Starting phenix.real_space_refine on Tue Aug 26 15:36:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1f_35921/08_2025/8j1f_35921_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1f_35921/08_2025/8j1f_35921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j1f_35921/08_2025/8j1f_35921_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1f_35921/08_2025/8j1f_35921_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1f_35921/08_2025/8j1f_35921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1f_35921/08_2025/8j1f_35921.map" } resolution = 3.62 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= 0.022 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 S 104 5.16 5 Cl 8 4.86 5 C 12448 2.51 5 N 3160 2.21 5 O 3396 1.98 5 H 19280 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38396 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9557 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 20, 'TRANS': 566} Chain breaks: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.88, per 1000 atoms: 0.28 Number of scatterers: 38396 At special positions: 0 Unit cell: (147.87, 147.87, 119.04, 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) Cl 8 17.00 S 104 16.00 O 3396 8.00 N 3160 7.00 C 12448 6.00 H 19280 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.94 Conformation dependent library (CDL) restraints added in 839.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 67.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.943A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.777A pdb=" N LEU A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.502A pdb=" N ASN A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.613A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.506A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.676A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.862A pdb=" N GLY A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.530A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.758A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.745A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.657A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 504 through 531 removed outlier: 3.515A pdb=" N PHE A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 569 Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.632A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 633 removed outlier: 3.624A pdb=" N PHE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.694A pdb=" N ILE A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 removed outlier: 4.009A pdb=" N SER A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 725 Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.913A pdb=" N LYS A 730 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.578A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.943A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.777A pdb=" N LEU B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.502A pdb=" N ASN B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.613A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.506A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.677A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.862A pdb=" N GLY B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.530A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.758A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.745A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 465 removed outlier: 3.657A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 491 Processing helix chain 'B' and resid 504 through 531 removed outlier: 3.515A pdb=" N PHE B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 569 Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.631A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 633 removed outlier: 3.624A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 680 removed outlier: 3.694A pdb=" N ILE B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 removed outlier: 4.009A pdb=" N SER B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 725 Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.912A pdb=" N LYS B 730 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 748 removed outlier: 3.579A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.942A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.777A pdb=" N LEU C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.503A pdb=" N ASN C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.614A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.506A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.676A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.862A pdb=" N GLY C 279 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 322 through 331 Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.530A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.758A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 451 removed outlier: 3.745A pdb=" N ALA C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 465 removed outlier: 3.657A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 491 Processing helix chain 'C' and resid 504 through 531 removed outlier: 3.515A pdb=" N PHE C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 569 Processing helix chain 'C' and resid 575 through 589 Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.632A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 633 removed outlier: 3.624A pdb=" N PHE C 611 " --> pdb=" O GLN C 607 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 680 removed outlier: 3.695A pdb=" N ILE C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 679 " --> pdb=" O LYS C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 688 removed outlier: 4.009A pdb=" N SER C 687 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 725 Processing helix chain 'C' and resid 726 through 730 removed outlier: 3.913A pdb=" N LYS C 730 " --> pdb=" O LYS C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 748 removed outlier: 3.578A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.943A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.777A pdb=" N LEU D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.502A pdb=" N ASN D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.614A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.506A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.676A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.862A pdb=" N GLY D 279 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 335 through 357 removed outlier: 3.530A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.758A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 451 removed outlier: 3.745A pdb=" N ALA D 451 " --> pdb=" O HIS D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 465 removed outlier: 3.657A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 491 Processing helix chain 'D' and resid 504 through 531 removed outlier: 3.515A pdb=" N PHE D 525 " --> pdb=" O GLY D 521 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 569 Processing helix chain 'D' and resid 575 through 589 Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.632A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY D 595 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 633 removed outlier: 3.624A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 631 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 680 removed outlier: 3.694A pdb=" N ILE D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 679 " --> pdb=" O LYS D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 688 removed outlier: 4.009A pdb=" N SER D 687 " --> pdb=" O GLU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 725 Processing helix chain 'D' and resid 726 through 730 removed outlier: 3.913A pdb=" N LYS D 730 " --> pdb=" O LYS D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 748 removed outlier: 3.578A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.936A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 414 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.936A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 414 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.936A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 414 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.935A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 414 " --> pdb=" O TYR D 411 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2928 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: 7.88 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19248 1.03 - 1.23: 44 1.23 - 1.42: 8180 1.42 - 1.62: 11168 1.62 - 1.81: 184 Bond restraints: 38824 Sorted by residual: bond pdb=" C25 XQ3 C 901 " pdb=" N22 XQ3 C 901 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C25 XQ3 A 901 " pdb=" N22 XQ3 A 901 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C25 XQ3 D 901 " pdb=" N22 XQ3 D 901 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C25 XQ3 B 901 " pdb=" N22 XQ3 B 901 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C07 XQ3 B 901 " pdb=" N06 XQ3 B 901 " ideal model delta sigma weight residual 1.349 1.457 -0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 38819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.74: 70008 7.74 - 15.49: 20 15.49 - 23.23: 12 23.23 - 30.97: 24 30.97 - 38.71: 16 Bond angle restraints: 70080 Sorted by residual: angle pdb=" C PRO D 638 " pdb=" CA PRO D 638 " pdb=" HA PRO D 638 " ideal model delta sigma weight residual 109.00 70.29 38.71 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C PRO A 638 " pdb=" CA PRO A 638 " pdb=" HA PRO A 638 