Starting phenix.real_space_refine on Thu Mar 5 14:14:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mij_23853/03_2026/7mij_23853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mij_23853/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mij_23853/03_2026/7mij_23853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mij_23853/03_2026/7mij_23853.map" model { file = "/net/cci-nas-00/data/ceres_data/7mij_23853/03_2026/7mij_23853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mij_23853/03_2026/7mij_23853.cif" } 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-5986/lib/python3.9/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: 5.03, per 1000 atoms: 0.22 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: 1.75 Conformation dependent library (CDL) restraints added in 786.7 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: 0.63 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: 3.23 Time building geometry restraints manager: 2.37 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: 13470 35.18 - 70.36: 654 70.36 - 105.53: 96 105.53 - 140.71: 36 140.71 - 175.89: 12 Dihedral angle restraints: 14268 sinusoidal: 6724 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 14265 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: 2.130 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.980 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 20.526 175.890 9360 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 covalent geometry : bond 0.00950 (23100) covalent geometry : angle 1.37936 (30912) SS BOND : bond 0.00124 ( 4) SS BOND : angle 1.30842 ( 8) hydrogen bonds : bond 0.33357 ( 1108) hydrogen bonds : angle 7.36727 ( 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 : 0.751 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: 0.6946 time to fit residues: 336.7914 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 : 0.639 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4198 r_free = 0.4198 target = 0.198296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165548 restraints weight = 17119.148| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 0.92 r_work: 0.3580 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.3406 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23104 Z= 0.150 Angle : 0.573 8.163 30920 Z= 0.310 Chirality : 0.039 0.135 3324 Planarity : 0.005 0.056 3704 Dihedral : 24.315 150.715 4328 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.24 % Allowed : 7.06 % Favored : 90.70 % 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: -0.70 (0.15), residues: 2548 helix: 0.15 (0.12), residues: 1580 sheet: 0.83 (0.52), 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 D 540 PHE 0.019 0.002 PHE A 449 TRP 0.012 0.001 TRP C 692 HIS 0.004 0.001 HIS C 523 Details of bonding type rmsd covalent geometry : bond 0.00254 (23100) covalent geometry : angle 0.57289 (30912) SS BOND : bond 0.00007 ( 4) SS BOND : angle 0.12863 ( 8) hydrogen bonds : bond 0.08098 ( 1108) hydrogen bonds : angle 4.08731 ( 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 348 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 0.785 Fit side-chains REVERT: A 327 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6529 (mmm-85) REVERT: A 682 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: A 736 GLU cc_start: 0.8384 (tt0) cc_final: 0.8174 (pt0) REVERT: A 751 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6572 (tt0) REVERT: B 121 LYS cc_start: 0.6824 (mptm) cc_final: 0.6599 (mptt) REVERT: B 645 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5900 (mp10) REVERT: B 682 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8158 (tp30) REVERT: C 121 LYS cc_start: 0.6810 (mptm) cc_final: 0.6557 (mptt) REVERT: C 645 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5874 (mp10) REVERT: C 682 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: D 121 LYS cc_start: 0.6809 (mptm) cc_final: 0.6561 (mptt) REVERT: D 645 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5869 (mp10) REVERT: D 682 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8164 (tp30) outliers start: 51 outliers final: 4 residues processed: 322 average time/residue: 0.7220 time to fit residues: 260.2742 Evaluate side-chains 275 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 262 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 751 GLU 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: 0.7980 chunk 182 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4184 r_free = 0.4184 target = 0.196677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162380 restraints weight = 17165.415| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.06 r_work: 0.3611 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3422 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23104 Z= 0.143 Angle : 0.537 7.004 30920 Z= 0.288 Chirality : 0.039 0.135 3324 Planarity : 0.004 0.047 3704 Dihedral : 22.472 152.308 4328 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.50 % Allowed : 8.03 % Favored : 89.47 % 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: 0.46 (0.16), residues: 2548 helix: 1.19 (0.13), residues: 1584 sheet: 0.92 (0.51), residues: 88 loop : -1.41 (0.19), residues: 876 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 0.019 0.001 PHE D 316 TRP 0.011 0.001 TRP C 692 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00245 (23100) covalent geometry : angle 0.53713 (30912) SS BOND : bond 0.00023 ( 4) SS BOND : angle 0.14584 ( 8) hydrogen bonds : bond 0.07310 ( 1108) hydrogen bonds : angle 3.93444 ( 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 330 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 327 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6846 (tpp-160) REVERT: A 479 MET cc_start: 0.1110 (OUTLIER) cc_final: 0.0747 (tmm) REVERT: A 501 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 121 LYS cc_start: 0.6749 (mptm) cc_final: 0.6510 (mptt) REVERT: B 276 GLU cc_start: 0.7566 (pm20) cc_final: 0.7314 (mp0) REVERT: B 327 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6228 (mmm-85) REVERT: B 645 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5906 (mp10) REVERT: B 682 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: C 121 LYS cc_start: 0.6730 (mptm) cc_final: 0.6487 (mptt) REVERT: C 327 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6204 (mmm-85) REVERT: C 645 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5863 (mp10) REVERT: C 682 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8095 (tp30) REVERT: D 121 LYS cc_start: 0.6743 (mptm) cc_final: 0.6499 (mptt) REVERT: D 327 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6210 (mmm-85) REVERT: D 645 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.5868 (mp10) REVERT: D 682 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8095 (tp30) outliers start: 57 outliers final: 11 residues processed: 305 average time/residue: 0.7331 time to fit residues: 250.2198 Evaluate side-chains 262 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 327 ARG 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 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 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 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: 1.9990 chunk 13 optimal weight: 0.0010 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 750 ASN B 580 GLN C 580 GLN D 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.195686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.162572 restraints weight = 16967.494| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 0.97 r_work: 0.3511 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work: 0.3305 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23104 Z= 0.149 Angle : 0.545 7.313 30920 Z= 0.291 Chirality : 0.040 0.142 3324 Planarity : 0.004 0.044 3704 Dihedral : 21.346 153.089 4328 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.63 % Allowed : 9.21 % Favored : 88.16 % 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: 0.71 (0.16), residues: 2548 helix: 1.43 (0.13), residues: 1612 sheet: 0.90 (0.50), residues: 88 loop : -1.49 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 225 TYR 0.025 0.002 TYR A 540 PHE 0.025 0.002 PHE D 449 TRP 0.012 0.001 TRP C 493 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00256 (23100) covalent geometry : angle 0.54501 (30912) SS BOND : bond 0.00017 ( 4) SS BOND : angle 0.26004 ( 8) hydrogen bonds : bond 0.07522 ( 1108) hydrogen bonds : angle 3.94137 ( 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 319 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7103 (OUTLIER) cc_final: 0.6843 (t) REVERT: A 158 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6701 (tt) REVERT: A 173 MET cc_start: 0.8366 (mtt) cc_final: 0.8131 (mtt) REVERT: A 253 LYS cc_start: 0.6634 (mmmt) cc_final: 0.6373 (mmmt) REVERT: A 327 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6420 (mmm-85) REVERT: A 501 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 682 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: A 728 PHE cc_start: 0.8506 (m-80) cc_final: 0.8253 (m-80) REVERT: B 121 LYS cc_start: 0.6825 (mptm) cc_final: 0.6497 (mptt) REVERT: B 158 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6691 (tt) REVERT: B 276 GLU cc_start: 0.7600 (pm20) cc_final: 0.7328 (pm20) REVERT: B 327 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6383 (mmm-85) REVERT: B 682 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: B 728 PHE cc_start: 0.8477 (m-80) cc_final: 0.8213 (m-80) REVERT: B 750 ASN cc_start: 0.8348 (m110) cc_final: 0.7956 (t0) REVERT: C 121 LYS cc_start: 0.6782 (mptm) cc_final: 0.6464 (mptt) REVERT: C 127 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6872 (t) REVERT: C 158 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6673 (tt) REVERT: C 327 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6358 (mmm-85) REVERT: C 682 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: C 728 PHE cc_start: 0.8468 (m-80) cc_final: 0.8209 (m-80) REVERT: C 750 ASN cc_start: 0.8291 (m110) cc_final: 0.7952 (t0) REVERT: D 121 LYS cc_start: 0.6788 (mptm) cc_final: 0.6473 (mptt) REVERT: D 127 VAL cc_start: 0.7111 (OUTLIER) cc_final: 0.6860 (t) REVERT: D 158 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6655 (tt) REVERT: D 327 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6372 (mmm-85) REVERT: D 