Starting phenix.real_space_refine on Sat Jul 4 19:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mij_23853/07_2026/7mij_23853.map" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 124 5.16 5 Na 2 4.78 5 C 15040 2.51 5 N 3460 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23010 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "C" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "A" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 626 Unusual residues: {' NA': 2, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 4.38, per 1000 atoms: 0.19 Number of scatterers: 23010 At special positions: 0 Unit cell: (126.42, 126.42, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 36 15.00 Na 2 11.00 O 4348 8.00 N 3460 7.00 C 15040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 920.9 milliseconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 65.8% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.628A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.896A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.544A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.930A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.899A pdb=" N GLY A 258 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.585A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.534A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 508 removed outlier: 4.145A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.517A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.652A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.578A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 685 removed outlier: 3.663A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.597A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.896A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.545A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.930A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.899A pdb=" N GLY B 258 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.586A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.533A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 508 removed outlier: 4.145A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.516A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.654A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.577A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.577A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.663A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.597A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.897A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.545A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.930A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.899A pdb=" N GLY C 258 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.586A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.534A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 removed outlier: 4.146A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 519 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.517A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.654A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.578A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 685 removed outlier: 3.662A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.598A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.897A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.545A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.931A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.898A pdb=" N GLY D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.586A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.972A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.534A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 4.145A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 519 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.517A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.653A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.577A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.578A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 685 removed outlier: 3.663A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.827A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.599A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 7.096A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 7.096A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 7.096A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 