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C PRO B 638 " pdb=" CA PRO B 638 " pdb=" HA PRO B 638 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C PRO C 638 " pdb=" CA PRO C 638 " pdb=" HA PRO C 638 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" N PRO B 638 " pdb=" CA PRO B 638 " pdb=" HA PRO B 638 " ideal model delta sigma weight residual 110.00 73.41 36.59 3.00e+00 1.11e-01 1.49e+02 ... (remaining 70075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 17517 30.55 - 61.10: 675 61.10 - 91.65: 56 91.65 - 122.20: 8 122.20 - 152.74: 12 Dihedral angle restraints: 18268 sinusoidal: 9908 harmonic: 8360 Sorted by residual: dihedral pdb=" C ASN A 637 " pdb=" N ASN A 637 " pdb=" CA ASN A 637 " pdb=" CB ASN A 637 " ideal model delta harmonic sigma weight residual -122.60 -134.72 12.12 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C ASN C 637 " pdb=" N ASN C 637 " pdb=" CA ASN C 637 " pdb=" CB ASN C 637 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 18265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3000 0.101 - 0.202: 28 0.202 - 0.303: 0 0.303 - 0.404: 0 0.404 - 0.505: 8 Chirality restraints: 3036 Sorted by residual: chirality pdb=" CA ASN A 637 " pdb=" N ASN A 637 " pdb=" C ASN A 637 " pdb=" CB ASN A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA ASN D 637 " pdb=" N ASN D 637 " pdb=" C ASN D 637 " pdb=" CB ASN D 637 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA ASN B 637 " pdb=" N ASN B 637 " pdb=" C ASN B 637 " pdb=" CB ASN B 637 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 3033 not shown) Planarity restraints: 5528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 XQ3 D 901 " 0.036 2.00e-02 2.50e+03 4.59e-02 5.26e+01 pdb=" C08 XQ3 D 901 " 0.087 2.00e-02 2.50e+03 pdb=" C09 XQ3 D 901 " -0.070 2.00e-02 2.50e+03 pdb=" C10 XQ3 D 901 " -0.033 2.00e-02 2.50e+03 pdb=" C11 XQ3 D 901 " -0.006 2.00e-02 2.50e+03 pdb=" C12 XQ3 D 901 " 0.027 2.00e-02 2.50e+03 pdb=" C13 XQ3 D 901 " 0.034 2.00e-02 2.50e+03 pdb=" C14 XQ3 D 901 " 0.009 2.00e-02 2.50e+03 pdb=" C15 XQ3 D 901 " -0.024 2.00e-02 2.50e+03 pdb=" S16 XQ3 D 901 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 XQ3 B 901 " -0.036 2.00e-02 2.50e+03 4.58e-02 5.25e+01 pdb=" C08 XQ3 B 901 " -0.087 2.00e-02 2.50e+03 pdb=" C09 XQ3 B 901 " 0.070 2.00e-02 2.50e+03 pdb=" C10 XQ3 B 901 " 0.033 2.00e-02 2.50e+03 pdb=" C11 XQ3 B 901 " 0.006 2.00e-02 2.50e+03 pdb=" C12 XQ3 B 901 " -0.027 2.00e-02 2.50e+03 pdb=" C13 XQ3 B 901 " -0.034 2.00e-02 2.50e+03 pdb=" C14 XQ3 B 901 " -0.009 2.00e-02 2.50e+03 pdb=" C15 XQ3 B 901 " 0.024 2.00e-02 2.50e+03 pdb=" S16 XQ3 B 901 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 XQ3 A 901 " 0.036 2.00e-02 2.50e+03 4.58e-02 5.24e+01 pdb=" C08 XQ3 A 901 " 0.087 2.00e-02 2.50e+03 pdb=" C09 XQ3 A 901 " -0.070 2.00e-02 2.50e+03 pdb=" C10 XQ3 A 901 " -0.033 2.00e-02 2.50e+03 pdb=" C11 XQ3 A 901 " -0.006 2.00e-02 2.50e+03 pdb=" C12 XQ3 A 901 " 0.027 2.00e-02 2.50e+03 pdb=" C13 XQ3 A 901 " 0.034 2.00e-02 2.50e+03 pdb=" C14 XQ3 A 901 " 0.009 2.00e-02 2.50e+03 pdb=" C15 XQ3 A 901 " -0.024 2.00e-02 2.50e+03 pdb=" S16 XQ3 A 901 " -0.060 2.00e-02 2.50e+03 ... (remaining 5525 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 3141 2.20 - 2.80: 82179 2.80 - 3.40: 108696 3.40 - 4.00: 135055 4.00 - 4.60: 209740 Nonbonded interactions: 538811 Sorted by model distance: nonbonded pdb=" OE1 GLU C 760 " pdb=" H GLU C 760 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU B 760 " pdb=" H GLU B 760 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU D 760 " pdb=" H GLU D 760 " model vdw 1.607 2.450 nonbonded pdb=" OE1 GLU A 760 " pdb=" H GLU A 760 " model vdw 1.607 2.450 nonbonded pdb=" O PRO B 298 " pdb="HD21 ASN B 302 " model vdw 1.616 2.450 ... (remaining 538806 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.650 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 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 : 0.004 0.108 19544 Z= 0.210 Angle : 0.700 17.731 26488 Z= 0.330 Chirality : 0.043 0.505 3036 Planarity : 0.004 0.062 3276 Dihedral : 16.030 152.744 7224 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.41 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.13 (0.18), residues: 2308 helix: 0.16 (0.14), residues: 1288 sheet: -2.44 (0.58), residues: 84 loop : -1.84 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 616 TYR 0.018 0.001 TYR B 236 PHE 0.015 0.001 PHE B 615 TRP 0.016 0.001 TRP C 409 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00432 (19544) covalent geometry : angle 0.69970 (26488) hydrogen bonds : bond 0.25303 ( 1012) hydrogen bonds : angle 8.33738 ( 2928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 TYR cc_start: 0.6884 (t80) cc_final: 0.6246 (t80) REVERT: A 680 MET cc_start: 0.7376 (ppp) cc_final: 0.7104 (ppp) REVERT: A 713 MET cc_start: 0.8715 (tmm) cc_final: 0.8407 (tmm) REVERT: B 314 MET cc_start: 0.6355 (mtt) cc_final: 0.6135 (mtt) REVERT: B 553 TYR cc_start: 0.6882 (t80) cc_final: 0.6250 (t80) REVERT: B 680 MET cc_start: 0.7369 (ppp) cc_final: 0.7088 (ppp) REVERT: B 713 MET cc_start: 0.8702 (tmm) cc_final: 0.8403 (tmm) REVERT: C 553 TYR cc_start: 0.6905 (t80) cc_final: 0.6274 (t80) REVERT: C 680 MET cc_start: 0.7389 (ppp) cc_final: 0.7116 (ppp) REVERT: C 713 MET cc_start: 0.8706 (tmm) cc_final: 0.8407 (tmm) REVERT: D 553 TYR cc_start: 0.6907 (t80) cc_final: 0.6276 (t80) REVERT: D 680 MET cc_start: 0.7389 (ppp) cc_final: 0.7113 (ppp) REVERT: D 713 MET cc_start: 0.8711 (tmm) cc_final: 0.8411 (tmm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2933 time to fit residues: 113.2594 Evaluate side-chains 213 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.184176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.151019 restraints weight = 128382.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.156730 restraints weight = 60886.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.160328 restraints weight = 38969.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.162445 restraints weight = 29719.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.163674 restraints weight = 25240.747| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19544 Z= 0.188 Angle : 0.694 12.385 26488 Z= 0.356 Chirality : 0.045 0.507 3036 Planarity : 0.005 0.056 3276 Dihedral : 12.721 155.172 2744 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.89 % Favored : 91.94 % Rotamer: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.30 (0.17), residues: 2308 helix: -0.06 (0.13), residues: 1344 sheet: -2.69 (0.58), residues: 84 loop : -1.88 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 594 TYR 0.016 0.002 TYR A 621 PHE 0.023 0.002 PHE C 615 TRP 0.011 0.001 TRP A 409 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00413 (19544) covalent geometry : angle 0.69388 (26488) hydrogen bonds : bond 0.05900 ( 1012) hydrogen bonds : angle 5.76805 ( 2928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.8922 (tmm) cc_final: 0.8677 (tmm) REVERT: A 743 ASP cc_start: 0.6552 (t0) cc_final: 0.6127 (t0) REVERT: B 713 MET cc_start: 0.8932 (tmm) cc_final: 0.8676 (tmm) REVERT: B 743 ASP cc_start: 0.6573 (t0) cc_final: 0.6142 (t0) REVERT: C 680 MET cc_start: 0.7336 (ppp) cc_final: 0.7129 (ppp) REVERT: C 713 MET cc_start: 0.8934 (tmm) cc_final: 0.8672 (tmm) REVERT: C 743 ASP cc_start: 0.6546 (t0) cc_final: 0.6113 (t0) REVERT: D 602 TYR cc_start: 0.6687 (m-80) cc_final: 0.6425 (m-80) REVERT: D 680 MET cc_start: 0.7307 (ppp) cc_final: 0.7101 (ppp) REVERT: D 713 MET cc_start: 0.8933 (tmm) cc_final: 0.8669 (tmm) REVERT: D 743 ASP cc_start: 0.6582 (t0) cc_final: 0.6141 (t0) outliers start: 2 outliers final: 2 residues processed: 254 average time/residue: 0.2709 time to fit residues: 109.3838 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 557 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 123 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN D 588 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.182844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.148844 restraints weight = 128884.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.154597 restraints weight = 61351.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.158208 restraints weight = 39420.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.160281 restraints weight = 30181.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.161514 restraints weight = 25754.943| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19544 Z= 0.191 Angle : 0.676 12.749 26488 Z= 0.341 Chirality : 0.045 0.519 3036 Planarity : 0.004 0.052 3276 Dihedral : 12.310 153.123 2744 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.15 % Favored : 91.51 % Rotamer: Outliers : 0.38 % Allowed : 9.04 % Favored : 90.58 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.42 (0.18), residues: 2308 helix: -0.06 (0.13), residues: 1368 sheet: -3.50 (0.51), residues: 84 loop : -2.04 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 594 TYR 0.020 0.002 TYR C 621 PHE 0.018 0.002 PHE D 756 TRP 0.008 0.001 TRP C 409 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00421 (19544) covalent geometry : angle 0.67597 (26488) hydrogen bonds : bond 0.05206 ( 1012) hydrogen bonds : angle 5.30960 ( 2928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 TYR cc_start: 0.6885 (m-80) cc_final: 0.6562 (m-80) REVERT: A 713 MET cc_start: 0.8918 (tmm) cc_final: 0.8672 (tmm) REVERT: B 602 TYR cc_start: 0.6937 (m-80) cc_final: 0.6621 (m-80) REVERT: B 713 MET cc_start: 0.8924 (tmm) cc_final: 0.8658 (tmm) REVERT: C 602 TYR cc_start: 0.6911 (m-80) cc_final: 0.6584 (m-80) REVERT: C 713 MET cc_start: 0.8930 (tmm) cc_final: 0.8669 (tmm) REVERT: D 602 TYR cc_start: 0.6865 (m-80) cc_final: 0.6636 (m-80) REVERT: D 713 MET cc_start: 0.8932 (tmm) cc_final: 0.8668 (tmm) outliers start: 8 outliers final: 8 residues processed: 236 average time/residue: 0.2813 time to fit residues: 103.9940 Evaluate side-chains 226 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 588 ASN C 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.178607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.144273 restraints weight = 129286.