682 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: D 728 PHE cc_start: 0.8481 (m-80) cc_final: 0.8217 (m-80) REVERT: D 750 ASN cc_start: 0.8300 (m110) cc_final: 0.7972 (t0) outliers start: 60 outliers final: 13 residues processed: 288 average time/residue: 0.7385 time to fit residues: 237.8084 Evaluate side-chains 267 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 682 GLU 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 158 LEU 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 184 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 479 MET 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 479 MET 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: 6.9990 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 224 optimal weight: 0.0030 chunk 107 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4208 r_free = 0.4208 target = 0.199142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.168199 restraints weight = 17204.610| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 0.90 r_work: 0.3584 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work: 0.3370 rms_B_bonded: 4.57 restraints_weight: 0.1250 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 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 = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3156 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= 0.117 Angle : 0.482 7.550 30920 Z= 0.257 Chirality : 0.038 0.126 3324 Planarity : 0.003 0.039 3704 Dihedral : 20.100 149.901 4328 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.19 % Allowed : 9.74 % Favored : 88.07 % 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: 1.17 (0.17), residues: 2548 helix: 1.83 (0.13), residues: 1620 sheet: 0.95 (0.51), residues: 88 loop : -1.42 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.022 0.001 TYR C 540 PHE 0.023 0.001 PHE D 449 TRP 0.013 0.001 TRP A 493 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00199 (23100) covalent geometry : angle 0.48161 (30912) SS BOND : bond 0.00023 ( 4) SS BOND : angle 0.21667 ( 8) hydrogen bonds : bond 0.05773 ( 1108) hydrogen bonds : angle 3.65784 ( 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 322 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7116 (OUTLIER) cc_final: 0.6888 (t) REVERT: A 253 LYS cc_start: 0.6688 (mmmt) cc_final: 0.6353 (mmmt) REVERT: A 728 PHE cc_start: 0.8510 (m-80) cc_final: 0.8294 (m-80) REVERT: B 121 LYS cc_start: 0.6760 (mptm) cc_final: 0.6446 (mptt) REVERT: B 173 MET cc_start: 0.8321 (mtt) cc_final: 0.8100 (mtt) REVERT: B 276 GLU cc_start: 0.7635 (pm20) cc_final: 0.7371 (pm20) REVERT: B 327 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6181 (mmm-85) REVERT: B 682 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: B 728 PHE cc_start: 0.8455 (m-80) cc_final: 0.8188 (m-80) REVERT: C 121 LYS cc_start: 0.6727 (mptm) cc_final: 0.6408 (mptt) REVERT: C 158 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6646 (tt) REVERT: C 173 MET cc_start: 0.8340 (mtt) cc_final: 0.8108 (mtt) REVERT: C 327 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6133 (mmm-85) REVERT: C 682 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8067 (tp30) REVERT: C 728 PHE cc_start: 0.8464 (m-80) cc_final: 0.8207 (m-80) REVERT: C 750 ASN cc_start: 0.8282 (m110) cc_final: 0.7941 (t0) REVERT: D 121 LYS cc_start: 0.6729 (mptm) cc_final: 0.6409 (mptt) REVERT: D 158 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6660 (tt) REVERT: D 173 MET cc_start: 0.8325 (mtt) cc_final: 0.8093 (mtt) REVERT: D 327 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6151 (mmm-85) REVERT: D 682 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8053 (tp30) REVERT: D 728 PHE cc_start: 0.8468 (m-80) cc_final: 0.8208 (m-80) REVERT: D 750 ASN cc_start: 0.8295 (m110) cc_final: 0.7949 (t0) outliers start: 50 outliers final: 7 residues processed: 298 average time/residue: 0.7374 time to fit residues: 245.9757 Evaluate side-chains 269 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 462 ARG 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 682 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 0.0870 chunk 223 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 236 optimal weight: 0.6980 chunk 220 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 234 optimal weight: 7.9990 chunk 156 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4207 r_free = 0.4207 target = 0.199156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.164444 restraints weight = 17192.141| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.24 r_work: 0.3579 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work: 0.3420 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3332 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= 0.113 Angle : 0.474 7.741 30920 Z= 0.252 Chirality : 0.037 0.126 3324 Planarity : 0.003 0.036 3704 Dihedral : 19.518 148.045 4328 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.89 % Allowed : 10.57 % Favored : 87.54 % 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: 1.43 (0.17), residues: 2548 helix: 2.05 (0.13), residues: 1616 sheet: 0.93 (0.50), residues: 88 loop : -1.30 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 