing sheet with id=AD3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD4, first strand: chain 'D' and resid 489 through 491 removed outlier: 3.513A pdb=" N THR D 736 " --> pdb=" O ASP D 490 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.490A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3438 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: 4.90 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8027 1.34 - 1.46: 6267 1.46 - 1.58: 11220 1.58 - 1.70: 1 1.70 - 1.83: 195 Bond restraints: 25710 Sorted by residual: bond pdb=" C2 A1AB5 C1401 " pdb=" N1 A1AB5 C1401 " ideal model delta sigma weight residual 1.275 1.450 -0.175 2.00e-02 2.50e+03 7.70e+01 bond pdb=" C2 A1AB5 D1302 " pdb=" N1 A1AB5 D1302 " ideal model delta sigma weight residual 1.275 1.446 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" C2 A1AB5 C1403 " pdb=" N1 A1AB5 C1403 " ideal model delta sigma weight residual 1.275 1.445 -0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" C2 A1AB5 A1302 " pdb=" N1 A1AB5 A1302 " ideal model delta sigma weight residual 1.275 1.444 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C3 A1AB5 C1403 " pdb=" N2 A1AB5 C1403 " ideal model delta sigma weight residual 1.290 1.451 -0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 25705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 34669 5.25 - 10.49: 58 10.49 - 15.74: 3 15.74 - 20.99: 0 20.99 - 26.24: 8 Bond angle restraints: 34738 Sorted by residual: angle pdb=" C THR D 394 " pdb=" N VAL D 395 " pdb=" CA VAL D 395 " ideal model delta sigma weight residual 121.97 132.98 -11.01 1.00e+00 1.00e+00 1.21e+02 angle pdb=" C4 A1AB5 A1302 " pdb=" C3 A1AB5 A1302 " pdb=" N2 A1AB5 A1302 " ideal model delta sigma weight residual 116.15 89.91 26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C4 A1AB5 C1403 " pdb=" C3 A1AB5 C1403 " pdb=" N2 A1AB5 C1403 " ideal model delta sigma weight residual 116.15 90.12 26.03 3.00e+00 1.11e-01 7.53e+01 angle pdb=" C4 A1AB5 D1302 " pdb=" C3 A1AB5 D1302 " pdb=" N2 A1AB5 D1302 " ideal model delta sigma weight residual 116.15 90.41 25.74 3.00e+00 1.11e-01 7.36e+01 angle pdb=" C10 A1AB5 C1401 " pdb=" C3 A1AB5 C1401 " pdb=" C4 A1AB5 C1401 " ideal model delta sigma weight residual 118.62 142.97 -24.35 3.00e+00 1.11e-01 6.59e+01 ... (remaining 34733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13871 17.86 - 35.73: 1090 35.73 - 53.59: 248 53.59 - 71.45: 46 71.45 - 89.31: 46 Dihedral angle restraints: 15301 sinusoidal: 6136 harmonic: 9165 Sorted by residual: dihedral pdb=" C GLU B 705 " pdb=" N GLU B 705 " pdb=" CA GLU B 705 " pdb=" CB GLU B 705 " ideal model delta harmonic sigma weight residual -122.60 -141.46 18.86 0 2.50e+00 1.60e-01 5.69e+01 dihedral pdb=" CA LYS D 393 " pdb=" C LYS D 393 " pdb=" N THR D 394 " pdb=" CA THR D 394 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA PHE C 546 " pdb=" C PHE C 546 " pdb=" N SER C 547 " pdb=" CA SER C 547 " ideal model delta harmonic sigma weight residual -180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 15298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3822 0.139 - 0.277: 7 0.277 - 0.416: 0 0.416 - 0.555: 0 0.555 - 0.693: 1 Chirality restraints: 3830 Sorted by residual: chirality pdb=" CA GLU B 705 " pdb=" N GLU B 705 " pdb=" C GLU B 705 " pdb=" CB GLU B 705 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CG LEU A 184 " pdb=" CB LEU A 184 " pdb=" CD1 LEU A 184 " pdb=" CD2 LEU A 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA PRO D 593 " pdb=" N PRO D 593 " pdb=" C PRO D 593 " pdb=" CB PRO D 593 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 3827 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 628 " -0.579 9.50e-02 1.11e+02 2.60e-01 4.12e+01 pdb=" NE ARG C 628 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 628 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 628 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 628 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 506 " 0.052 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO C 507 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 704 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C LEU B 704 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU B 704 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 705 " -0.013 2.00e-02 2.50e+03 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 0.67 - 1.52: 4 1.52 - 2.36: 57 2.36 - 3.21: 24121 3.21 - 4.05: 64723 4.05 - 4.90: 117897 Warning: very small nonbonded interaction distances. Nonbonded interactions: 206802 Sorted by model distance: nonbonded pdb=" CD GLU D 705 " pdb=" OE2 GLU D1301 " model vdw 0.673 3.270 nonbonded pdb=" OE2 GLU D 705 " pdb=" OE2 GLU D1301 " model vdw 0.804 3.040 nonbonded pdb=" OE2 GLU D 705 " pdb=" CD GLU D1301 " model vdw 0.902 3.270 nonbonded pdb=" CD GLU D 705 " pdb=" CD GLU D1301 " model vdw 1.373 3.500 nonbonded pdb=" CG GLU D 705 " pdb=" OE2 GLU D1301 " model vdw 1.576 3.440 ... (remaining 206797 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 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 772 or (resid 773 and (name N o \ r name CA or name C or name O or name CB )) or resid 774 through 817 or (resid 8 \ 18 through 819 and (name N or name CA or name C or name O or name CB )) or resid \ 1301)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 772 or (resid 773 and (name N o \ r name CA or name C or name O or name CB )) or resid 774 through 1301)) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1402)) selection = (chain 'D' and (resid 10 through 772 or (resid 773 and (name N or name CA or nam \ e C or name O or name CB )) or resid 774 through 1301)) } 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.950 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.868 25719 Z= 0.831 Angle : 0.777 26.235 34752 Z= 0.405 Chirality : 0.043 0.693 3830 Planarity : 0.006 0.260 4395 Dihedral : 14.498 89.314 9428 Min Nonbonded Distance : 0.673 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 0.48 % Allowed : 9.99 % Favored : 89.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.15), residues: 3164 helix: 1.47 (0.14), residues: 1417 sheet: -0.25 (0.29), residues: 357 loop : -0.59 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 594 TYR 0.017 0.001 TYR A 533 PHE 0.029 0.002 PHE A 296 TRP 0.014 0.002 TRP B 605 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00699 (25710) covalent geometry : angle 0.77657 (34738) SS BOND : bond 0.00834 ( 7) SS BOND : angle 1.26400 ( 14) hydrogen bonds : bond 0.15550 ( 1188) hydrogen bonds : angle 5.83094 ( 3438) Misc. bond : bond 0.86055 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 737 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7979 (m-30) cc_final: 0.7350 (t0) REVERT: A 382 LEU cc_start: 0.8657 (pp) cc_final: 0.8410 (tp) REVERT: A 463 MET cc_start: 0.8509 (mmm) cc_final: 0.8247 (mmt) REVERT: A 518 LEU cc_start: 0.9037 (mt) cc_final: 0.8045 (mt) REVERT: A 539 VAL cc_start: 0.9615 (t) cc_final: 0.8852 (m) REVERT: A 573 ILE cc_start: 0.8896 (tt) cc_final: 0.8376 (tt) REVERT: A 584 PHE cc_start: 0.8762 (t80) cc_final: 0.8377 (t80) REVERT: A 585 MET cc_start: 0.8776 (mmt) cc_final: 0.8543 (mmm) REVERT: A 611 ILE cc_start: 0.9562 (mm) cc_final: 0.9250 (mm) REVERT: A 613 ILE cc_start: 0.9338 (mm) cc_final: 0.8530 (tp) REVERT: A 661 ARG cc_start: 0.9077 (mmt180) cc_final: 0.8405 (ttp80) REVERT: A 670 MET cc_start: 0.9208 (mtp) cc_final: 0.8882 (mtp) REVERT: A 789 LEU cc_start: 0.8254 (tp) cc_final: 0.7925 (tp) REVERT: A 805 LEU cc_start: 0.9004 (tt) cc_final: 0.8621 (mm) REVERT: B 25 GLU cc_start: 0.8563 (mp0) cc_final: 0.8239 (mp0) REVERT: B 175 GLU cc_start: 0.9483 (mp0) cc_final: 0.9233 (pm20) REVERT: B 214 HIS cc_start: 0.8185 (p90) cc_final: 0.7560 (p-80) REVERT: B 255 VAL cc_start: 0.8989 (t) cc_final: 0.8779 (p) REVERT: B 362 GLU cc_start: 0.8847 (tt0) cc_final: 0.8454 (mm-30) REVERT: B 378 ASP cc_start: 0.8851 (m-30) cc_final: 0.8639 (m-30) REVERT: B 514 VAL cc_start: 0.7643 (t) cc_final: 0.7395 (p) REVERT: B 533 TYR cc_start: 0.8185 (t80) cc_final: 0.7856 (t80) REVERT: B 534 ILE cc_start: 0.9102 (mt) cc_final: 0.8710 (tt) REVERT: B 540 LEU cc_start: 0.8580 (tp) cc_final: 0.8258 (tp) REVERT: B 573 ILE cc_start: 0.8803 (tp) cc_final: 0.8030 (tp) REVERT: B 601 VAL cc_start: 0.9151 (t) cc_final: 0.8651 (p) REVERT: B 608 PHE cc_start: 0.8953 (t80) cc_final: 0.8564 (t80) REVERT: B 614 SER cc_start: 0.9682 (m) cc_final: 0.9362 (t) REVERT: B 620 LEU cc_start: 0.8761 (tp) cc_final: 0.8519 (tt) REVERT: B 798 ILE cc_start: 0.8976 (mt) cc_final: 0.8324 (tt) REVERT: C 79 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8581 (pttm) REVERT: C 107 HIS cc_start: 0.7998 (m90) cc_final: 0.7540 (m-70) REVERT: C 161 THR cc_start: 0.9336 (m) cc_final: 0.9047 (p) REVERT: C 188 LYS cc_start: 0.8885 (mttt) cc_final: 0.8337 (tptp) REVERT: C 200 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8782 (tttt) REVERT: C 284 LEU cc_start: 0.8889 (tp) cc_final: 0.8684 (mt) REVERT: C 518 LEU cc_start: 0.8994 (mt) cc_final: 0.6804 (mt) REVERT: C 540 LEU cc_start: 0.8718 (tp) cc_final: 0.8507 (tp) REVERT: C 584 PHE cc_start: 0.8691 (t80) cc_final: 0.8283 (t80) REVERT: C 585 MET cc_start: 0.8663 (mmt) cc_final: 0.8262 (mmm) REVERT: C 601 VAL cc_start: 0.9332 (t) cc_final: 0.8967 (p) REVERT: C 611 ILE cc_start: 0.9511 (mm) cc_final: 0.9075 (mm) REVERT: C 613 ILE cc_start: 0.9236 (mm) cc_final: 0.7969 (tp) REVERT: C 617 THR cc_start: 0.9557 (m) cc_final: 0.9290 (t) REVERT: C 630 VAL cc_start: 0.8177 (m) cc_final: 0.7937 (p) REVERT: C 638 ASP cc_start: 0.9022 (m-30) cc_final: 0.8003 (m-30) REVERT: C 659 PHE cc_start: 0.8972 (m-80) cc_final: 0.8741 (m-10) REVERT: C 703 LEU cc_start: 0.9251 (mt) cc_final: 0.8704 (mt) REVERT: C 789 LEU cc_start: 0.8294 (tp) cc_final: 0.7989 (mt) REVERT: C 805 LEU cc_start: 0.8886 (tt) cc_final: 0.8570 (mm) REVERT: D 18 PHE cc_start: 0.8807 (m-80) cc_final: 0.8295 (m-10) REVERT: D 138 ASP cc_start: 0.7437 (t0) cc_final: 0.7105 (t0) REVERT: D 165 VAL cc_start: 0.9248 (p) cc_final: 0.8642 (p) REVERT: D 175 GLU cc_start: 0.8676 (mp0) cc_final: 0.8458 (mp0) REVERT: D 177 TYR cc_start: 0.8786 (m-80) cc_final: 0.8488 (m-80) REVERT: D 208 VAL cc_start: 0.8648 (t) cc_final: 0.8247 (t) REVERT: D 232 LEU cc_start: 0.8876 (pt) cc_final: 0.8676 (pp) REVERT: D 293 THR cc_start: 0.8132 (m) cc_final: 0.7856 (p) REVERT: D 373 TYR cc_start: 0.7879 (p90) cc_final: 0.7038 (p90) REVERT: D 378 ASP cc_start: 0.8582 (m-30) cc_final: 0.7942 (m-30) REVERT: D 463 MET cc_start: 0.4924 (mmp) cc_final: 0.3479 (mtt) REVERT: D 502 ILE cc_start: 0.8193 (mt) cc_final: 0.7987 (mp) REVERT: D 514 VAL cc_start: 0.8101 (t) cc_final: 0.7839 (p) REVERT: D 521 LEU cc_start: 0.9361 (mt) cc_final: 0.8992 (mt) REVERT: D 534 ILE cc_start: 0.8954 (mt) cc_final: 0.8552 (tt) REVERT: D 587 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8436 (mp10) REVERT: D 601 VAL cc_start: 0.9387 (t) cc_final: 0.9020 (p) REVERT: D 610 LEU cc_start: 0.9305 (tp) cc_final: 0.8859 (tt) REVERT: D 611 ILE cc_start: 0.9668 (mm) cc_final: 0.9388 (mm) REVERT: D 612 ILE cc_start: 0.9631 (mm) cc_final: 0.9224 (tt) REVERT: D 614 SER cc_start: 0.9613 (m) cc_final: 0.9234 (t) REVERT: D 624 LEU cc_start: 0.8959 (mt) cc_final: 0.8551 (mm) REVERT: D 795 VAL cc_start: 0.9249 (p) cc_final: 0.8733 (m) outliers start: 13 outliers final: 3 residues processed: 745 average time/residue: 0.1616 time to fit residues: 184.5626 Evaluate side-chains 421 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 418 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.065006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045809 restraints weight = 140039.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047435 restraints weight = 92624.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048556 restraints weight = 69361.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049403 restraints weight = 56417.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049994 restraints weight = 48288.852| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25719 Z= 0.137 Angle : 0.606 10.400 34752 Z= 0.318 Chirality : 0.043 0.222 3830 Planarity : 0.005 0.059 4395 Dihedral : 4.783 64.697 3519 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3164 helix: 1.53 (0.14), residues: 1453 sheet: -0.28 (0.27), residues: 404 loop : -0.53 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 628 TYR 0.022 0.001 TYR B 177 PHE 0.032 0.002 PHE D 237 TRP 0.030 0.002 TRP C 526 HIS 0.008 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00304 (25710) covalent geometry : angle 0.60429 (34738) SS BOND : bond 0.00304 ( 7) SS BOND : angle 2.64089 ( 14) hydrogen bonds : bond 0.03894 ( 1188) hydrogen bonds : angle 4.59989 ( 3438) Misc. bond : bond 0.00688 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 499 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8263 (m-30) cc_final: 0.7899 (t0) REVERT: A 463 MET cc_start: 0.9084 (mmm) cc_final: 0.8438 (mmt) REVERT: A 527 MET cc_start: 0.9081 (mmp) cc_final: 0.8057 (mmp) REVERT: A 531 PHE cc_start: 0.9531 (m-10) cc_final: 0.9238 (m-80) REVERT: A 541 PHE cc_start: 0.9110 (t80) cc_final: 0.8891 (t80) REVERT: A 661 ARG cc_start: 0.9164 (mmt180) cc_final: 0.8423 (ttp80) REVERT: A 796 PHE cc_start: 0.9147 (m-80) cc_final: 0.8875 (m-80) REVERT: B 17 LEU cc_start: 0.8879 (tp) cc_final: 0.8505 (tp) REVERT: B 167 ASN cc_start: 0.8128 (m-40) cc_final: 0.7697 (m-40) REVERT: B 175 GLU cc_start: 0.9531 (mp0) cc_final: 0.9310 (pm20) REVERT: B 245 PHE cc_start: 0.9120 (m-80) cc_final: 0.8878 (m-10) REVERT: B 292 MET cc_start: 0.7482 (ppp) cc_final: 0.7183 (ppp) REVERT: B 378 ASP cc_start: 0.8740 (m-30) cc_final: 0.8488 (m-30) REVERT: B 463 MET cc_start: 0.8404 (mmp) cc_final: 0.8142 (mmm) REVERT: B 517 PHE cc_start: 0.9174 (p90) cc_final: 0.8846 (p90) REVERT: B 525 ILE cc_start: 0.9495 (mt) cc_final: 0.9244 (mt) REVERT: B 533 TYR cc_start: 0.8907 (t80) cc_final: 0.8192 (t80) REVERT: B 614 SER cc_start: 0.9862 (m) cc_final: 0.9642 (t) REVERT: B 708 MET cc_start: 0.9854 (ttp) cc_final: 0.9402 (ptm) REVERT: C 74 PHE cc_start: 0.8941 (t80) cc_final: 0.8515 (t80) REVERT: C 79 LYS cc_start: 0.8900 (ptmm) cc_final: 0.8670 (pttm) REVERT: C 107 HIS cc_start: 0.8407 (m90) cc_final: 0.8038 (m90) REVERT: C 159 GLN cc_start: 0.7687 (mp10) cc_final: 0.7484 (mp10) REVERT: C 161 THR cc_start: 0.9008 (m) cc_final: 0.8622 (p) REVERT: C 180 LEU cc_start: 0.8928 (tt) cc_final: 0.8622 (mt) REVERT: C 188 LYS cc_start: 0.9309 (mttt) cc_final: 0.8961 (tptp) REVERT: C 196 CYS cc_start: 0.7511 (m) cc_final: 0.6241 (m) REVERT: C 200 LYS cc_start: 0.9505 (mmmt) cc_final: 0.8782 (tttt) REVERT: C 361 MET cc_start: 0.7454 (mpp) cc_final: 0.6945 (mpp) REVERT: C 479 LEU cc_start: 0.9235 (tp) cc_final: 0.8879 (tp) REVERT: C 518 LEU cc_start: 0.9409 (mt) cc_final: 0.9023 (mt) REVERT: C 527 MET cc_start: 0.8984 (mmp) cc_final: 0.8362 (mmp) REVERT: C 531 PHE cc_start: 0.9591 (m-10) cc_final: 0.9295 (m-80) REVERT: C 541 PHE cc_start: 0.9275 (t80) cc_final: 0.8887 (t80) REVERT: C 587 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8279 (mm-40) REVERT: C 670 MET cc_start: 0.8982 (ptp) cc_final: 0.8496 (ptp) REVERT: C 705 GLU cc_start: 0.8847 (pm20) cc_final: 0.8537 (pm20) REVERT: C 721 MET cc_start: 0.7908 (pmm) cc_final: 0.7610 (pmm) REVERT: D 18 PHE cc_start: 0.9159 (m-80) cc_final: 0.8859 (m-10) REVERT: D 83 ASN cc_start: 0.8764 (p0) cc_final: 0.8046 (p0) REVERT: D 93 HIS cc_start: 0.8467 (m-70) cc_final: 0.7992 (m-70) REVERT: D 138 ASP cc_start: 0.7829 (t0) cc_final: 0.7549 (t0) REVERT: D 151 ASP cc_start: 0.9166 (m-30) cc_final: 0.8854 (m-30) REVERT: D 165 VAL cc_start: 0.9480 (p) cc_final: 0.9264 (p) REVERT: D 177 TYR cc_start: 0.8823 (m-80) cc_final: 0.8156 (m-80) REVERT: D 193 ILE cc_start: 0.9373 (mp) cc_final: 0.8876 (mp) REVERT: D 204 ILE cc_start: 0.9095 (mm) cc_final: 0.8653 (mm) REVERT: D 293 THR cc_start: 0.8097 (m) cc_final: 0.7894 (p) REVERT: D 378 ASP cc_start: 0.8258 (m-30) cc_final: 0.7195 (m-30) REVERT: D 479 LEU cc_start: 0.9088 (tt) cc_final: 0.8854 (mm) REVERT: D 496 MET cc_start: 0.8053 (ppp) cc_final: 0.7629 (ppp) REVERT: D 514 VAL cc_start: 0.9002 (t) cc_final: 0.8742 (p) REVERT: D 517 PHE cc_start: 0.8857 (p90) cc_final: 0.8178 (p90) REVERT: D 525 ILE cc_start: 0.9435 (mt) cc_final: 0.8948 (mt) REVERT: D 541 PHE cc_start: 0.8928 (t80) cc_final: 0.8469 (t80) REVERT: D 610 LEU cc_start: 0.9721 (tp) cc_final: 0.9459 (tp) REVERT: D 611 ILE cc_start: 0.9739 (mm) cc_final: 0.9501 (mt) REVERT: D 614 SER cc_start: 0.9832 (m) cc_final: 0.9612 (t) REVERT: D 795 VAL cc_start: 0.9372 (p) cc_final: 0.9000 (m) outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.1502 time to fit residues: 119.9447 Evaluate side-chains 348 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 22 optimal weight: 0.0470 chunk 64 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 279 optimal weight: 0.4980 chunk 188 optimal weight: 0.0060 chunk 191 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.065297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046421 restraints weight = 139347.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048020 restraints weight = 92470.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049153 restraints weight = 69348.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049984 restraints weight = 56309.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.050583 restraints weight = 48254.461| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25719 Z= 0.114 Angle : 0.578 10.495 34752 Z= 0.298 Chirality : 0.042 0.204 3830 Planarity : 0.004 0.064 4395 Dihedral : 4.473 63.405 3519 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.07 % Favored : 96.74 % Rotamer: Outliers : 0.15 % Allowed : 2.32 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3164 helix: 1.51 (0.14), residues: 1449 sheet: -0.38 (0.27), residues: 387 loop : -0.46 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.014 0.001 TYR D 128 PHE 0.027 0.001 PHE D 237 TRP 0.044 0.002 TRP D 158 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00251 (25710) covalent geometry : angle 0.57641 (34738) SS BOND : bond 0.00226 ( 7) SS BOND : angle 2.13174 ( 14) hydrogen bonds : bond 0.03580 ( 1188) hydrogen bonds : angle 4.44789 ( 3438) Misc. bond : bond 0.00678 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 461 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8258 (m-30) cc_final: 0.7840 (t0) REVERT: A 431 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8962 (mm-30) REVERT: A 463 MET cc_start: 0.8998 (mmm) cc_final: 0.8250 (mmt) REVERT: A 503 MET cc_start: 0.6516 (tpt) cc_final: 0.6312 (tpt) REVERT: A 531 PHE cc_start: 0.9535 (m-10) cc_final: 0.9240 (m-80) REVERT: A 541 PHE cc_start: 0.9073 (t80) cc_final: 0.8398 (t80) REVERT: A 573 ILE cc_start: 0.9038 (tp) cc_final: 0.8737 (tp) REVERT: A 661 ARG cc_start: 0.9164 (mmt180) cc_final: 0.8404 (ttp80) REVERT: B 17 LEU cc_start: 0.8915 (tp) cc_final: 0.8540 (tp) REVERT: B 125 ILE cc_start: 0.9460 (tp) cc_final: 0.9171 (pt) REVERT: B 137 TYR cc_start: 0.8681 (p90) cc_final: 0.8471 (p90) REVERT: B 167 ASN cc_start: 0.8239 (m-40) cc_final: 0.7667 (m-40) REVERT: B 175 GLU cc_start: 0.9550 (mp0) cc_final: 0.9301 (pm20) REVERT: B 188 LYS cc_start: 0.9269 (tmmt) cc_final: 0.9060 (tptp) REVERT: B 193 ILE cc_start: 0.8922 (mp) cc_final: 0.8573 (mm) REVERT: B 221 ILE cc_start: 0.9396 (mt) cc_final: 0.8782 (mt) REVERT: B 292 MET cc_start: 0.7485 (ppp) cc_final: 0.7114 (ppp) REVERT: B 378 ASP cc_start: 0.8709 (m-30) cc_final: 0.8422 (m-30) REVERT: B 408 MET cc_start: 0.7951 (tpp) cc_final: 0.7340 (tpp) REVERT: B 463 MET cc_start: 0.8419 (mmp) cc_final: 0.8166 (mmm) REVERT: B 517 PHE cc_start: 0.9137 (p90) cc_final: 0.8879 (p90) REVERT: B 518 LEU cc_start: 0.9511 (mt) cc_final: 0.9057 (mt) REVERT: B 533 TYR cc_start: 0.8850 (t80) cc_final: 0.8220 (t80) REVERT: B 587 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8497 (mp10) REVERT: B 614 SER cc_start: 0.9810 (m) cc_final: 0.9561 (t) REVERT: C 74 PHE cc_start: 0.8863 (t80) cc_final: 0.8648 (t80) REVERT: C 79 LYS cc_start: 0.8985 (ptmm) cc_final: 0.8697 (pttm) REVERT: C 107 HIS cc_start: 0.8337 (m90) cc_final: 0.7895 (m90) REVERT: C 125 ILE cc_start: 0.9606 (mt) cc_final: 0.9395 (mt) REVERT: C 131 ASP cc_start: 0.8168 (t0) cc_final: 0.7437 (t0) REVERT: C 159 GLN cc_start: 0.7748 (mp10) cc_final: 0.7239 (mp10) REVERT: C 161 THR cc_start: 0.9060 (m) cc_final: 0.8685 (p) REVERT: C 188 LYS cc_start: 0.9351 (mttt) cc_final: 0.9042 (tptp) REVERT: C 196 CYS cc_start: 0.7583 (m) cc_final: 0.5894 (m) REVERT: C 200 LYS cc_start: 0.9499 (mmmt) cc_final: 0.8777 (tttt) REVERT: C 479 LEU cc_start: 0.9281 (tp) cc_final: 0.8864 (tp) REVERT: C 503 MET cc_start: 0.8788 (tpt) cc_final: 0.8570 (tpt) REVERT: C 527 MET cc_start: 0.8905 (mmp) cc_final: 0.8286 (mmp) REVERT: C 531 PHE cc_start: 0.9579 (m-10) cc_final: 0.9260 (m-80) REVERT: C 541 PHE cc_start: 0.9297 (t80) cc_final: 0.8973 (t80) REVERT: C 587 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8533 (mm-40) REVERT: C 617 THR cc_start: 0.9699 (m) cc_final: 0.9471 (p) REVERT: C 705 GLU cc_start: 0.8811 (pm20) cc_final: 0.7359 (pm20) REVERT: C 708 MET cc_start: 0.8730 (mmp) cc_final: 0.8516 (mmp) REVERT: D 83 ASN cc_start: 0.8866 (p0) cc_final: 0.8323 (p0) REVERT: D 93 HIS cc_start: 0.8403 (m-70) cc_final: 0.8040 (m-70) REVERT: D 138 ASP cc_start: 0.7790 (t0) cc_final: 0.7526 (t0) REVERT: D 151 ASP cc_start: 0.9058 (m-30) cc_final: 0.8852 (m-30) REVERT: D 293 THR cc_start: 0.8167 (m) cc_final: 0.7933 (p) REVERT: D 378 ASP cc_start: 0.8347 (m-30) cc_final: 0.6941 (m-30) REVERT: D 463 MET cc_start: 0.7107 (mmp) cc_final: 0.6576 (mmp) REVERT: D 496 MET cc_start: 0.8314 (ppp) cc_final: 0.7874 (ppp) REVERT: D 514 VAL cc_start: 0.8964 (t) cc_final: 0.8626 (p) REVERT: D 517 PHE cc_start: 0.8871 (p90) cc_final: 0.8215 (p90) REVERT: D 518 LEU cc_start: 0.9311 (mp) cc_final: 0.9096 (mp) REVERT: D 541 PHE cc_start: 0.9021 (t80) cc_final: 0.8578 (t80) REVERT: D 587 GLN cc_start: 0.8429 (mp10) cc_final: 0.8177 (mp10) REVERT: D 614 SER cc_start: 0.9839 (m) cc_final: 0.9476 (t) REVERT: D 629 MET cc_start: 0.7410 (tpp) cc_final: 0.6941 (mmt) REVERT: D 795 VAL cc_start: 0.9349 (p) cc_final: 0.8985 (m) outliers start: 4 outliers final: 1 residues processed: 461 average time/residue: 0.1681 time to fit residues: 125.4150 Evaluate side-chains 336 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 315 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.058099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.039851 restraints weight = 153917.