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.150128 restraints weight = 62539.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.153717 restraints weight = 40270.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.155884 restraints weight = 30784.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.157158 restraints weight = 26111.436| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19544 Z= 0.206 Angle : 0.668 12.943 26488 Z= 0.339 Chirality : 0.045 0.520 3036 Planarity : 0.004 0.052 3276 Dihedral : 12.586 163.922 2744 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.84 % Favored : 90.81 % Rotamer: Outliers : 1.01 % Allowed : 10.91 % Favored : 88.08 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.50 (0.18), residues: 2308 helix: -0.13 (0.13), residues: 1376 sheet: -3.80 (0.51), residues: 84 loop : -2.06 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 446 TYR 0.020 0.002 TYR B 621 PHE 0.022 0.002 PHE A 756 TRP 0.008 0.001 TRP D 409 HIS 0.004 0.001 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00457 (19544) covalent geometry : angle 0.66780 (26488) hydrogen bonds : bond 0.04676 ( 1012) hydrogen bonds : angle 5.14773 ( 2928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 TYR cc_start: 0.6973 (m-80) cc_final: 0.6747 (m-80) REVERT: A 713 MET cc_start: 0.8912 (tmm) cc_final: 0.8665 (tmm) REVERT: B 602 TYR cc_start: 0.6989 (m-80) cc_final: 0.6763 (m-80) REVERT: B 713 MET cc_start: 0.8918 (tmm) cc_final: 0.8662 (tmm) REVERT: C 713 MET cc_start: 0.8912 (tmm) cc_final: 0.8661 (tmm) REVERT: D 713 MET cc_start: 0.8913 (tmm) cc_final: 0.8659 (tmm) outliers start: 21 outliers final: 13 residues processed: 228 average time/residue: 0.2624 time to fit residues: 94.1903 Evaluate side-chains 225 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 189 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.181041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.147553 restraints weight = 129081.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.153478 restraints weight = 60749.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.157131 restraints weight = 38428.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.159319 restraints weight = 29065.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.160609 restraints weight = 24515.580| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19544 Z= 0.148 Angle : 0.620 12.999 26488 Z= 0.312 Chirality : 0.044 0.521 3036 Planarity : 0.004 0.047 3276 Dihedral : 12.586 169.825 2744 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.89 % Favored : 91.77 % Rotamer: Outliers : 0.58 % Allowed : 12.07 % Favored : 87.36 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.23 (0.18), residues: 2308 helix: 0.15 (0.14), residues: 1376 sheet: -4.04 (0.48), residues: 84 loop : -2.02 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 594 TYR 0.021 0.002 TYR A 621 PHE 0.018 0.001 PHE A 756 TRP 0.009 0.001 TRP A 409 HIS 0.003 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00328 (19544) covalent geometry : angle 0.62010 (26488) hydrogen bonds : bond 0.04330 ( 1012) hydrogen bonds : angle 4.89282 ( 2928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 230 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.8905 (tmm) cc_final: 0.8655 (tmm) REVERT: B 713 MET cc_start: 0.8911 (tmm) cc_final: 0.8646 (tmm) REVERT: C 713 MET cc_start: 0.8909 (tmm) cc_final: 0.8650 (tmm) REVERT: D 713 MET cc_start: 0.8908 (tmm) cc_final: 0.8655 (tmm) outliers start: 12 outliers final: 8 residues processed: 238 average time/residue: 0.3049 time to fit residues: 114.9587 Evaluate side-chains 231 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 54 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.182525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.148846 restraints weight = 128627.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.154525 restraints weight = 60630.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.158289 restraints weight = 38692.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.160416 restraints weight = 29431.