7.097A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3216 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: 4.09 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.44: 5981 1.44 - 1.56: 13410 1.56 - 1.69: 77 1.69 - 1.82: 204 Bond restraints: 23100 Sorted by residual: bond pdb=" C21 POV B 909 " pdb=" O21 POV B 909 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV C 909 " pdb=" O21 POV C 909 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV A 911 " pdb=" O21 POV A 911 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV B 901 " pdb=" O21 POV B 901 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV A 905 " pdb=" O21 POV A 905 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 23095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 29726 2.80 - 5.60: 770 5.60 - 8.41: 232 8.41 - 11.21: 107 11.21 - 14.01: 77 Bond angle restraints: 30912 Sorted by residual: angle pdb=" C LYS D 614 " pdb=" N ASP D 615 " pdb=" CA ASP D 615 " ideal model delta sigma weight residual 120.82 129.64 -8.82 1.50e+00 4.44e-01 3.46e+01 angle pdb=" C LYS A 614 " pdb=" N ASP A 615 " pdb=" CA ASP A 615 " ideal model delta sigma weight residual 120.82 129.61 -8.79 1.50e+00 4.44e-01 3.44e+01 angle pdb=" C LYS C 614 " pdb=" N ASP C 615 " pdb=" CA ASP C 615 " ideal model delta sigma weight residual 120.82 129.59 -8.77 1.50e+00 4.44e-01 3.42e+01 angle pdb=" C LYS B 614 " pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta sigma weight residual 120.82 129.55 -8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" N GLN A 313 " pdb=" CA GLN A 313 " pdb=" CB GLN A 313 " ideal model delta sigma weight residual 110.80 103.81 6.99 1.49e+00 4.50e-01 2.20e+01 ... (remaining 30907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13357 35.18 - 70.36: 555 70.36 - 105.53: 92 105.53 - 140.71: 36 140.71 - 175.89: 12 Dihedral angle restraints: 14052 sinusoidal: 6508 harmonic: 7544 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 14049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2604 0.054 - 0.109: 588 0.109 - 0.163: 94 0.163 - 0.217: 31 0.217 - 0.272: 7 Chirality restraints: 3324 Sorted by residual: chirality pdb=" CA ASN A 314 " pdb=" N ASN A 314 " pdb=" C ASN A 314 " pdb=" CB ASN A 314 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN D 314 " pdb=" N ASN D 314 " pdb=" C ASN D 314 " pdb=" CB ASN D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASN C 314 " pdb=" N ASN C 314 " pdb=" C ASN C 314 " pdb=" CB ASN C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 3321 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 311 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS B 311 " -0.058 2.00e-02 2.50e+03 pdb=" O LYS B 311 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 312 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 509 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO B 510 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " -0.052 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO D 510 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " -0.043 5.00e-02 4.00e+02 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6551 2.84 - 3.35: 19720 3.35 - 3.87: 35478 3.87 - 4.38: 43603 4.38 - 4.90: 72412 Nonbonded interactions: 177764 Sorted by model distance: nonbonded pdb=" O ALA A 206 " pdb=" O HOH A1001 " model vdw 2.320 3.040 nonbonded pdb=" O GLN A 255 " pdb=" O HOH A1002 " model vdw 2.327 3.040 nonbonded pdb=" O GLN C 255 " pdb=" O HOH C1001 " model vdw 2.339 3.040 nonbonded pdb=" O GLN D 255 " pdb=" O HOH D1001 " model vdw 2.342 3.040 nonbonded pdb=" O THR A 393 " pdb=" O HOH A1003 " model vdw 2.343 3.040 ... (remaining 177759 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 118 through 906) selection = (chain 'B' and resid 118 through 906) selection = (chain 'C' and resid 118 through 906) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.610 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.090 23104 Z= 0.486 Angle : 1.379 14.011 30920 Z= 0.610 Chirality : 0.049 0.272 3324 Planarity : 0.006 0.079 3704 Dihedral : 19.919 175.890 9144 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.18 % Allowed : 4.96 % Favored : 94.87 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.12), residues: 2548 helix: -2.98 (0.09), residues: 1540 sheet: 0.69 (0.53), residues: 88 loop : -1.97 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 363 TYR 0.020 0.003 TYR A 540 PHE 0.041 0.003 PHE A 526 TRP 0.016 0.002 TRP B 692 HIS 0.007 0.002 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.49 (23100) covalent geometry : angle 1.37936 / 0.61 (30912) SS BOND : bond 0.00124 / 0.06 ( 4) SS BOND : angle 1.30842 / 0.82 ( 8) hydrogen bonds : bond 0.33357 / 21.89 ( 1108) hydrogen bonds : angle 7.36727 / 5.22 ( 3216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 428 time to evaluate : 0.919 Fit side-chains REVERT: A 479 MET cc_start: 0.1459 (ptp) cc_final: 0.1216 (tmm) REVERT: A 497 ILE cc_start: 0.7532 (mt) cc_final: 0.6777 (mp) REVERT: A 501 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6339 (mp0) REVERT: B 497 ILE cc_start: 0.7663 (mt) cc_final: 0.7146 (mp) REVERT: B 501 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6280 (mp0) REVERT: B 578 MET cc_start: 0.8127 (tpp) cc_final: 0.7827 (tpp) REVERT: C 497 ILE cc_start: 0.7666 (mt) cc_final: 0.6923 (mp) REVERT: C 501 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6314 (mp0) REVERT: C 578 MET cc_start: 0.8144 (tpp) cc_final: 0.7920 (tpp) REVERT: D 497 ILE cc_start: 0.7678 (mt) cc_final: 0.7162 (mp) REVERT: D 501 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6308 (mp0) REVERT: D 578 MET cc_start: 0.8137 (tpp) cc_final: 0.7902 (tpp) outliers start: 4 outliers final: 0 residues processed: 431 average time/residue: 0.6359 time to fit residues: 310.4889 Evaluate side-chains 265 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 220 ASN A 227 GLN A 274 GLN A 426 HIS A 477 HIS A 523 HIS A 643 ASN A 647 ASN A 750 ASN B 220 ASN B 227 GLN B 274 GLN B 426 HIS B 477 HIS B 523 HIS B 643 ASN B 647 ASN C 220 ASN C 227 GLN C 274 GLN C 426 HIS C 477 HIS C 523 HIS C 643 ASN C 647 ASN C 750 ASN D 220 ASN D 227 GLN D 274 GLN D 426 HIS D 477 HIS D 523 HIS D 643 ASN D 647 ASN D 750 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.198928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167095 restraints weight = 17161.118| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.88 r_work: 0.3605 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23104 Z= 0.148 Angle : 0.566 8.093 30920 Z= 0.307 Chirality : 0.039 0.136 3324 Planarity : 0.005 0.056 3704 Dihedral : 23.599 150.476 4112 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.15 % Allowed : 7.06 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 2548 helix: 0.08 (0.12), residues: 1580 sheet: 0.85 (0.53), residues: 88 loop : -1.61 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 714 TYR 0.023 0.002 TYR A 540 PHE 0.019 0.002 PHE A 449 TRP 0.013 0.001 TRP B 692 HIS 0.004 0.001 HIS B 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (23100) covalent geometry : angle 0.56574 / 0.31 (30912) SS BOND : bond 0.00014 / 0.01 ( 4) SS BOND : angle 0.15237 / 0.10 ( 8) hydrogen bonds : bond 0.07696 / 5.05 ( 1108) hydrogen bonds : angle 4.05337 / 2.86 ( 3216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.542 Fit side-chains REVERT: A 578 MET cc_start: 0.8799 (tpp) cc_final: 0.8583 (tpp) REVERT: A 682 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: B 121 LYS cc_start: 0.6731 (mptm) cc_final: 0.6514 (mptt) REVERT: B 327 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6082 (mmm-85) REVERT: B 645 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5824 (mp10) REVERT: B 682 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7923 (tp30) REVERT: C 121 LYS cc_start: 0.6758 (mptm) cc_final: 0.6533 (mptt) REVERT: C 645 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5814 (mp10) REVERT: C 682 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: D 121 LYS cc_start: 0.6753 (mptm) cc_final: 0.6537 (mptt) REVERT: D 645 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5810 (mp10) REVERT: D 682 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7902 (tp30) outliers start: 49 outliers final: 4 residues processed: 316 average time/residue: 0.6444 time to fit residues: 228.9939 Evaluate side-chains 260 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 98 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 130 optimal weight: 0.0050 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 750 ASN B 580 GLN C 580 GLN C 750 ASN D 580 GLN D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.195778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164434 restraints weight = 17060.626| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 0.88 r_work: 0.3511 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work: 0.3286 rms_B_bonded: 4.42 restraints_weight: 0.1250 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23104 Z= 0.151 Angle : 0.552 6.915 30920 Z= 0.297 Chirality : 0.039 0.139 3324 Planarity : 0.004 0.045 3704 Dihedral : 22.017 152.716 4112 