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.041254 restraints weight = 100850.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.042225 restraints weight = 75745.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.042913 restraints weight = 61984.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043356 restraints weight = 53842.927| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25719 Z= 0.270 Angle : 0.753 14.557 34752 Z= 0.395 Chirality : 0.045 0.184 3830 Planarity : 0.005 0.060 4395 Dihedral : 5.193 54.917 3519 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.46 % Favored : 95.35 % Rotamer: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.15), residues: 3164 helix: 0.99 (0.14), residues: 1458 sheet: -0.63 (0.27), residues: 383 loop : -0.50 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 308 TYR 0.028 0.002 TYR A 286 PHE 0.045 0.003 PHE D 237 TRP 0.055 0.003 TRP C 526 HIS 0.009 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00565 (25710) covalent geometry : angle 0.75257 (34738) SS BOND : bond 0.00455 ( 7) SS BOND : angle 1.90891 ( 14) hydrogen bonds : bond 0.04711 ( 1188) hydrogen bonds : angle 5.19855 ( 3438) Misc. bond : bond 0.00726 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 378 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.9361 (mm) cc_final: 0.8946 (tp) REVERT: A 113 MET cc_start: 0.9163 (mpp) cc_final: 0.8929 (mpp) REVERT: A 195 ASP cc_start: 0.8800 (t0) cc_final: 0.8536 (t0) REVERT: A 214 HIS cc_start: 0.9149 (p-80) cc_final: 0.8910 (p-80) REVERT: A 431 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9101 (mm-30) REVERT: A 463 MET cc_start: 0.8761 (mmm) cc_final: 0.8406 (mmm) REVERT: A 527 MET cc_start: 0.9090 (mmp) cc_final: 0.7881 (mmm) REVERT: A 531 PHE cc_start: 0.9557 (m-10) cc_final: 0.9225 (m-80) REVERT: A 541 PHE cc_start: 0.9203 (t80) cc_final: 0.8843 (t80) REVERT: A 661 ARG cc_start: 0.9209 (mmt180) cc_final: 0.8566 (ttp80) REVERT: A 666 VAL cc_start: 0.9113 (p) cc_final: 0.8825 (p) REVERT: A 732 TYR cc_start: 0.8906 (m-10) cc_final: 0.8642 (m-10) REVERT: B 25 GLU cc_start: 0.8981 (mp0) cc_final: 0.8476 (mp0) REVERT: B 175 GLU cc_start: 0.9613 (mp0) cc_final: 0.9374 (mp0) REVERT: B 192 VAL cc_start: 0.9661 (t) cc_final: 0.9444 (m) REVERT: B 193 ILE cc_start: 0.9512 (mp) cc_final: 0.9161 (mm) REVERT: B 292 MET cc_start: 0.8111 (ppp) cc_final: 0.7677 (ppp) REVERT: B 378 ASP cc_start: 0.9012 (m-30) cc_final: 0.8698 (m-30) REVERT: B 408 MET cc_start: 0.8754 (tpp) cc_final: 0.8261 (tpp) REVERT: B 463 MET cc_start: 0.8955 (mmp) cc_final: 0.8737 (mmp) REVERT: B 496 MET cc_start: 0.9215 (tpp) cc_final: 0.8864 (ttm) REVERT: B 509 LYS cc_start: 0.8773 (pttm) cc_final: 0.8512 (pptt) REVERT: B 533 TYR cc_start: 0.9214 (t80) cc_final: 0.8710 (t80) REVERT: B 670 MET cc_start: 0.9003 (mtt) cc_final: 0.8719 (mmt) REVERT: B 721 MET cc_start: 0.9265 (pmm) cc_final: 0.8790 (pmm) REVERT: C 25 GLU cc_start: 0.9198 (mp0) cc_final: 0.8804 (mm-30) REVERT: C 292 MET cc_start: 0.9420 (ppp) cc_final: 0.9042 (ppp) REVERT: C 428 LEU cc_start: 0.9867 (tp) cc_final: 0.9640 (mp) REVERT: C 479 LEU cc_start: 0.9255 (tp) cc_final: 0.8998 (tp) REVERT: C 527 MET cc_start: 0.8949 (mmp) cc_final: 0.8463 (mmp) REVERT: C 531 PHE cc_start: 0.9603 (m-10) cc_final: 0.9278 (m-80) REVERT: C 541 PHE cc_start: 0.9303 (t80) cc_final: 0.8859 (t80) REVERT: C 587 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8190 (mm-40) REVERT: C 705 GLU cc_start: 0.8878 (pm20) cc_final: 0.8091 (pm20) REVERT: C 708 MET cc_start: 0.9200 (mmp) cc_final: 0.8885 (mmp) REVERT: C 721 MET cc_start: 0.8924 (pmm) cc_final: 0.8557 (pmm) REVERT: C 732 TYR cc_start: 0.8348 (m-10) cc_final: 0.7703 (m-10) REVERT: D 83 ASN cc_start: 0.9049 (p0) cc_final: 0.8213 (p0) REVERT: D 93 HIS cc_start: 0.9043 (m-70) cc_final: 0.8407 (m-70) REVERT: D 113 MET cc_start: 0.8976 (tpp) cc_final: 0.8110 (tpt) REVERT: D 127 TYR cc_start: 0.9058 (t80) cc_final: 0.8818 (t80) REVERT: D 138 ASP cc_start: 0.8678 (t0) cc_final: 0.8256 (t0) REVERT: D 177 TYR cc_start: 0.9423 (m-80) cc_final: 0.8957 (m-10) REVERT: D 284 LEU cc_start: 0.9184 (mm) cc_final: 0.8827 (tp) REVERT: D 378 ASP cc_start: 0.8751 (m-30) cc_final: 0.7664 (m-30) REVERT: D 463 MET cc_start: 0.7684 (mmp) cc_final: 0.7038 (mmm) REVERT: D 514 VAL cc_start: 0.9091 (t) cc_final: 0.8861 (p) REVERT: D 517 PHE cc_start: 0.9081 (p90) cc_final: 0.8567 (p90) REVERT: D 614 SER cc_start: 0.9835 (m) cc_final: 0.9534 (t) REVERT: D 795 VAL cc_start: 0.9137 (p) cc_final: 0.8817 (m) outliers start: 5 outliers final: 1 residues processed: 383 average time/residue: 0.1629 time to fit residues: 102.0518 Evaluate side-chains 282 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 248 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 101 optimal weight: 0.0060 chunk 267 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.039897 restraints weight = 151377.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041278 restraints weight = 99000.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.042225 restraints weight = 74273.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042903 restraints weight = 60877.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.043341 restraints weight = 52927.674| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25719 Z= 0.201 Angle : 0.627 10.636 34752 Z= 0.330 Chirality : 0.043 0.195 3830 Planarity : 0.004 0.090 4395 Dihedral : 4.899 55.887 3519 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.73 % Rotamer: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3164 helix: 1.09 (0.14), residues: 1479 sheet: -0.67 (0.27), residues: 396 loop : -0.54 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.025 0.002 TYR D 177 PHE 0.018 0.002 PHE C 659 TRP 0.038 0.002 TRP C 526 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00417 (25710) covalent geometry : angle 0.62617 (34738) SS BOND : bond 0.01071 ( 7) SS BOND : angle 1.53699 ( 14) hydrogen bonds : bond 0.03909 ( 1188) hydrogen bonds : angle 4.90419 ( 3438) Misc. bond : bond 0.00647 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9179 (m-80) cc_final: 0.8656 (m-10) REVERT: A 97 ILE cc_start: 0.9420 (mm) cc_final: 0.9151 (tp) REVERT: A 136 LEU cc_start: 0.9655 (mm) cc_final: 0.9368 (mm) REVERT: A 140 ASP cc_start: 0.9128 (t0) cc_final: 0.8778 (t0) REVERT: A 159 