Starting phenix.real_space_refine on Sun Sep 13 02:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uw6_20918/09_2026/6uw6_20918.cif" } resolution = 3.66 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= 0.006 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 116 5.16 5 C 13100 2.51 5 N 3272 2.21 5 O 3572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20072 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4910 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 25 Restraints were copied for chains: B, C, D Time building chain proxies: 5.04, per 1000 atoms: 0.25 Number of scatterers: 20072 At special positions: 0 Unit cell: (161.7, 161.7, 119.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 12 15.00 O 3572 8.00 N 3272 7.00 C 13100 6.00 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: 1.86 Conformation dependent library (CDL) restraints added in 875.1 milliseconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 64.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.806A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.642A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.855A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.997A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.694A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.322A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.534A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.645A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 425 through 461 removed outlier: 3.856A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 507 removed outlier: 6.867A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 541 removed outlier: 3.832A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.168A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.605A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 607 removed outlier: 3.995A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.516A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.603A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 4.122A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.569A pdb=" N LYS A 743 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.806A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.643A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.855A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.996A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.694A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.323A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.534A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.644A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 425 through 461 removed outlier: 3.856A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 507 removed outlier: 6.866A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 541 removed outlier: 3.832A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.169A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.605A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 607 removed outlier: 3.995A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 4.517A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.602A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 4.122A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 748 removed outlier: 3.569A pdb=" N LYS B 743 " --> pdb=" O TRP B 739 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.805A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.642A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.855A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.997A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.695A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.323A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.534A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.645A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 425 through 461 removed outlier: 3.857A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 507 removed outlier: 6.867A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 541 removed outlier: 3.832A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.168A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.605A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 607 removed outlier: 3.994A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 4.516A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.603A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 4.122A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 748 removed outlier: 3.569A pdb=" N LYS C 743 " --> pdb=" O TRP C 739 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.805A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.643A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.855A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.997A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.694A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 removed outlier: 4.322A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.534A pdb=" N GLY D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.645A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 425 through 461 removed outlier: 3.857A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 507 removed outlier: 6.866A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 541 removed outlier: 3.832A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 4.168A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.605A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 607 removed outlier: 3.995A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 4.517A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.603A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 4.122A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 748 removed outlier: 3.568A pdb=" N LYS D 743 " --> pdb=" O TRP D 739 