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.68 % Allowed : 7.81 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2548 helix: 1.13 (0.13), residues: 1588 sheet: 0.99 (0.51), residues: 88 loop : -1.50 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 371 TYR 0.024 0.002 TYR B 540 PHE 0.020 0.002 PHE C 316 TRP 0.011 0.001 TRP D 692 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (23100) covalent geometry : angle 0.55168 / 0.30 (30912) SS BOND : bond 0.00012 / 0.01 ( 4) SS BOND : angle 0.14751 / 0.11 ( 8) hydrogen bonds : bond 0.07821 / 5.11 ( 1108) hydrogen bonds : angle 3.98386 / 2.80 ( 3216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 278 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 276 GLU cc_start: 0.7540 (pm20) cc_final: 0.7258 (pm20) REVERT: A 479 MET cc_start: 0.0827 (OUTLIER) cc_final: 0.0601 (tmm) REVERT: A 501 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 728 PHE cc_start: 0.8492 (m-80) cc_final: 0.8232 (m-80) REVERT: B 121 LYS cc_start: 0.6848 (mptm) cc_final: 0.6481 (mptt) REVERT: B 210 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: B 276 GLU cc_start: 0.7571 (pm20) cc_final: 0.7342 (pm20) REVERT: B 327 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6351 (mmm-85) REVERT: B 645 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5887 (mp10) REVERT: B 682 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: C 121 LYS cc_start: 0.6852 (mptm) cc_final: 0.6474 (mptt) REVERT: C 276 GLU cc_start: 0.7465 (pm20) cc_final: 0.7151 (mp0) REVERT: C 327 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6293 (mmm-85) REVERT: C 501 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 645 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5839 (mp10) REVERT: C 682 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: D 121 LYS cc_start: 0.6847 (mptm) cc_final: 0.6471 (mptt) REVERT: D 276 GLU cc_start: 0.7474 (pm20) cc_final: 0.7166 (mp0) REVERT: D 327 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6305 (mmm-85) REVERT: D 501 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7000 (mm-30) REVERT: D 645 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: D 682 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8230 (tp30) outliers start: 61 outliers final: 14 residues processed: 312 average time/residue: 0.6537 time to fit residues: 229.9133 Evaluate side-chains 270 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 0.2980 chunk 13 optimal weight: 0.0970 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.198445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.164176 restraints weight = 17202.460| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.92 r_work: 0.3649 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work: 0.3446 rms_B_bonded: 4.99 restraints_weight: 0.1250 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23104 Z= 0.124 Angle : 0.495 7.248 30920 Z= 0.265 Chirality : 0.038 0.153 3324 Planarity : 0.004 0.041 3704 Dihedral : 20.427 150.993 4112 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.37 % Allowed : 8.99 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2548 helix: 1.57 (0.13), residues: 1612 sheet: 0.94 (0.50), residues: 88 loop : -1.48 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 371 TYR 0.023 0.001 TYR D 540 PHE 0.025 0.001 PHE D 449 TRP 0.010 0.001 TRP A 493 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (23100) covalent geometry : angle 0.49545 / 0.27 (30912) SS BOND : bond 0.00018 / 0.01 ( 4) SS BOND : angle 0.22422 / 0.14 ( 8) hydrogen bonds : bond 0.06193 / 4.06 ( 1108) hydrogen bonds : angle 3.73254 / 2.63 ( 3216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7089 (OUTLIER) cc_final: 0.6859 (t) REVERT: A 253 LYS cc_start: 0.6578 (mmmt) cc_final: 0.6299 (mmmt) REVERT: A 479 MET cc_start: 0.1115 (OUTLIER) cc_final: 0.0786 (tmm) REVERT: A 682 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: B 121 LYS cc_start: 0.6705 (mptm) cc_final: 0.6492 (mptt) REVERT: B 276 GLU cc_start: 0.7596 (pm20) cc_final: 0.7392 (pm20) REVERT: B 327 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6320 (mmm-85) REVERT: B 479 MET cc_start: 0.1406 (ptt) cc_final: 0.0890 (tmm) REVERT: B 682 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: C 121 LYS cc_start: 0.6701 (mptm) cc_final: 0.6475 (mptt) REVERT: C 158 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6582 (tt) REVERT: C 327 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6136 (mmm-85) REVERT: C 479 MET cc_start: 0.1393 (ptt) cc_final: 0.0879 (tmm) REVERT: C 682 