225 TYR 0.021 0.001 TYR A 540 PHE 0.024 0.001 PHE A 449 TRP 0.015 0.001 TRP A 493 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00195 (23100) covalent geometry : angle 0.47451 (30912) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.40430 ( 8) hydrogen bonds : bond 0.05558 ( 1108) hydrogen bonds : angle 3.58830 ( 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 295 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7094 (OUTLIER) cc_final: 0.6882 (t) REVERT: A 158 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6621 (tt) REVERT: A 253 LYS cc_start: 0.6589 (mmmt) cc_final: 0.6350 (mmmt) REVERT: A 750 ASN cc_start: 0.8256 (m110) cc_final: 0.7956 (t0) REVERT: B 121 LYS cc_start: 0.6763 (mptm) cc_final: 0.6457 (mptt) REVERT: B 158 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6607 (tt) REVERT: B 173 MET cc_start: 0.8341 (mtt) cc_final: 0.8116 (mtt) REVERT: B 276 GLU cc_start: 0.7628 (pm20) cc_final: 0.7420 (pm20) REVERT: B 327 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6219 (mmm-85) REVERT: B 682 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: C 121 LYS cc_start: 0.6735 (mptm) cc_final: 0.6398 (mptt) REVERT: C 327 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6166 (mmm-85) REVERT: C 682 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: C 750 ASN cc_start: 0.8236 (m110) cc_final: 0.7952 (t0) REVERT: D 121 LYS cc_start: 0.6745 (mptm) cc_final: 0.6406 (mptt) REVERT: D 173 MET cc_start: 0.8336 (mtt) cc_final: 0.8098 (mtt) REVERT: D 327 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6136 (mmm-85) REVERT: D 682 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: D 728 PHE cc_start: 0.8400 (m-80) cc_final: 0.8194 (m-80) REVERT: D 750 ASN cc_start: 0.8245 (m110) cc_final: 0.7958 (t0) outliers start: 43 outliers final: 11 residues processed: 278 average time/residue: 0.7322 time to fit residues: 228.2891 Evaluate side-chains 256 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 458 VAL 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 327 ARG Chi-restraints excluded: chain C residue 462 ARG 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 458 VAL Chi-restraints excluded: chain D residue 462 ARG 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: 2.9990 chunk 236 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN C 580 GLN C 647 ASN D 580 GLN D 647 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.192533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.159067 restraints weight = 16609.819| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 0.99 r_work: 0.3490 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.3325 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.3325 ------------------------------------------------------------------------------- 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: 22 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23104 Z= 0.192 Angle : 0.623 8.161 30920 Z= 0.332 Chirality : 0.042 0.147 3324 Planarity : 0.005 0.043 3704 Dihedral : 20.369 153.987 4328 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.19 % Allowed : 10.39 % Favored : 87.41 % 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: 0.98 (0.16), residues: 2548 helix: 1.67 (0.13), residues: 1608 sheet: 0.86 (0.51), residues: 88 loop : -1.39 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 729 TYR 0.025 0.002 TYR A 540 PHE 0.026 0.002 PHE A 316 TRP 0.024 0.002 TRP D 493 HIS 0.007 0.002 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00351 (23100) covalent geometry : angle 0.62255 (30912) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.52576 ( 8) hydrogen bonds : bond 0.08923 ( 1108) hydrogen bonds : angle 4.10658 ( 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 315 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6605 (tt) REVERT: A 253 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6313 (mmmt) REVERT: A 750 ASN cc_start: 0.8214 (m110) cc_final: 0.7925 (t0) REVERT: B 121 LYS cc_start: 0.6855 (mptm) cc_final: 0.6529 (mptt) REVERT: B 158 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6523 (tt) REVERT: B 327 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6414 (mmm-85) REVERT: B 682 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: B 728 PHE cc_start: 0.8408 (m-80) cc_final: 0.8186 (m-80) REVERT: B 750 ASN cc_start: 0.8207 (m110) cc_final: 0.7917 (t0) REVERT: C 121 LYS cc_start: 0.6828 (mptm) cc_final: 0.6506 (mptt) REVERT: C 158 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6521 (tt) REVERT: C 327 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6414 (mmm-85) REVERT: C 682 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: C 750 ASN cc_start: 0.8186 (m110) cc_final: 0.7904 (t0) REVERT: D 121 LYS cc_start: 0.6829 (mptm) cc_final: 0.6505 (mptt) REVERT: D 158 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6477 (tt) REVERT: D 327 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6419 (mmm-85) REVERT: D 682 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: D 720 LEU cc_start: 0.8333 (tp) cc_final: 0.8055 (tp) REVERT: D 728 PHE cc_start: 0.8405 (m-80) cc_final: 0.8191 (m-80) REVERT: D 750 ASN cc_start: 0.8187 (m110) cc_final: 