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.765A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.764A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.765A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.764A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3060 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: 2.99 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6085 1.34 - 1.46: 4181 1.46 - 1.58: 9726 1.58 - 1.70: 260 1.70 - 1.81: 220 Bond restraints: 20472 Sorted by residual: bond pdb=" C16 6OU A 802 " pdb=" O18 6OU A 802 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C16 6OU D 802 " pdb=" O18 6OU D 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C16 6OU B 802 " pdb=" O18 6OU B 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 6OU C 802 " pdb=" O18 6OU C 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C16 6OU C 804 " pdb=" O18 6OU C 804 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 20467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 26951 3.37 - 6.74: 507 6.74 - 10.11: 105 10.11 - 13.47: 13 13.47 - 16.84: 12 Bond angle restraints: 27588 Sorted by residual: angle pdb=" N GLU A 196 " pdb=" CA GLU A 196 " pdb=" C GLU A 196 " ideal model delta sigma weight residual 111.28 121.86 -10.58 1.09e+00 8.42e-01 9.43e+01 angle pdb=" N GLU C 196 " pdb=" CA GLU C 196 " pdb=" C GLU C 196 " ideal model delta sigma weight residual 111.28 121.86 -10.58 1.09e+00 8.42e-01 9.42e+01 angle pdb=" N GLU D 196 " pdb=" CA GLU D 196 " pdb=" C GLU D 196 " ideal model delta sigma weight residual 111.28 121.85 -10.57 1.09e+00 8.42e-01 9.41e+01 angle pdb=" N GLU B 196 " pdb=" CA GLU B 196 " pdb=" C GLU B 196 " ideal model delta sigma weight residual 111.28 121.84 -10.56 1.09e+00 8.42e-01 9.39e+01 angle pdb=" N ALA D 218 " pdb=" CA ALA D 218 " pdb=" C ALA D 218 " ideal model delta sigma weight residual 112.38 120.81 -8.43 1.22e+00 6.72e-01 4.77e+01 ... (remaining 27583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 10756 20.26 - 40.52: 1156 40.52 - 60.78: 172 60.78 - 81.04: 36 81.04 - 101.29: 16 Dihedral angle restraints: 12136 sinusoidal: 5052 harmonic: 7084 Sorted by residual: dihedral pdb=" CA LEU A 484 " pdb=" C LEU A 484 " pdb=" N LEU A 485 " pdb=" CA LEU A 485 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU B 484 " pdb=" C LEU B 484 " pdb=" N LEU B 485 " pdb=" CA LEU B 485 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LEU D 484 " pdb=" C LEU D 484 " pdb=" N LEU D 485 " pdb=" CA LEU D 485 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 12133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2940 0.115 - 0.230: 152 0.230 - 0.345: 8 0.345 - 0.460: 0 0.460 - 0.575: 12 Chirality restraints: 3112 Sorted by residual: chirality pdb=" C20 6OU D 802 " pdb=" C19 6OU D 802 " pdb=" C21 6OU D 802 " pdb=" O30 6OU D 802 " both_signs ideal model delta sigma weight residual False 2.35 2.92 -0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" C20 6OU B 802 " pdb=" C19 6OU B 802 " pdb=" C21 6OU B 802 " pdb=" O30 6OU B 802 " both_signs ideal model delta sigma weight residual False 2.35 2.92 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" C20 6OU A 802 " pdb=" C19 6OU A 802 " pdb=" C21 6OU A 802 " pdb=" O30 6OU A 802 " both_signs ideal model delta sigma weight residual False 2.35 2.92 -0.57 2.00e-01 2.50e+01 8.24e+00 ... (remaining 3109 not shown) Planarity restraints: 3392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO B 181 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO D 181 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO C 181 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.037 5.00e-02 4.00e+02 ... (remaining 3389 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6272 2.82 - 3.34: 17879 3.34 - 3.86: 30993 3.86 - 4.38: 35286 4.38 - 4.90: 62494 Nonbonded interactions: 152924 Sorted by model distance: nonbonded pdb=" OG1 THR A 343 " pdb=" OE1 GLN A 346 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR D 343 " pdb=" OE1 GLN D 346 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR B 343 " pdb=" OE1 GLN B 346 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR C 343 " pdb=" OE1 GLN C 346 " model vdw 2.299 3.040 nonbonded pdb=" O SER C 518 " pdb=" OG SER C 518 " model vdw 2.312 3.040 ... (remaining 152919 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.700 Find NCS groups from input model: 0.160 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.015 0.141 20472 Z= 0.690 Angle : 1.236 16.843 27588 Z= 0.628 Chirality : 0.067 0.575 3112 Planarity : 0.007 0.068 3392 Dihedral : 16.705 101.294 7536 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.12), residues: 2376 helix: -2.93 (0.08), residues: 1540 sheet: -2.37 (0.50), residues: 84 loop : -3.55 (0.17), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 698 TYR 0.022 0.003 TYR B 208 PHE 0.019 0.002 PHE C 592 TRP 0.020 0.002 TRP C 710 HIS 0.006 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.01462 / 0.69 (20472) covalent geometry : angle 1.23629 / 0.63 (27588) hydrogen bonds : bond 0.14945 / 10.08 ( 1040) hydrogen bonds : angle 5.85154 / 4.02 ( 3060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.8485 (tp) cc_final: 0.8252 (pt) REVERT: A 590 PHE cc_start: 0.8515 (t80) cc_final: 0.8216 (t80) REVERT: B 128 SER cc_start: 0.8889 (m) cc_final: 0.8493 (p) REVERT: B 591 LEU cc_start: 0.8699 (mt) cc_final: 0.8485 (mp) REVERT: C 128 SER cc_start: 0.8793 (m) cc_final: 0.8411 (p) REVERT: C 493 TRP cc_start: 0.7023 (t-100) cc_final: 0.6757 (t-100) REVERT: C 555 MET cc_start: 0.7900 (ttp) cc_final: 0.7628 (ttm) REVERT: C 590 PHE cc_start: 0.8558 (t80) cc_final: 0.8321 (t80) REVERT: C 710 TRP cc_start: 0.7181 (t60) cc_final: 0.6946 (t60) REVERT: D 128 SER cc_start: 0.8718 (m) cc_final: 0.8321 (p) REVERT: D 368 LYS cc_start: 0.8295 (tptp) cc_final: 0.8086 (pttm) REVERT: D 591 LEU cc_start: 0.8792 (mt) cc_final: 0.8551 (mp) REVERT: D 631 GLU cc_start: 0.8255 (tp30) cc_final: 0.7785 (tp30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1447 time to fit residues: 78.5801 Evaluate side-chains 233 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 417 HIS A 430 HIS A 523 HIS B 220 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 394 ASN B 417 HIS B 430 HIS B 523 HIS C 220 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 394 ASN C 417 HIS C 430 HIS C 523 HIS D 160 HIS D 220 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 394 ASN D 417 HIS D 430 HIS D 523 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.163240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127633 restraints weight = 25884.