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: C 728 PHE cc_start: 0.8377 (m-80) cc_final: 0.8167 (m-80) REVERT: C 750 ASN cc_start: 0.8255 (m110) cc_final: 0.7937 (t0) REVERT: D 121 LYS cc_start: 0.6727 (mptm) cc_final: 0.6498 (mptt) REVERT: D 158 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6476 (tt) REVERT: D 327 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6156 (mmm-85) REVERT: D 479 MET cc_start: 0.1353 (ptt) cc_final: 0.0856 (tmm) REVERT: D 682 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: D 728 PHE cc_start: 0.8388 (m-80) cc_final: 0.8168 (m-80) REVERT: D 750 ASN cc_start: 0.8269 (m110) cc_final: 0.7963 (t0) outliers start: 54 outliers final: 11 residues processed: 291 average time/residue: 0.6564 time to fit residues: 214.4827 Evaluate side-chains 267 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 112 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.193405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.159497 restraints weight = 16659.980| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.05 r_work: 0.3537 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work: 0.3357 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23104 Z= 0.170 Angle : 0.580 7.542 30920 Z= 0.310 Chirality : 0.040 0.139 3324 Planarity : 0.004 0.045 3704 Dihedral : 20.470 153.786 4112 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.24 % Allowed : 10.00 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2548 helix: 1.58 (0.13), residues: 1584 sheet: 0.90 (0.51), residues: 88 loop : -1.33 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 729 TYR 0.026 0.002 TYR D 540 PHE 0.023 0.002 PHE D 316 TRP 0.014 0.002 TRP B 493 HIS 0.006 0.002 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (23100) covalent geometry : angle 0.58006 / 0.31 (30912) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.26652 / 0.18 ( 8) hydrogen bonds : bond 0.08281 / 5.40 ( 1108) hydrogen bonds : angle 4.03175 / 2.83 ( 3216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6628 (tt) REVERT: A 253 LYS cc_start: 0.6607 (mmmt) cc_final: 0.6340 (mmmt) REVERT: A 327 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6188 (mmm-85) REVERT: A 645 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5690 (tp40) REVERT: A 682 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: B 121 LYS cc_start: 0.6797 (mptm) cc_final: 0.6498 (mptt) REVERT: B 276 GLU cc_start: 0.7593 (pm20) cc_final: 0.7382 (pm20) REVERT: B 327 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6447 (mmm-85) REVERT: B 645 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.6056 (mp10) REVERT: B 682 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: B 728 PHE cc_start: 0.8349 (m-80) cc_final: 0.8133 (m-80) REVERT: B 750 ASN cc_start: 0.8238 (m110) cc_final: 0.7945 (t0) REVERT: C 121 LYS cc_start: 0.6779 (mptm) cc_final: 0.6481 (mptt) REVERT: C 158 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6626 (tt) REVERT: C 327 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6378 (mmm-85) REVERT: C 645 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.6041 (mp10) REVERT: C 682 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: C 728 PHE cc_start: 0.8368 (m-80) cc_final: 0.8152 (m-80) REVERT: C 750 ASN cc_start: 0.8221 (m110) cc_final: 0.7935 (t0) REVERT: D 121 LYS cc_start: 0.6787 (mptm) cc_final: 0.6491 (mptt) REVERT: D 158 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6629 (tt) REVERT: D 327 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6380 (mmm-85) REVERT: D 645 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: D 682 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: D 728 PHE cc_start: 0.8378 (m-80) cc_final: 0.8156 (m-80) REVERT: D 750 ASN cc_start: 0.8227 (m110) cc_final: 0.7948 (t0) outliers start: 51 outliers final: 16 residues processed: 282 average time/residue: 0.6650 time to fit residues: 210.2489 Evaluate side-chains 279 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 220 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 647 ASN B 580 GLN B 647 ASN C 178 ASN C 580 GLN C 647 ASN D 580 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.190608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158761 restraints weight = 16421.427| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 0.88 r_work: 0.3467 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.3327 rms_B_bonded: 3.63 restraints_weight: 0.1250 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23104 Z= 0.233 Angle : 0.715 7.615 30920 Z= 0.380 Chirality : 0.045 0.162 