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.161604 restraints weight = 24856.414| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19544 Z= 0.167 Angle : 0.626 13.123 26488 Z= 0.315 Chirality : 0.044 0.524 3036 Planarity : 0.004 0.045 3276 Dihedral : 12.371 166.125 2744 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.71 % Favored : 90.94 % Rotamer: Outliers : 0.87 % Allowed : 12.69 % Favored : 86.44 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -1.25 (0.18), residues: 2308 helix: 0.07 (0.13), residues: 1416 sheet: -4.14 (0.49), residues: 84 loop : -2.00 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 594 TYR 0.021 0.002 TYR B 621 PHE 0.018 0.002 PHE A 756 TRP 0.008 0.001 TRP A 409 HIS 0.003 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00372 (19544) covalent geometry : angle 0.62554 (26488) hydrogen bonds : bond 0.04206 ( 1012) hydrogen bonds : angle 4.83986 ( 2928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.8918 (tmm) cc_final: 0.8681 (tmm) REVERT: B 713 MET cc_start: 0.8929 (tmm) cc_final: 0.8677 (tmm) REVERT: C 713 MET cc_start: 0.8923 (tmm) cc_final: 0.8677 (tmm) REVERT: D 713 MET cc_start: 0.8917 (tmm) cc_final: 0.8680 (tmm) outliers start: 18 outliers final: 14 residues processed: 230 average time/residue: 0.2920 time to fit residues: 106.1007 Evaluate side-chains 228 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 153 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.184579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.151567 restraints weight = 128734.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.157424 restraints weight = 59759.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.161067 restraints weight = 37641.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.163231 restraints weight = 28391.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.164382 restraints weight = 24018.474| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19544 Z= 0.126 Angle : 0.609 13.106 26488 Z= 0.301 Chirality : 0.043 0.523 3036 Planarity : 0.004 0.042 3276 Dihedral : 12.327 171.403 2744 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.11 % Favored : 92.55 % Rotamer: Outliers : 0.48 % Allowed : 13.17 % Favored : 86.35 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.97 (0.18), residues: 2308 helix: 0.32 (0.14), residues: 1412 sheet: -4.17 (0.47), residues: 84 loop : -1.90 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 594 TYR 0.021 0.002 TYR A 621 PHE 0.014 0.001 PHE C 615 TRP 0.009 0.001 TRP A 409 HIS 0.002 0.000 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00279 (19544) covalent geometry : angle 0.60856 (26488) hydrogen bonds : bond 0.03975 ( 1012) hydrogen bonds : angle 4.64433 ( 2928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 MET cc_start: 0.8910 (tmm) cc_final: 0.8708 (tmm) REVERT: B 713 MET cc_start: 0.8901 (tmm) cc_final: 0.8692 (tmm) REVERT: C 713 MET cc_start: 0.8919 (tmm) cc_final: 0.8704 (tmm) REVERT: D 713 MET cc_start: 0.8921 (tmm) cc_final: 0.8707 (tmm) outliers start: 10 outliers final: 6 residues processed: 231 average time/residue: 0.2918 time to fit residues: 106.1955 Evaluate side-chains 231 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 198 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 588 ASN D 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.183298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.150147 restraints weight = 128385.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.155814 restraints weight = 60527.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.159343 restraints weight = 38471.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.161470 restraints weight = 29344.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.162643 restraints weight = 24862.498| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19544 Z= 0.156 Angle : 0.612 13.220 26488 Z= 0.306 Chirality : 0.044 0.526 3036 Planarity : 0.004 0.041 3276 Dihedral : 12.193 167.852 2744 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.01 % Favored : 90.81 % Rotamer: Outliers : 0.72 % Allowed : 13.46 % Favored : 85.82 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.95 (0.18), residues: 2308 helix: 0.36 (0.14), residues: 1408 sheet: -4.17 (0.48), residues: 84 loop : -1.95 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.021 0.002 TYR A 621 PHE 0.016 0.001 PHE A 756 TRP 0.007 0.001 TRP B 409 HIS 0.003 0.000 HIS C 388 Details of bonding type rmsd covalent geometry : bond 0.00352 (19544) covalent geometry : angle 0.61214 (26488) hydrogen bonds : bond 0.03980 ( 1012) hydrogen bonds : angle 4.68389 ( 2928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 713 MET cc_start: 0.8925 (tmm) cc_final: 0.8719 (tmm) REVERT: D 713 MET cc_start: 0.8927 (tmm) cc_final: 0.8722 (tmm) outliers start: 15 outliers final: 11 residues processed: 233 average time/residue: 0.3157 time to fit residues: 115.8045 Evaluate side-chains 236 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 63 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN C 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.184242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.151172 restraints weight = 128634.