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130390 restraints weight = 19197.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132307 restraints weight = 15684.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133621 restraints weight = 13672.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134395 restraints weight = 12418.345| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20472 Z= 0.143 Angle : 0.575 5.936 27588 Z= 0.303 Chirality : 0.039 0.169 3112 Planarity : 0.004 0.052 3392 Dihedral : 9.871 102.722 2840 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.69 % Allowed : 15.60 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.16), residues: 2376 helix: -0.73 (0.12), residues: 1572 sheet: -1.88 (0.55), residues: 84 loop : -2.94 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 716 TYR 0.013 0.001 TYR A 260 PHE 0.008 0.001 PHE A 522 TRP 0.011 0.001 TRP A 433 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (20472) covalent geometry : angle 0.57514 / 0.30 (27588) hydrogen bonds : bond 0.03806 / 2.50 ( 1040) hydrogen bonds : angle 3.76564 / 2.61 ( 3060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8630 (pp) REVERT: A 590 PHE cc_start: 0.8440 (t80) cc_final: 0.8090 (t80) REVERT: A 626 SER cc_start: 0.8522 (m) cc_final: 0.8157 (p) REVERT: A 702 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7172 (tt0) REVERT: B 422 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8615 (pp) REVERT: B 430 HIS cc_start: 0.7740 (m-70) cc_final: 0.7440 (m-70) REVERT: B 575 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: C 369 ARG cc_start: 0.7270 (ttp80) cc_final: 0.7006 (ttp80) REVERT: C 422 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8667 (pp) REVERT: C 575 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: C 590 PHE cc_start: 0.8532 (t80) cc_final: 0.8221 (t80) REVERT: C 626 SER cc_start: 0.8502 (m) cc_final: 0.8131 (p) REVERT: D 368 LYS cc_start: 0.8330 (tptp) cc_final: 0.7888 (pttm) REVERT: D 422 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8688 (pp) REVERT: D 626 SER cc_start: 0.8562 (m) cc_final: 0.8248 (p) REVERT: D 631 GLU cc_start: 0.8093 (tp30) cc_final: 0.7865 (tp30) outliers start: 36 outliers final: 10 residues processed: 294 average time/residue: 0.1334 time to fit residues: 62.8791 Evaluate side-chains 242 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 636 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN A 274 GLN B 143 GLN B 160 HIS B 274 GLN C 143 GLN C 160 HIS C 274 GLN D 274 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126654 restraints weight = 25765.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129463 restraints weight = 19013.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131410 restraints weight = 15479.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132713 restraints weight = 13456.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133536 restraints weight = 12228.403| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20472 Z= 0.135 Angle : 0.549 9.743 27588 Z= 0.283 Chirality : 0.038 0.137 3112 Planarity : 0.003 0.037 3392 Dihedral : 9.150 92.181 2840 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.91 % Allowed : 18.75 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2376 helix: 0.13 (0.13), residues: 1568 sheet: -1.85 (0.54), residues: 84 loop : -2.71 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 122 TYR 0.014 0.001 TYR D 260 PHE 0.008 0.001 PHE C 715 TRP 0.015 0.001 TRP D 710 HIS 0.006 0.001 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (20472) covalent geometry : angle 0.54932 / 0.28 (27588) hydrogen bonds : bond 0.03511 / 2.29 ( 1040) hydrogen bonds : angle 3.57734 / 2.47 ( 3060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 251 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: A 626 SER cc_start: 0.8494 (m) cc_final: 0.8262 (p) REVERT: A 702 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7220 (tt0) REVERT: B 193 PHE cc_start: 0.7874 (t80) cc_final: 0.7658 (t80) REVERT: B 508 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7602 (tp) REVERT: B 575 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: B 626 SER cc_start: 0.8585 (m) cc_final: 0.8270 (p) REVERT: C 422 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8783 (pp) REVERT: C 575 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: C 626 SER cc_start: 0.8496 (m) cc_final: 0.8275 (p) REVERT: D 368 LYS cc_start: 0.8222 (tptp) cc_final: 0.7685 (pttm) REVERT: D 369 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7093 (ttp80) REVERT: D 422 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8790 (pp) REVERT: D 430 HIS cc_start: 0.7694 (m-70) cc_final: 0.7470 (m170) REVERT: D 626 SER cc_start: 0.8445 (m) cc_final: 0.8240 (p) REVERT: D 631 GLU cc_start: 0.8071 (tp30) cc_final: 0.7817 (tp30) outliers start: 62 outliers final: 19 residues processed: 292 average time/residue: 0.1429 time to fit residues: 66.2233 Evaluate side-chains 247 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 636 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124987 restraints weight = 25941.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127558 restraints weight = 19584.