3324 Planarity : 0.006 0.053 3704 Dihedral : 21.365 158.272 4112 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.24 % Allowed : 10.26 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2548 helix: 1.15 (0.12), residues: 1588 sheet: 0.80 (0.51), residues: 88 loop : -1.64 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 716 TYR 0.033 0.003 TYR A 540 PHE 0.034 0.003 PHE C 449 TRP 0.021 0.002 TRP C 493 HIS 0.008 0.002 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.23 (23100) covalent geometry : angle 0.71456 / 0.38 (30912) SS BOND : bond 0.00252 / 0.12 ( 4) SS BOND : angle 0.69490 / 0.43 ( 8) hydrogen bonds : bond 0.10243 / 6.67 ( 1108) hydrogen bonds : angle 4.37175 / 3.06 ( 3216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6649 (tt) REVERT: A 253 LYS cc_start: 0.6693 (mmmt) cc_final: 0.6356 (mmmt) REVERT: A 327 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6252 (mmm-85) REVERT: A 682 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: B 327 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6440 (mmm-85) REVERT: B 645 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.6083 (mp10) REVERT: B 682 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8283 (tp30) REVERT: B 728 PHE cc_start: 0.8357 (m-80) cc_final: 0.8140 (m-80) REVERT: B 750 ASN cc_start: 0.8112 (m110) cc_final: 0.7822 (t0) REVERT: C 158 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6613 (tt) REVERT: C 327 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6389 (mmm-85) REVERT: C 645 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6084 (mp10) REVERT: C 682 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: C 750 ASN cc_start: 0.8124 (m110) cc_final: 0.7835 (t0) REVERT: D 158 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6607 (tt) REVERT: D 327 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6396 (mmm-85) REVERT: D 645 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6073 (mp10) REVERT: D 682 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: D 750 ASN cc_start: 0.8127 (m110) cc_final: 0.7851 (t0) outliers start: 51 outliers final: 21 residues processed: 303 average time/residue: 0.6293 time to fit residues: 215.0921 Evaluate side-chains 288 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 174 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 21 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 647 ASN B 580 GLN C 580 GLN C 647 ASN D 580 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.195891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162540 restraints weight = 16892.994| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 0.90 r_work: 0.3625 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23104 Z= 0.133 Angle : 0.514 6.715 30920 Z= 0.277 Chirality : 0.039 0.129 3324 Planarity : 0.003 0.045 3704 Dihedral : 20.030 152.999 4112 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.28 % Allowed : 9.96 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.16), residues: 2548 helix: 1.74 (0.13), residues: 1608 sheet: 0.79 (0.51), residues: 88 loop : -1.53 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 225 TYR 0.023 0.002 TYR D 540 PHE 0.029 0.001 PHE B 449 TRP 0.015 0.001 TRP A 493 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (23100) covalent geometry : angle 0.51352 / 0.28 (30912) SS BOND : bond 0.00064 / 0.03 ( 4) SS BOND : angle 0.59695 / 0.38 ( 8) hydrogen bonds : bond 0.06550 / 4.28 ( 1108) hydrogen bonds : angle 3.81473 / 2.69 ( 3216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.6488 (mmmt) cc_final: 0.6287 (mmmt) REVERT: A 327 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5990 (mmm-85) REVERT: B 327 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6076 (mmm-85) REVERT: B 682 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: B 750 ASN cc_start: 0.7869 (m110) cc_final: 0.7648 (t0) REVERT: C 158 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6355 (tt) REVERT: C 327 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6036 (mmm-85) REVERT: C 682 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: C 750 ASN cc_start: 0.7857 (m110) cc_final: 0.7643 (t0) REVERT: D 158 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6350 (tt) REVERT: D 327 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6041 (mmm-85) REVERT: D 682 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: D 750 ASN cc_start: 0.7861 (m110) cc_final: 0.7648 (t0) outliers start: 52 outliers final: 11 residues processed: 293 average time/residue: 0.6502 time to fit residues: 214.6976 