0.7903 (t0) outliers start: 50 outliers final: 14 residues processed: 295 average time/residue: 0.7037 time to fit residues: 233.9699 Evaluate side-chains 267 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 458 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 458 VAL 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 458 VAL Chi-restraints excluded: chain C residue 462 ARG 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 682 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 194 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.196788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162388 restraints weight = 16906.230| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.06 r_work: 0.3620 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3432 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3323 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= 0.128 Angle : 0.504 7.919 30920 Z= 0.269 Chirality : 0.038 0.129 3324 Planarity : 0.003 0.038 3704 Dihedral : 19.659 151.693 4328 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.40 % Allowed : 11.23 % Favored : 87.37 % 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: 1.22 (0.17), residues: 2548 helix: 1.90 (0.13), residues: 1636 sheet: 0.82 (0.51), residues: 88 loop : -1.51 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.020 0.001 TYR A 540 PHE 0.028 0.001 PHE A 449 TRP 0.021 0.001 TRP A 493 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00219 (23100) covalent geometry : angle 0.50360 (30912) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.66744 ( 8) hydrogen bonds : bond 0.06294 ( 1108) hydrogen bonds : angle 3.73016 ( 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 299 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7142 (OUTLIER) cc_final: 0.6915 (t) REVERT: A 158 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6587 (tt) REVERT: A 253 LYS cc_start: 0.6533 (mmmt) cc_final: 0.6312 (mmmt) REVERT: A 750 ASN cc_start: 0.8160 (m110) cc_final: 0.7934 (t0) REVERT: B 121 LYS cc_start: 0.6740 (mptm) cc_final: 0.6461 (mptt) REVERT: B 158 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6520 (tt) REVERT: B 314 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7304 (m-40) REVERT: B 327 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6167 (mmm-85) REVERT: B 682 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: B 750 ASN cc_start: 0.8168 (m110) cc_final: 0.7922 (t0) REVERT: C 121 LYS cc_start: 0.6740 (mptm) cc_final: 0.6455 (mptt) REVERT: C 158 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6514 (tt) REVERT: C 327 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6248 (mmm-85) REVERT: C 682 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: C 750 ASN cc_start: 0.8162 (m110) cc_final: 0.7924 (t0) REVERT: D 121 LYS cc_start: 0.6758 (mptm) cc_final: 0.6477 (mptt) REVERT: D 158 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6514 (tt) REVERT: D 327 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6248 (mmm-85) REVERT: D 682 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: D 750 ASN cc_start: 0.8172 (m110) cc_final: 0.7943 (t0) outliers start: 32 outliers final: 12 residues processed: 288 average time/residue: 0.7167 time to fit residues: 232.0802 Evaluate side-chains 266 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 458 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 314 ASN 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 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 485 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 195 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 250 optimal weight: 0.0050 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.194217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164956 restraints weight = 16794.883| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 0.66 r_work: 0.3660 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3255 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= 0.158 Angle : 0.561 8.428 30920 Z= 0.298 Chirality : 0.040 0.137 3324 Planarity : 0.004 0.040 3704 Dihedral : 19.772 152.916 4328 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.27 % Allowed : 11.71 % Favored : 87.02 % 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: 1.09 (0.16), residues: 2548 helix: 1.81 (0.13), residues: 1632 sheet: 0.69 (0.51), residues: 88 loop : -1.55 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 462 TYR 0.022 0.002 TYR C 540 PHE 0.021 0.002 PHE B 316 TRP 0.027 0.002 TRP D 493 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00277 (23100) covalent geometry : angle 0.56143 (30912) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.71157 ( 8) hydrogen bonds : bond 0.07710 ( 1108) hydrogen bonds : angle 3.92089 ( 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 284 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6214 (tt) REVERT: A 327 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.5886 (mmm-85) REVERT: A 750 ASN cc_start: 0.7858 (m110) cc_final: 0.7649 (t0) REVERT: B 327 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6115 (mmm-85) REVERT: B 682 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: B 720 