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8904 (tp-100) REVERT: A 195 ASP cc_start: 0.8862 (t0) cc_final: 0.8644 (t0) REVERT: A 463 MET cc_start: 0.8892 (mmm) cc_final: 0.8632 (mmm) REVERT: A 527 MET cc_start: 0.8900 (mmp) cc_final: 0.7779 (mmm) REVERT: A 531 PHE cc_start: 0.9505 (m-10) cc_final: 0.9217 (m-80) REVERT: A 541 PHE cc_start: 0.9147 (t80) cc_final: 0.8779 (t80) REVERT: A 661 ARG cc_start: 0.9163 (mmt180) cc_final: 0.8508 (ttp80) REVERT: A 670 MET cc_start: 0.9204 (ptt) cc_final: 0.8858 (ppp) REVERT: A 674 MET cc_start: 0.9312 (ptm) cc_final: 0.8918 (ptt) REVERT: A 732 TYR cc_start: 0.8898 (m-10) cc_final: 0.8641 (m-80) REVERT: B 25 GLU cc_start: 0.9030 (mp0) cc_final: 0.8640 (mp0) REVERT: B 93 HIS cc_start: 0.8887 (m90) cc_final: 0.8655 (m-70) REVERT: B 175 GLU cc_start: 0.9562 (mp0) cc_final: 0.9244 (pm20) REVERT: B 192 VAL cc_start: 0.9646 (t) cc_final: 0.9382 (m) REVERT: B 193 ILE cc_start: 0.9420 (mp) cc_final: 0.9115 (mm) REVERT: B 221 ILE cc_start: 0.9472 (mt) cc_final: 0.9126 (mm) REVERT: B 292 MET cc_start: 0.8051 (ppp) cc_final: 0.7608 (ppp) REVERT: B 378 ASP cc_start: 0.8947 (m-30) cc_final: 0.8640 (m-30) REVERT: B 380 MET cc_start: 0.7849 (tpt) cc_final: 0.7647 (tmm) REVERT: B 408 MET cc_start: 0.8853 (tpp) cc_final: 0.8371 (tpp) REVERT: B 496 MET cc_start: 0.9188 (tpp) cc_final: 0.8860 (ttm) REVERT: B 509 LYS cc_start: 0.8745 (pttm) cc_final: 0.8494 (pptt) REVERT: B 533 TYR cc_start: 0.9177 (t80) cc_final: 0.8522 (t80) REVERT: B 670 MET cc_start: 0.9017 (mtt) cc_final: 0.8740 (mmt) REVERT: B 721 MET cc_start: 0.9261 (pmm) cc_final: 0.9009 (pmm) REVERT: B 799 LEU cc_start: 0.9506 (tt) cc_final: 0.9146 (mm) REVERT: C 25 GLU cc_start: 0.9242 (mp0) cc_final: 0.9030 (mp0) REVERT: C 117 LEU cc_start: 0.9342 (tt) cc_final: 0.9015 (mp) REVERT: C 292 MET cc_start: 0.9260 (ppp) cc_final: 0.8960 (ppp) REVERT: C 496 MET cc_start: 0.9007 (tmm) cc_final: 0.8662 (tmm) REVERT: C 527 MET cc_start: 0.8901 (mmp) cc_final: 0.8231 (mmp) REVERT: C 531 PHE cc_start: 0.9531 (m-10) cc_final: 0.9119 (m-80) REVERT: C 541 PHE cc_start: 0.9230 (t80) cc_final: 0.9008 (t80) REVERT: C 661 ARG cc_start: 0.8977 (mpt90) cc_final: 0.8572 (ttp80) REVERT: C 705 GLU cc_start: 0.8854 (pm20) cc_final: 0.8010 (pm20) REVERT: C 708 MET cc_start: 0.9346 (mmp) cc_final: 0.9005 (mmp) REVERT: C 721 MET cc_start: 0.8844 (pmm) cc_final: 0.8407 (pmm) REVERT: D 83 ASN cc_start: 0.9070 (p0) cc_final: 0.8277 (p0) REVERT: D 93 HIS cc_start: 0.9095 (m-70) cc_final: 0.8480 (m-70) REVERT: D 113 MET cc_start: 0.9045 (tpp) cc_final: 0.8163 (tpp) REVERT: D 138 ASP cc_start: 0.8414 (t0) cc_final: 0.7851 (t0) REVERT: D 151 ASP cc_start: 0.9294 (m-30) cc_final: 0.9086 (m-30) REVERT: D 241 GLU cc_start: 0.8684 (tp30) cc_final: 0.8365 (tp30) REVERT: D 284 LEU cc_start: 0.9345 (mm) cc_final: 0.9063 (mm) REVERT: D 378 ASP cc_start: 0.8635 (m-30) cc_final: 0.7702 (m-30) REVERT: D 463 MET cc_start: 0.7517 (mmp) cc_final: 0.6856 (mmm) REVERT: D 517 PHE cc_start: 0.9149 (p90) cc_final: 0.8597 (p90) REVERT: D 585 MET cc_start: 0.8598 (mmm) cc_final: 0.8048 (mmm) REVERT: D 614 SER cc_start: 0.9790 (m) cc_final: 0.9466 (t) REVERT: D 795 VAL cc_start: 0.9031 (p) cc_final: 0.8581 (m) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.1614 time to fit residues: 94.6006 Evaluate side-chains 257 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 276 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 253 optimal weight: 0.8980 chunk 277 optimal weight: 0.0010 chunk 200 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.059476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.041159 restraints weight = 152562.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042614 restraints weight = 99477.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.043628 restraints weight = 74419.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.044335 restraints weight = 60564.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044665 restraints weight = 52452.688| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25719 Z= 0.112 Angle : 0.566 11.313 34752 Z= 0.291 Chirality : 0.042 0.205 3830 Planarity : 0.004 0.083 4395 Dihedral : 4.526 57.480 3519 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3164 helix: 1.33 (0.14), residues: 1483 sheet: -0.57 (0.27), residues: 397 loop : -0.47 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 178 TYR 0.017 0.001 TYR A 286 PHE 0.017 0.001 PHE C 796 TRP 0.025 0.001 TRP C 526 HIS 0.007 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00248 (25710) covalent geometry : angle 0.56530 (34738) SS BOND : bond 0.00272 ( 7) SS BOND : angle 1.42579 ( 14) hydrogen bonds : bond 0.03464 ( 1188) hydrogen bonds : angle 4.56391 ( 3438) Misc. bond : bond 0.00507 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9153 (m-80) cc_final: 0.8604 (m-10) REVERT: A 97 ILE cc_start: 0.9394 (mm) cc_final: 0.9182 (tp) REVERT: A 136 LEU cc_start: 0.9631 (mm) cc_final: 0.9301 (mm) REVERT: A 140 ASP cc_start: 0.9103 (t0) cc_final: 0.8874 (t0) REVERT: A 159 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8843 (tp-100) REVERT: A 214 HIS cc_start: 0.9092 (p-80) cc_final: 0.8786 (p-80) REVERT: A 463 MET cc_start: 0.8912 (mmm) cc_final: 0.8508 (mmm) REVERT: A 476 ILE cc_start: 0.8364 (mm) cc_final: 0.8148 (tp) REVERT: A 527 MET cc_start: 0.8860 (mmp) cc_final: 0.7692 (mmm) REVERT: A 531 PHE cc_start: 0.9489 (m-10) cc_final: 0.9180 (m-80) REVERT: A 541 PHE cc_start: 0.9118 (t80) cc_final: 0.8559 (t80) REVERT: A 585 MET cc_start: 0.9424 (mmm) cc_final: 0.8968 (tpp) REVERT: A 661 ARG cc_start: 0.9182 (mmt180) cc_final: 0.8480 (ttp80) REVERT: A 670 MET cc_start: 0.9186 (ptt) cc_final: 0.8899 (ppp) REVERT: A 674 MET cc_start: 0.9263 (ptm) cc_final: 0.8916 (ptt) REVERT: A 732 TYR cc_start: 0.8785 (m-10) cc_final: 0.8537 (m-10) REVERT: B 25 GLU cc_start: 0.9010 (mp0) cc_final: 0.8487 (mp0) REVERT: B 93 HIS cc_start: 0.8778 (m90) cc_final: 0.8531 (m-70) REVERT: B 124 LEU cc_start: 0.9632 (mm) cc_final: 0.9286 (mm) REVERT: B 167 ASN cc_start: 0.9156 (t0) cc_final: 0.8931 (t0) REVERT: B 175 GLU cc_start: 0.9546 (mp0) cc_final: 0.9204 (pm20) REVERT: B 192 VAL cc_start: 0.9634 (t) cc_final: 0.9424 (m) REVERT: B 292 MET cc_start: 0.8064 (ppp) cc_final: 0.7606 (ppp) REVERT: B 378 ASP cc_start: 0.8875 (m-30) cc_final: 0.8563 (m-30) REVERT: B 496 MET cc_start: 0.9120 (tpp) cc_final: 0.8744 (ttp) REVERT: B 503 MET cc_start: 0.8519 (mmm) cc_final: 0.8098 (mmm) REVERT: B 509 LYS cc_start: 0.8775 (pttm) cc_final: 0.8501 (pptt) REVERT: B 518 LEU cc_start: 0.9420 (mt) cc_final: 0.8868 (tt) REVERT: B 533 TYR cc_start: 0.9135 (t80) cc_final: 0.8354 (t80) REVERT: B 670 MET cc_start: 0.9039 (mtt) cc_final: 0.8824 (mmt) REVERT: B 799 LEU cc_start: 0.9501 (tt) cc_final: 0.9126 (mm) REVERT: C 25 GLU cc_start: 0.9310 (mp0) cc_final: 0.8766 (mm-30) REVERT: C 117 LEU cc_start: 0.9246 (tt) cc_final: 0.8943 (mp) REVERT: C 496 MET cc_start: 0.9010 (tmm) cc_final: 0.8745 (tmm) REVERT: C 518 LEU cc_start: 0.9158 (mt) cc_final: 0.8909 (mt) REVERT: C 527 MET cc_start: 0.8876 (mmp) cc_final: 0.8210 (mmp) REVERT: C 531 PHE cc_start: 0.9497 (m-10) cc_final: 0.9085 (m-80) REVERT: C 541 PHE cc_start: 0.9195 (t80) cc_final: 0.8956 (t80) REVERT: C 587 