Evaluate side-chains 266 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 194 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 647 ASN B 647 ASN C 580 GLN C 647 ASN D 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.193866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160546 restraints weight = 16601.894| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 0.98 r_work: 0.3513 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work: 0.3373 rms_B_bonded: 3.60 restraints_weight: 0.1250 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23104 Z= 0.156 Angle : 0.561 8.176 30920 Z= 0.299 Chirality : 0.040 0.136 3324 Planarity : 0.004 0.046 3704 Dihedral : 19.856 152.516 4112 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.80 % Allowed : 11.58 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.16), residues: 2548 helix: 1.73 (0.13), residues: 1608 sheet: 0.71 (0.51), residues: 88 loop : -1.55 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 729 TYR 0.024 0.002 TYR D 540 PHE 0.020 0.002 PHE B 316 TRP 0.023 0.002 TRP D 493 HIS 0.005 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 (23100) covalent geometry : angle 0.56082 / 0.30 (30912) SS BOND : bond 0.00127 / 0.06 ( 4) SS BOND : angle 0.74650 / 0.49 ( 8) hydrogen bonds : bond 0.07672 / 5.01 ( 1108) hydrogen bonds : angle 3.94724 / 2.77 ( 3216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6626 (tt) REVERT: A 253 LYS cc_start: 0.6698 (mmmt) cc_final: 0.6381 (mmmt) REVERT: A 327 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6124 (mmm-85) REVERT: B 327 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6397 (mmm-85) REVERT: B 682 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: B 720 LEU cc_start: 0.8197 (tp) cc_final: 0.7960 (tp) REVERT: B 750 ASN cc_start: 0.8149 (m110) cc_final: 0.7826 (t0) REVERT: C 158 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6521 (tt) REVERT: C 327 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6260 (mmm-85) REVERT: C 682 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8083 (tp30) REVERT: C 720 LEU cc_start: 0.8159 (tp) cc_final: 0.7950 (tp) REVERT: C 728 PHE cc_start: 0.8363 (m-80) cc_final: 0.8127 (m-80) REVERT: C 750 ASN cc_start: 0.8099 (m110) cc_final: 0.7812 (t0) REVERT: D 158 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6520 (tt) REVERT: D 327 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6364 (mmm-85) REVERT: D 682 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: D 720 LEU cc_start: 0.8167 (tp) cc_final: 0.7956 (tp) REVERT: D 728 PHE cc_start: 0.8368 (m-80) cc_final: 0.8133 (m-80) REVERT: D 750 ASN cc_start: 0.8093 (m110) cc_final: 0.7822 (t0) outliers start: 41 outliers final: 19 residues processed: 287 average time/residue: 0.6797 time to fit residues: 219.2833 Evaluate side-chains 283 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 195 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 251 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 647 ASN C 647 ASN D 580 GLN D 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.193510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.160208 restraints weight = 16760.223| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 0.97 r_work: 0.3514 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work: 0.3343 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23104 Z= 0.163 Angle : 0.574 8.043 30920 Z= 0.306 Chirality : 0.040 0.136 3324 Planarity : 0.004 0.046 3704 Dihedral : 19.809 153.160 4112 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.02 % Allowed : 11.40 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2548 helix: 1.70 (0.13), residues: 1608 sheet: 0.52 (0.51), residues: 88 loop : -1.55 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 729 TYR 0.024 0.002 TYR A 540 PHE 0.032 0.002 PHE B 449 TRP 0.028 0.002 TRP D 493 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (23100) covalent geometry : angle 0.57363 / 0.31 (30912) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.97994 / 0.65 ( 8) hydrogen bonds : bond 0.07895 / 5.16 ( 1108) hydrogen bonds : angle 3.97300 / 2.79 ( 3216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6612 (tt) REVERT: A 253 LYS cc_start: 0.6707 (mmmt) cc_final: 0.6382 (mmmt) REVERT: A 327 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6171 (mmm-85) REVERT: B 327 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6429 (mmm-85) REVERT: B 682 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: B 750 ASN cc_start: 0.8230 (m110) cc_final: 0.7911 (t0) REVERT: C 