LEU cc_start: 0.8150 (tp) cc_final: 0.7916 (tp) REVERT: B 750 ASN cc_start: 0.7823 (m110) cc_final: 0.7606 (t0) REVERT: C 158 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6155 (tt) REVERT: C 327 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6092 (mmm-85) REVERT: C 682 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: C 720 LEU cc_start: 0.8162 (tp) cc_final: 0.7927 (tp) REVERT: D 158 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6123 (tt) REVERT: D 327 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6102 (mmm-85) REVERT: D 682 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7779 (tp30) outliers start: 29 outliers final: 14 residues processed: 275 average time/residue: 0.7641 time to fit residues: 236.5352 Evaluate side-chains 273 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 713 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 458 VAL 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 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 485 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 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 647 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.157534 restraints weight = 16453.568| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 0.96 r_work: 0.3479 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.3332 rms_B_bonded: 3.56 restraints_weight: 0.1250 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3155 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 8.141 30920 Z= 0.378 Chirality : 0.045 0.158 3324 Planarity : 0.005 0.050 3704 Dihedral : 20.853 158.605 4328 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.45 % Allowed : 11.49 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2548 helix: 1.29 (0.12), residues: 1624 sheet: 0.71 (0.52), residues: 88 loop : -1.61 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 462 TYR 0.028 0.003 TYR A 540 PHE 0.029 0.003 PHE B 316 TRP 0.045 0.003 TRP B 493 HIS 0.009 0.003 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00440 (23100) covalent geometry : angle 0.71509 (30912) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.94223 ( 8) hydrogen bonds : bond 0.10069 ( 1108) hydrogen bonds : angle 4.32559 ( 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 295 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.790 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: 0.6607 (tt) REVERT: A 327 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6152 (mmm-85) REVERT: A 750 ASN cc_start: 0.8127 (m110) cc_final: 0.7855 (t0) REVERT: B 327 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6356 (mmm-85) REVERT: B 682 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: B 720 LEU cc_start: 0.8242 (tp) cc_final: 0.7967 (tp) REVERT: B 750 ASN cc_start: 0.8120 (m110) cc_final: 0.7856 (t0) REVERT: C 158 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6525 (tt) REVERT: C 327 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6317 (mmm-85) REVERT: C 682 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: C 720 LEU cc_start: 0.8256 (tp) cc_final: 0.7994 (tp) REVERT: D 158 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6471 (tt) REVERT: D 327 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6344 (mmm-85) REVERT: D 682 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8223 (tp30) outliers start: 33 outliers final: 16 residues processed: 287 average time/residue: 0.7136 time to fit residues: 229.9862 Evaluate side-chains 281 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 485 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 458 VAL 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 458 VAL Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 485 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 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 580 GLN D 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.195926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162416 restraints weight = 16964.405| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.01 r_work: 0.3530 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work: 0.3397 rms_B_bonded: 3.83 restraints_weight: 0.1250 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3386 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= 0.136 Angle : 0.530 8.236 30920 Z= 0.281 Chirality : 0.039 0.141 3324 Planarity : 0.003 0.042 3704 Dihedral : 19.861 153.463 4328 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.23 % Allowed : 11.97 % Favored : 86.80 % 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: 1.11 (0.16), residues: 2548 helix: 1.83 (0.13), residues: 1632 sheet: 0.61 (0.51), residues: 88 loop : -1.54 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 462 TYR 0.020 0.002 TYR A 540 PHE 0.019 0.002 PHE B 316 TRP 0.029 0.002 TRP B 493 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00234 (23100) covalent geometry : angle 0.52978 (30912) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.93459 ( 8) hydrogen bonds : bond 0.06611 ( 1108) hydrogen bonds : angle 3.80100 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13054.14 seconds wall clock time: 221 minutes 7.61 seconds (13267.61 seconds total)