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8296 (mm-40) REVERT: C 661 ARG cc_start: 0.9016 (mpt90) cc_final: 0.8558 (ttp80) REVERT: C 705 GLU cc_start: 0.8844 (pm20) cc_final: 0.7945 (pm20) REVERT: C 708 MET cc_start: 0.9333 (mmp) cc_final: 0.9037 (mmp) REVERT: C 721 MET cc_start: 0.8581 (pmm) cc_final: 0.8164 (pmm) REVERT: D 83 ASN cc_start: 0.9055 (p0) cc_final: 0.8280 (p0) REVERT: D 93 HIS cc_start: 0.9055 (m-70) cc_final: 0.8533 (m-70) REVERT: D 113 MET cc_start: 0.9157 (tpp) cc_final: 0.7582 (tpp) REVERT: D 138 ASP cc_start: 0.8122 (t0) cc_final: 0.7569 (t0) REVERT: D 151 ASP cc_start: 0.9277 (m-30) cc_final: 0.9040 (t0) REVERT: D 225 LEU cc_start: 0.8844 (mm) cc_final: 0.8572 (mm) REVERT: D 241 GLU cc_start: 0.8724 (tp30) cc_final: 0.8393 (tp30) REVERT: D 284 LEU cc_start: 0.9355 (mm) cc_final: 0.8467 (mm) REVERT: D 378 ASP cc_start: 0.8507 (m-30) cc_final: 0.7575 (m-30) REVERT: D 463 MET cc_start: 0.7455 (mmp) cc_final: 0.6623 (mmp) REVERT: D 517 PHE cc_start: 0.9045 (p90) cc_final: 0.8507 (p90) REVERT: D 614 SER cc_start: 0.9765 (m) cc_final: 0.9434 (t) REVERT: D 629 MET cc_start: 0.7703 (mmm) cc_final: 0.7472 (mmm) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1583 time to fit residues: 97.8096 Evaluate side-chains 278 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 235 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 286 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.040573 restraints weight = 153283.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.041892 restraints weight = 103159.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.042833 restraints weight = 78798.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.043486 restraints weight = 65046.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.043898 restraints weight = 56819.279| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25719 Z= 0.145 Angle : 0.581 11.819 34752 Z= 0.302 Chirality : 0.042 0.206 3830 Planarity : 0.004 0.071 4395 Dihedral : 4.538 58.611 3519 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3164 helix: 1.31 (0.14), residues: 1484 sheet: -0.64 (0.27), residues: 398 loop : -0.43 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.015 0.001 TYR A 286 PHE 0.015 0.001 PHE C 796 TRP 0.044 0.002 TRP C 526 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00313 (25710) covalent geometry : angle 0.58048 (34738) SS BOND : bond 0.00247 ( 7) SS BOND : angle 1.80979 ( 14) hydrogen bonds : bond 0.03484 ( 1188) hydrogen bonds : angle 4.63692 ( 3438) Misc. bond : bond 0.00540 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9233 (m-80) cc_final: 0.8986 (m-80) REVERT: A 136 LEU cc_start: 0.9641 (mm) cc_final: 0.9344 (mm) REVERT: A 140 ASP cc_start: 0.9109 (t0) cc_final: 0.8832 (t0) REVERT: A 159 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8743 (tp-100) REVERT: A 214 HIS cc_start: 0.9146 (p-80) cc_final: 0.8809 (p-80) REVERT: A 463 MET cc_start: 0.8862 (mmm) cc_final: 0.8119 (mmm) REVERT: A 476 ILE cc_start: 0.8460 (mm) cc_final: 0.8252 (tp) REVERT: A 479 LEU cc_start: 0.9019 (tp) cc_final: 0.8773 (tp) REVERT: A 527 MET cc_start: 0.8857 (mmp) cc_final: 0.7673 (mmm) REVERT: A 531 PHE cc_start: 0.9492 (m-10) cc_final: 0.9180 (m-80) REVERT: A 541 PHE cc_start: 0.9075 (t80) cc_final: 0.8525 (t80) REVERT: A 661 ARG cc_start: 0.9178 (mmt180) cc_final: 0.8476 (ttp80) REVERT: A 670 MET cc_start: 0.9177 (ptt) cc_final: 0.8937 (ppp) REVERT: A 674 MET cc_start: 0.9300 (ptm) cc_final: 0.8946 (ptt) REVERT: B 25 GLU cc_start: 0.9072 (mp0) cc_final: 0.8715 (mp0) REVERT: B 93 HIS cc_start: 0.8715 (m90) cc_final: 0.8454 (m-70) REVERT: B 175 GLU cc_start: 0.9532 (mp0) cc_final: 0.9204 (pm20) REVERT: B 192 VAL cc_start: 0.9640 (t) cc_final: 0.9380 (m) REVERT: B 193 ILE cc_start: 0.9421 (mp) cc_final: 0.9056 (mp) REVERT: B 292 MET cc_start: 0.8111 (ppp) cc_final: 0.7668 (ppp) REVERT: B 378 ASP cc_start: 0.8950 (m-30) cc_final: 0.8635 (m-30) REVERT: B 408 MET cc_start: 0.8263 (tpp) cc_final: 0.7624 (tpp) REVERT: B 496 MET cc_start: 0.9144 (tpp) cc_final: 0.8788 (ttp) REVERT: B 509 LYS cc_start: 0.8777 (pttm) cc_final: 0.8485 (pptt) REVERT: B 533 TYR cc_start: 0.9159 (t80) cc_final: 0.8399 (t80) REVERT: B 585 MET cc_start: 0.8144 (mmm) cc_final: 0.7403 (mmm) REVERT: B 721 MET cc_start: 0.9248 (pmm) cc_final: 0.8933 (pmm) REVERT: C 25 GLU cc_start: 0.9303 (mp0) cc_final: 0.9043 (mp0) REVERT: C 117 LEU cc_start: 0.9288 (tt) cc_final: 0.8993 (mp) REVERT: C 442 LEU cc_start: 0.9243 (mt) cc_final: 0.9024 (mt) REVERT: C 496 MET cc_start: 0.9023 (tmm) cc_final: 0.8782 (tmm) REVERT: C 527 MET cc_start: 0.8739 (mmp) cc_final: 0.8204 (mmp) REVERT: C 531 PHE cc_start: 0.9476 (m-10) cc_final: 0.9083 (m-80) REVERT: C 541 PHE cc_start: 0.9202 (t80) cc_final: 0.8947 (t80) REVERT: C 661 ARG cc_start: 0.9064 (mpt90) cc_final: 0.8511 (ttp80) REVERT: C 705 GLU cc_start: 0.8820 (pm20) cc_final: 0.7950 (pm20) REVERT: C 708 MET cc_start: 0.9411 (mmp) cc_final: 0.9076 (mmp) REVERT: C 721 MET cc_start: 0.8707 (pmm) cc_final: 0.8489 (pmm) REVERT: D 83 ASN cc_start: 0.9063 (p0) cc_final: 0.8284 (p0) REVERT: D 93 HIS cc_start: 0.9087 (m-70) cc_final: 0.8566 (m-70) REVERT: D 113 MET cc_start: 0.9099 (tpp) cc_final: 0.8770 (tpp) REVERT: D 138 ASP cc_start: 0.8083 (t0) cc_final: 0.7532 (t0) REVERT: D 241 GLU cc_start: 0.8718 (tp30) cc_final: 0.8440 (tp30) REVERT: D 463 MET cc_start: 0.7477 (mmp) cc_final: 0.6740 (mmp) REVERT: D 517 PHE cc_start: 0.9060 (p90) cc_final: 0.8825 (p90) REVERT: D 585 MET cc_start: 0.8513 (mmm) cc_final: 0.7743 (mmm) REVERT: D 614 SER cc_start: 0.9782 (m) cc_final: 0.9551 (p) REVERT: D 629 MET cc_start: 0.7552 (mmm) cc_final: 0.7331 (mmm) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.1582 time to fit residues: 91.3212 Evaluate side-chains 260 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 203 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 214 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041911 restraints weight = 149877.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043321 restraints weight = 100111.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.044246 restraints weight = 75762.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044947 restraints weight = 62474.