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.156959 restraints weight = 60041.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.160540 restraints weight = 37964.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.162644 restraints weight = 28803.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.163849 restraints weight = 24443.886| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19544 Z= 0.131 Angle : 0.608 13.381 26488 Z= 0.300 Chirality : 0.043 0.525 3036 Planarity : 0.004 0.040 3276 Dihedral : 12.102 167.238 2744 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.50 % Favored : 92.33 % Rotamer: Outliers : 0.38 % Allowed : 13.46 % Favored : 86.15 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.86 (0.18), residues: 2308 helix: 0.44 (0.14), residues: 1408 sheet: -4.18 (0.47), residues: 84 loop : -1.92 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.022 0.001 TYR B 621 PHE 0.015 0.001 PHE C 357 TRP 0.008 0.001 TRP A 409 HIS 0.002 0.000 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00293 (19544) covalent geometry : angle 0.60774 (26488) hydrogen bonds : bond 0.03883 ( 1012) hydrogen bonds : angle 4.59706 ( 2928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 234 average time/residue: 0.3075 time to fit residues: 112.7083 Evaluate side-chains 235 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 162 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.184898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.152475 restraints weight = 129059.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.158368 restraints weight = 60487.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.162008 restraints weight = 37728.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.164177 restraints weight = 28326.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.165418 restraints weight = 23788.543| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19544 Z= 0.121 Angle : 0.607 13.524 26488 Z= 0.297 Chirality : 0.043 0.529 3036 Planarity : 0.003 0.039 3276 Dihedral : 12.001 167.841 2744 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 0.53 % Allowed : 13.46 % Favored : 86.01 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.77 (0.18), residues: 2308 helix: 0.52 (0.14), residues: 1412 sheet: -4.19 (0.47), residues: 84 loop : -1.89 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 392 TYR 0.022 0.001 TYR B 621 PHE 0.015 0.001 PHE C 615 TRP 0.009 0.001 TRP D 409 HIS 0.002 0.000 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00272 (19544) covalent geometry : angle 0.60687 (26488) hydrogen bonds : bond 0.03753 ( 1012) hydrogen bonds : angle 4.51653 ( 2928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 234 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 PHE cc_start: 0.7317 (t80) cc_final: 0.6819 (t80) REVERT: B 525 PHE cc_start: 0.7314 (t80) cc_final: 0.6812 (t80) REVERT: C 525 PHE cc_start: 0.7315 (t80) cc_final: 0.6810 (t80) REVERT: D 525 PHE cc_start: 0.7319 (t80) cc_final: 0.6819 (t80) outliers start: 11 outliers final: 11 residues processed: 236 average time/residue: 0.3212 time to fit residues: 118.8895 Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 209 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.183640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.151099 restraints weight = 129396.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.157059 restraints weight = 60635.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.160716 restraints weight = 37999.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.162874 restraints weight = 28450.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.164146 restraints weight = 23886.143| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19544 Z= 0.151 Angle : 0.625 13.580 26488 Z= 0.307 Chirality : 0.044 0.530 3036 Planarity : 0.004 0.040 3276 Dihedral : 11.921 165.780 2744 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.06 % Favored : 90.77 % Rotamer: Outliers : 0.77 % Allowed : 13.27 % Favored : 85.96 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.85 (0.18), residues: 2308 helix: 0.45 (0.14), residues: 1408 sheet: -4.20 (0.47), residues: 84 loop : -1.91 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 392 TYR 0.019 0.002 TYR D 602 PHE 0.015 0.002 PHE C 615 TRP 0.006 0.001 TRP D 409 HIS 0.003 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00339 (19544) covalent geometry : angle 0.62450 (26488) hydrogen bonds : bond 0.03768 ( 1012) hydrogen bonds : angle 4.58350 ( 2928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5647.13 seconds wall clock time: 97 minutes 10.95 seconds (5830.95 seconds total)