158 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6532 (tt) REVERT: C 327 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6348 (mmm-85) REVERT: C 682 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8169 (tp30) REVERT: C 728 PHE cc_start: 0.8416 (m-80) cc_final: 0.8199 (m-80) REVERT: C 750 ASN cc_start: 0.8162 (m110) cc_final: 0.7893 (t0) REVERT: D 158 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6500 (tt) REVERT: D 327 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6348 (mmm-85) REVERT: D 682 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: D 728 PHE cc_start: 0.8423 (m-80) cc_final: 0.8202 (m-80) REVERT: D 750 ASN cc_start: 0.8165 (m110) cc_final: 0.7907 (t0) outliers start: 46 outliers final: 18 residues processed: 296 average time/residue: 0.6519 time to fit residues: 217.5046 Evaluate side-chains 285 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 647 ASN C 580 GLN C 647 ASN D 580 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.194034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160649 restraints weight = 16727.303| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 0.98 r_work: 0.3510 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work: 0.3358 rms_B_bonded: 3.90 restraints_weight: 0.1250 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23104 Z= 0.156 Angle : 0.562 8.304 30920 Z= 0.299 Chirality : 0.040 0.133 3324 Planarity : 0.004 0.046 3704 Dihedral : 19.601 152.982 4112 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.67 % Allowed : 11.49 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 2548 helix: 1.78 (0.13), residues: 1608 sheet: 0.56 (0.51), residues: 88 loop : -1.51 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 729 TYR 0.022 0.002 TYR D 540 PHE 0.021 0.002 PHE A 316 TRP 0.031 0.002 TRP B 493 HIS 0.005 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (23100) covalent geometry : angle 0.56169 / 0.30 (30912) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 1.06557 / 0.70 ( 8) hydrogen bonds : bond 0.07589 / 4.95 ( 1108) hydrogen bonds : angle 3.92574 / 2.76 ( 3216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6634 (tt) REVERT: A 253 LYS cc_start: 0.6647 (mmmt) cc_final: 0.6329 (mmmt) REVERT: A 327 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6176 (mmm-85) REVERT: B 327 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6409 (mmm-85) REVERT: B 682 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: B 750 ASN cc_start: 0.8182 (m110) cc_final: 0.7861 (t0) REVERT: C 158 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6544 (tt) REVERT: C 327 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6387 (mmm-85) REVERT: C 682 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: C 728 PHE cc_start: 0.8417 (m-80) cc_final: 0.8197 (m-80) REVERT: C 750 ASN cc_start: 0.8142 (m110) cc_final: 0.7857 (t0) REVERT: D 158 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6491 (tt) REVERT: D 327 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6399 (mmm-85) REVERT: D 682 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: D 728 PHE cc_start: 0.8421 (m-80) cc_final: 0.8211 (m-80) REVERT: D 750 ASN cc_start: 0.8142 (m110) cc_final: 0.7867 (t0) outliers start: 38 outliers final: 20 residues processed: 286 average time/residue: 0.6426 time to fit residues: 207.2580 Evaluate side-chains 279 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.195723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164106 restraints weight = 16929.241| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 0.86 r_work: 0.3647 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23104 Z= 0.138 Angle : 0.531 8.370 30920 Z= 0.283 Chirality : 0.039 0.141 3324 Planarity : 0.003 0.044 3704 Dihedral : 19.020 151.278 4112 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.54 % Allowed : 12.02 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.16), residues: 2548 helix: 1.92 (0.13), residues: 1612 sheet: 0.54 (0.51), residues: 88 loop : -1.45 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 337 TYR 0.020 0.002 TYR A 540 PHE 0.032 0.001 PHE B 449 TRP 0.026 0.002 TRP A 493 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (23100) covalent geometry : angle 0.53069 / 0.28 (30912) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 1.00438 / 0.66 ( 8) hydrogen bonds : bond 0.06751 / 4.41 ( 1108) hydrogen bonds : angle 3.78761 / 2.66 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11415.90 seconds wall clock time: 193 minutes 49.18 seconds (11629.18 seconds total)