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045398 restraints weight = 54385.859| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25719 Z= 0.102 Angle : 0.564 12.031 34752 Z= 0.288 Chirality : 0.042 0.193 3830 Planarity : 0.004 0.074 4395 Dihedral : 4.319 62.485 3519 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.15), residues: 3164 helix: 1.41 (0.14), residues: 1484 sheet: -0.44 (0.28), residues: 369 loop : -0.47 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.015 0.001 TYR A 286 PHE 0.015 0.001 PHE A 88 TRP 0.031 0.001 TRP C 526 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00224 (25710) covalent geometry : angle 0.56307 (34738) SS BOND : bond 0.00250 ( 7) SS BOND : angle 1.54683 ( 14) hydrogen bonds : bond 0.03177 ( 1188) hydrogen bonds : angle 4.42964 ( 3438) Misc. bond : bond 0.00457 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9218 (m-80) cc_final: 0.8604 (m-10) REVERT: A 82 VAL cc_start: 0.9520 (p) cc_final: 0.9318 (p) REVERT: A 136 LEU cc_start: 0.9626 (mm) cc_final: 0.9327 (mm) REVERT: A 140 ASP cc_start: 0.9173 (t0) cc_final: 0.8880 (t0) REVERT: A 159 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8701 (tp-100) REVERT: A 214 HIS cc_start: 0.9075 (p-80) cc_final: 0.8848 (p-80) REVERT: A 334 LYS cc_start: 0.9413 (mtmt) cc_final: 0.9132 (mttt) REVERT: A 356 TYR cc_start: 0.8984 (p90) cc_final: 0.8255 (p90) REVERT: A 463 MET cc_start: 0.8902 (mmm) cc_final: 0.8154 (mmm) REVERT: A 476 ILE cc_start: 0.8347 (mm) cc_final: 0.8076 (tp) REVERT: A 479 LEU cc_start: 0.8909 (tp) cc_final: 0.8632 (tp) REVERT: A 527 MET cc_start: 0.8822 (mmp) cc_final: 0.7598 (mmm) REVERT: A 531 PHE cc_start: 0.9469 (m-10) cc_final: 0.9175 (m-80) REVERT: A 585 MET cc_start: 0.9432 (mmm) cc_final: 0.9160 (mmm) REVERT: A 661 ARG cc_start: 0.9166 (mmt180) cc_final: 0.8435 (ttp80) REVERT: A 670 MET cc_start: 0.9155 (ptt) cc_final: 0.8895 (ppp) REVERT: A 674 MET cc_start: 0.9226 (ptm) cc_final: 0.8901 (ptt) REVERT: A 732 TYR cc_start: 0.8752 (m-10) cc_final: 0.8478 (m-10) REVERT: B 25 GLU cc_start: 0.9023 (mp0) cc_final: 0.8560 (mp0) REVERT: B 93 HIS cc_start: 0.8578 (m90) cc_final: 0.8350 (m-70) REVERT: B 175 GLU cc_start: 0.9522 (mp0) cc_final: 0.9164 (pm20) REVERT: B 192 VAL cc_start: 0.9629 (t) cc_final: 0.9317 (m) REVERT: B 193 ILE cc_start: 0.9463 (mp) cc_final: 0.9053 (mp) REVERT: B 292 MET cc_start: 0.8134 (ppp) cc_final: 0.7695 (ppp) REVERT: B 378 ASP cc_start: 0.8915 (m-30) cc_final: 0.8582 (m-30) REVERT: B 408 MET cc_start: 0.8236 (tpp) cc_final: 0.7557 (tpp) REVERT: B 509 LYS cc_start: 0.8790 (pttm) cc_final: 0.8499 (pptt) REVERT: B 518 LEU cc_start: 0.9292 (mt) cc_final: 0.8732 (tt) REVERT: B 585 MET cc_start: 0.7988 (mmm) cc_final: 0.7152 (mmm) REVERT: B 799 LEU cc_start: 0.9496 (tt) cc_final: 0.9133 (mm) REVERT: C 25 GLU cc_start: 0.9321 (mp0) cc_final: 0.8784 (mm-30) REVERT: C 160 VAL cc_start: 0.9612 (t) cc_final: 0.9346 (m) REVERT: C 425 CYS cc_start: 0.9676 (m) cc_final: 0.9451 (m) REVERT: C 479 LEU cc_start: 0.9295 (tp) cc_final: 0.9084 (pp) REVERT: C 496 MET cc_start: 0.9042 (tmm) cc_final: 0.8814 (tmm) REVERT: C 503 MET cc_start: 0.8556 (tpt) cc_final: 0.8322 (tpt) REVERT: C 527 MET cc_start: 0.8659 (mmp) cc_final: 0.8035 (mmp) REVERT: C 531 PHE cc_start: 0.9463 (m-10) cc_final: 0.9080 (m-80) REVERT: C 541 PHE cc_start: 0.9147 (t80) cc_final: 0.8904 (t80) REVERT: C 661 ARG cc_start: 0.9068 (mpt90) cc_final: 0.8490 (ttp80) REVERT: C 705 GLU cc_start: 0.8798 (pm20) cc_final: 0.7984 (pm20) REVERT: C 708 MET cc_start: 0.9389 (mmp) cc_final: 0.9047 (mmp) REVERT: C 721 MET cc_start: 0.8246 (pmm) cc_final: 0.7741 (pmm) REVERT: D 83 ASN cc_start: 0.9100 (p0) cc_final: 0.8453 (p0) REVERT: D 93 HIS cc_start: 0.8969 (m-70) cc_final: 0.8352 (m-70) REVERT: D 113 MET cc_start: 0.9186 (tpp) cc_final: 0.7801 (tpp) REVERT: D 138 ASP cc_start: 0.7820 (t0) cc_final: 0.7226 (t0) REVERT: D 241 GLU cc_start: 0.8661 (tp30) cc_final: 0.8403 (tp30) REVERT: D 284 LEU cc_start: 0.9454 (mm) cc_final: 0.8631 (mm) REVERT: D 463 MET cc_start: 0.7305 (mmp) cc_final: 0.6691 (mmp) REVERT: D 517 PHE cc_start: 0.8954 (p90) cc_final: 0.8551 (p90) REVERT: D 518 LEU cc_start: 0.9173 (mp) cc_final: 0.8752 (mt) REVERT: D 585 MET cc_start: 0.8438 (mmm) cc_final: 0.7655 (mmm) REVERT: D 614 SER cc_start: 0.9776 (m) cc_final: 0.9422 (t) REVERT: D 629 MET cc_start: 0.7623 (mmm) cc_final: 0.7375 (mmm) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.1651 time to fit residues: 99.3123 Evaluate side-chains 272 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 146 optimal weight: 0.2980 chunk 160 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.059256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.041261 restraints weight = 152791.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.042660 restraints weight = 100764.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.043590 restraints weight = 76024.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.044286 restraints weight = 62572.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.044727 restraints weight = 54399.969| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.7476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25719 Z= 0.115 Angle : 0.561 12.396 34752 Z= 0.289 Chirality : 0.042 0.209 3830 Planarity : 0.004 0.061 4395 Dihedral : 4.308 62.963 3519 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 3164 helix: 1.42 (0.14), residues: 1482 sheet: -0.53 (0.28), residues: 374 loop : -0.42 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 141 TYR 0.014 0.001 TYR A 286 PHE 0.017 0.001 PHE A 607 TRP 0.026 0.001 TRP B 605 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00255 (25710) covalent geometry : angle 0.55985 (34738) SS BOND : bond 0.00334 ( 7) SS BOND : angle 1.62227 ( 14) hydrogen bonds : bond 0.03209 ( 1188) hydrogen bonds : angle 4.44464 ( 3438) Misc. bond : bond 0.00475 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9218 (m-80) cc_final: 0.8791 (m-10) REVERT: A 136 LEU cc_start: 0.9671 (mm) cc_final: 0.9362 (mm) REVERT: A 140 ASP cc_start: 0.9136 (t0) cc_final: 0.8882 (t0) REVERT: A 159 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8695 (tp-100) REVERT: A 214 HIS cc_start: 0.9132 (p-80) cc_final: 0.8789 (p-80) REVERT: A 356 TYR cc_start: 0.9034 (p90) cc_final: 0.8307 (p90) REVERT: A 463 MET cc_start: 0.8890 (mmm) cc_final: 0.8189 (mmm) REVERT: A 476 ILE cc_start: 0.8389 (mm) cc_final: 0.8147 (tp) REVERT: A 479 LEU cc_start: 0.8918 (tp) cc_final: 0.8686 (tp) REVERT: A 527 MET cc_start: 0.8727 (mmp) cc_final: 0.7549 (mmm) REVERT: A 531 PHE cc_start: 0.9481 (m-10) cc_final: 0.9139 (m-80) REVERT: A 541 PHE cc_start: 0.9113 (t80) cc_final: 0.8564 (t80) REVERT: A 585 MET cc_start: 0.9416 (mmm) cc_final: 0.8911 (tpp) REVERT: A 661 ARG cc_start: 0.9178 (mmt180) cc_final: 0.8465 (ttp80) REVERT: A 670 MET cc_start: 0.9163 (ptt) cc_final: 0.8897 (ppp) REVERT: A 674 MET cc_start: 0.9263 (ptm) cc_final: 0.8966 (ptt) REVERT: B 25 GLU cc_start: 0.9084 (mp0) cc_final: 0.8734 (mp0) REVERT: B 93 HIS cc_start: 0.8626 (m90) cc_final: 0.8391 (m-70) REVERT: B 175 GLU cc_start: 0.9521 (mp0) cc_final: 0.9169 (pm20) REVERT: B 192 VAL cc_start: 0.9613 (t) cc_final: 0.9313 (m) REVERT: B 193 ILE cc_start: 0.9397 (mp) cc_final: 0.8999 (mp) REVERT: B 292 MET cc_start: 0.8142 (ppp) cc_final: 0.7720 (ppp) REVERT: B 378 ASP cc_start: 0.8949 (m-30) cc_final: 0.8656 (m-30) REVERT: B 380 MET cc_start: 0.7858 (tpt) cc_final: 0.7643 (tmm) REVERT: B 408 MET cc_start: 0.8273 (tpp) cc_final: 0.7576 (tpp) REVERT: B 509 LYS cc_start: 0.8780 (pttm) cc_final: 0.8483 (pptt) REVERT: B 799 LEU cc_start: 0.9505 (tt) cc_final: 0.9136 (mm) REVERT: C 25 GLU cc_start: 0.9336 (mp0) cc_final: 0.8823 (mm-30) REVERT: C 442 LEU cc_start: 0.9269 (mt) cc_final: 0.9049 (mt) REVERT: C 503 MET cc_start: 0.8345 (tpt) cc_final: 0.8093 (tpt) REVERT: C 527 MET cc_start: 0.8719 (mmp) cc_final: 0.8190 (mmp) REVERT: C 531 PHE cc_start: 0.9460 (m-10) cc_final: 0.9095 (m-80) REVERT: C 541 PHE cc_start: 0.9168 (t80) cc_final: 0.8962 (t80) REVERT: C 661 ARG cc_start: 0.9073 (mpt90) cc_final: 0.8425 (ttp80) REVERT: C 705 GLU cc_start: 0.8758 (pm20) cc_final: 0.7967 (pm20) REVERT: C 708 MET cc_start: 0.9431 (mmp) cc_final: 0.9077 (mmp) REVERT: C 721 MET cc_start: 0.8435 (pmm) cc_final: 0.7880 (pmm) REVERT: D 83 ASN cc_start: 0.9089 (p0) cc_final: 0.8472 (p0) REVERT: D 93 HIS cc_start: 0.9011 (m-70) cc_final: 0.8410 (m-70) REVERT: D 113 MET cc_start: 0.9173 (tpp) cc_final: 0.7946 (tpp) REVERT: D 138 ASP cc_start: 0.7818 (t0) cc_final: 0.7190 (t0) REVERT: D 241 GLU cc_start: 0.8661 (tp30) cc_final: 0.8407 (tp30) REVERT: D 284 LEU cc_start: 0.9503 (mm) cc_final: 0.8755 (mm) REVERT: D 463 MET cc_start: 0.7412 (mmp) cc_final: 0.6808 (mmp) REVERT: D 517 PHE cc_start: 0.8950 (p90) cc_final: 0.8590 (p90) REVERT: D 518 LEU cc_start: 0.9136 (mp) cc_final: 0.8724 (mt) REVERT: D 585 MET cc_start: 0.8644 (mmm) cc_final: 0.8102 (mmm) REVERT: D 614 SER cc_start: 0.9787 (m) cc_final: 0.9410 (t) REVERT: D 629 MET cc_start: 0.7663 (mmm) cc_final: 0.7445 (mmm) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1634 time to fit residues: 94.0101 Evaluate side-chains 256 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 4 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.059316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.041364 restraints weight = 151304.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.042732 restraints weight = 101241.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.043642 restraints weight = 76794.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044352 restraints weight = 63374.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.044674 restraints weight = 54885.384| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25719 Z= 0.110 Angle : 0.569 12.470 34752 Z= 0.290 Chirality : 0.042 0.208 3830 Planarity : 0.004 0.063 4395 Dihedral : 4.268 60.997 3519 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3164 helix: 1.43 (0.14), residues: 1480 sheet: -0.54 (0.28), residues: 376 loop : -0.40 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 141 TYR 0.014 0.001 TYR A 286 PHE 0.019 0.001 PHE A 88 TRP 0.059 0.002 TRP B 578 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00245 (25710) covalent geometry : angle 0.56771 (34738) SS BOND : bond 0.00371 ( 7) SS BOND : angle 1.81497 ( 14) hydrogen bonds : bond 0.03189 ( 1188) hydrogen bonds : angle 4.41391 ( 3438) Misc. bond : bond 0.00469 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9210 (m-80) cc_final: 0.8809 (m-80) REVERT: A 136 LEU cc_start: 0.9671 (mm) cc_final: 0.9351 (mm) REVERT: A 140 ASP cc_start: 0.9113 (t0) cc_final: 0.8853 (t0) REVERT: A 159 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8483 (tm-30) REVERT: A 214 HIS cc_start: 0.9131 (p-80) cc_final: 0.8817 (p-80) REVERT: A 334 LYS cc_start: 0.9394 (mtmt) cc_final: 0.9144 (mttt) REVERT: A 356 TYR cc_start: 0.9006 (p90) cc_final: 0.8278 (p90) REVERT: A 361 MET cc_start: 0.7395 (ptp) cc_final: 0.7157 (ptp) REVERT: A 463 MET cc_start: 0.8905 (mmm) cc_final: 0.8207 (mmm) REVERT: A 476 ILE cc_start: 0.8364 (mm) cc_final: 0.8107 (tp) REVERT: A 479 LEU cc_start: 0.8849 (tp) cc_final: 0.8615 (tp) REVERT: A 527 MET cc_start: 0.8692 (mmp) cc_final: 0.7495 (mmm) REVERT: A 531 PHE cc_start: 0.9478 (m-10) cc_final: 0.9170 (m-80) REVERT: A 541 PHE cc_start: 0.9078 (t80) cc_final: 0.8531 (t80) REVERT: A 585 MET cc_start: 0.9436 (mmm) cc_final: 0.8945 (tpp) REVERT: A 661 ARG cc_start: 0.9169 (mmt180) cc_final: 0.8448 (ttp80) REVERT: A 670 MET cc_start: 0.9159 (ptt) cc_final: 0.8891 (ppp) REVERT: A 674 MET cc_start: 0.9249 (ptm) cc_final: 0.8949 (ptt) REVERT: B 25 GLU cc_start: 0.9063 (mp0) cc_final: 0.8689 (mp0) REVERT: B 93 HIS cc_start: 0.8663 (m90) cc_final: 0.8428 (m-70) REVERT: B 175 GLU cc_start: 0.9510 (mp0) cc_final: 0.9160 (pm20) REVERT: B 192 VAL cc_start: 0.9612 (t) cc_final: 0.9316 (m) REVERT: B 193 ILE cc_start: 0.9381 (mp) cc_final: 0.8998 (mp) REVERT: B 292 MET cc_start: 0.8142 (ppp) cc_final: 0.7750 (ppp) REVERT: B 378 ASP cc_start: 0.8970 (m-30) cc_final: 0.8691 (m-30) REVERT: B 408 MET cc_start: 0.8262 (tpp) cc_final: 0.7538 (tpp) REVERT: B 509 LYS cc_start: 0.8767 (pttm) cc_final: 0.8487 (pptt) REVERT: B 533 TYR cc_start: 0.9260 (t80) cc_final: 0.8554 (t80) REVERT: B 534 ILE cc_start: 0.9458 (tt) cc_final: 0.9219 (tt) REVERT: B 611 ILE cc_start: 0.9662 (mt) cc_final: 0.9299 (mt) REVERT: B 799 LEU cc_start: 0.9501 (tt) cc_final: 0.9132 (mm) REVERT: C 25 GLU cc_start: 0.9341 (mp0) cc_final: 0.8834 (mm-30) REVERT: C 117 LEU cc_start: 0.9300 (tt) cc_final: 0.9042 (mp) REVERT: C 442 LEU cc_start: 0.9293 (mt) cc_final: 0.9066 (mt) REVERT: C 503 MET cc_start: 0.8326 (tpt) cc_final: 0.8098 (tpt) REVERT: C 527 MET cc_start: 0.8649 (mmp) cc_final: 0.8067 (mmp) REVERT: C 531 PHE cc_start: 0.9462 (m-10) cc_final: 0.9098 (m-80) REVERT: C 541 PHE cc_start: 0.9150 (t80) cc_final: 0.8925 (t80) REVERT: C 661 ARG cc_start: 0.9076 (mpt90) cc_final: 0.8396 (ttp80) REVERT: C 705 GLU cc_start: 0.8781 (pm20) cc_final: 0.8054 (pm20) REVERT: C 708 MET cc_start: 0.9426 (mmp) cc_final: 0.9055 (mmp) REVERT: C 721 MET cc_start: 0.8403 (pmm) cc_final: 0.7875 (pmm) REVERT: D 83 ASN cc_start: 0.9099 (p0) cc_final: 0.8467 (p0) REVERT: D 93 HIS cc_start: 0.9002 (m-70) cc_final: 0.8419 (m-70) REVERT: D 113 MET cc_start: 0.9149 (tpp) cc_final: 0.7951 (tpp) REVERT: D 138 ASP cc_start: 0.7808 (t0) cc_final: 0.7178 (t0) REVERT: D 284 LEU cc_start: 0.9508 (mm) cc_final: 0.8708 (mm) REVERT: D 463 MET cc_start: 0.7290 (mmp) cc_final: 0.6714 (mmp) REVERT: D 517 PHE cc_start: 0.8920 (p90) cc_final: 0.8615 (p90) REVERT: D 518 LEU cc_start: 0.9166 (mp) cc_final: 0.8795 (mt) REVERT: D 585 MET cc_start: 0.8617 (mmm) cc_final: 0.8127 (mmm) REVERT: D 614 SER cc_start: 0.9785 (m) cc_final: 0.9417 (t) REVERT: D 629 MET cc_start: 0.7675 (mmm) cc_final: 0.7460 (mmm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1503 time to fit residues: 85.3115 Evaluate side-chains 261 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 275 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 287 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040431 restraints weight = 153291.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041798 restraints weight = 101619.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.042742 restraints weight = 76887.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.043371 restraints weight = 63137.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.043860 restraints weight = 55060.867| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25719 Z= 0.136 Angle : 0.586 12.417 34752 Z= 0.301 Chirality : 0.042 0.197 3830 Planarity : 0.004 0.064 4395 Dihedral : 4.323 58.085 3519 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.15), residues: 3164 helix: 1.36 (0.14), residues: 1484 sheet: -0.66 (0.28), residues: 387 loop : -0.39 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.014 0.001 TYR D 127 PHE 0.019 0.001 PHE B 607 TRP 0.056 0.002 TRP B 578 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00297 (25710) covalent geometry : angle 0.58532 (34738) SS BOND : bond 0.00274 ( 7) SS BOND : angle 1.73937 ( 14) hydrogen bonds : bond 0.03320 ( 1188) hydrogen bonds : angle 4.51511 ( 3438) Misc. bond : bond 0.00513 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3992.39 seconds wall clock time: 69 minutes 44.17 seconds (4184.17 seconds total)