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129362 restraints weight = 16224.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130474 restraints weight = 14258.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130910 restraints weight = 13063.165| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20472 Z= 0.170 Angle : 0.572 7.504 27588 Z= 0.294 Chirality : 0.039 0.129 3112 Planarity : 0.003 0.037 3392 Dihedral : 9.240 90.927 2840 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.26 % Allowed : 20.21 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2376 helix: 0.42 (0.13), residues: 1568 sheet: -1.93 (0.52), residues: 84 loop : -2.53 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 712 TYR 0.015 0.001 TYR A 260 PHE 0.027 0.001 PHE D 193 TRP 0.010 0.001 TRP A 433 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (20472) covalent geometry : angle 0.57242 / 0.29 (27588) hydrogen bonds : bond 0.03723 / 2.43 ( 1040) hydrogen bonds : angle 3.63057 / 2.51 ( 3060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: A 626 SER cc_start: 0.8498 (m) cc_final: 0.8284 (p) REVERT: B 193 PHE cc_start: 0.7761 (t80) cc_final: 0.7546 (t80) REVERT: B 368 LYS cc_start: 0.8253 (tptt) cc_final: 0.7959 (pttm) REVERT: B 508 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7547 (tp) REVERT: B 575 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: B 626 SER cc_start: 0.8581 (m) cc_final: 0.8289 (p) REVERT: C 422 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8826 (pp) REVERT: C 575 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: D 368 LYS cc_start: 0.8315 (tptp) cc_final: 0.8035 (tptm) REVERT: D 626 SER cc_start: 0.8471 (m) cc_final: 0.8271 (p) outliers start: 48 outliers final: 26 residues processed: 284 average time/residue: 0.1411 time to fit residues: 63.6945 Evaluate side-chains 253 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 8 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128963 restraints weight = 25814.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131666 restraints weight = 19400.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133540 restraints weight = 15981.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134711 restraints weight = 13970.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135681 restraints weight = 12743.902| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20472 Z= 0.105 Angle : 0.510 7.590 27588 Z= 0.262 Chirality : 0.037 0.117 3112 Planarity : 0.003 0.036 3392 Dihedral : 8.342 83.799 2840 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.44 % Allowed : 20.49 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2376 helix: 0.73 (0.13), residues: 1572 sheet: -1.36 (0.55), residues: 76 loop : -2.48 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 122 TYR 0.012 0.001 TYR A 594 PHE 0.023 0.001 PHE D 193 TRP 0.015 0.001 TRP B 710 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (20472) covalent geometry : angle 0.51043 / 0.26 (27588) hydrogen bonds : bond 0.02985 / 1.96 ( 1040) hydrogen bonds : angle 3.46811 / 2.40 ( 3060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: A 578 MET cc_start: 0.6935 (mmt) cc_final: 0.6235 (mtt) REVERT: B 122 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7884 (ptm160) REVERT: B 368 LYS cc_start: 0.7995 (tptt) cc_final: 0.7713 (pttm) REVERT: B 508 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7420 (tt) REVERT: B 575 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: B 590 PHE cc_start: 0.8343 (t80) cc_final: 0.7965 (t80) REVERT: C 575 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: C 590 PHE cc_start: 0.8386 (t80) cc_final: 0.8042 (t80) REVERT: D 368 LYS cc_start: 0.8194 (tptp) cc_final: 0.7957 (tptm) outliers start: 52 outliers final: 22 residues processed: 286 average time/residue: 0.1417 time to fit residues: 64.0737 Evaluate side-chains 243 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 716 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 212 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128726 restraints weight = 25690.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131407 restraints weight = 19215.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133254 restraints weight = 15832.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134313 restraints weight = 13855.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135308 restraints weight = 12688.957| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20472 Z= 0.109 Angle : 0.523 11.413 27588 Z= 0.264 Chirality : 0.037 0.115 3112 Planarity : 0.003 0.035 3392 Dihedral : 7.937 81.051 2840 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.73 % Allowed : 21.48 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2376 helix: 1.02 (0.13), residues: 1544 sheet: -1.72 (0.53), residues: 84 loop : -2.37 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.015 0.001 TYR A 213 PHE 0.029 0.001 PHE D 193 TRP 0.008 0.001 TRP C 433 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (20472) covalent geometry : angle 0.52334 / 0.26 (27588) hydrogen bonds : bond 0.02984 / 1.95 ( 1040) hydrogen bonds : angle 3.45338 / 2.39 ( 3060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5457 (tt0) REVERT: A 493 TRP cc_start: 0.7447 (t-100) cc_final: 0.6823 (t-100) REVERT: A 575 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 122 ARG cc_start: 0.8129 (ttp-170) cc_final: 0.7895 (ptm160) REVERT: B 368 LYS cc_start: 0.7969 (tptt) cc_final: 0.7739 (pttm) REVERT: B 508 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7418 (tt) REVERT: B 575 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 706 MET cc_start: 0.8298 (ttm) cc_final: 0.7986 (ttm) REVERT: C 575 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: D 255 GLN cc_start: 0.5956 (OUTLIER) cc_final: 0.5443 (tt0) outliers start: 58 outliers final: 40 residues processed: 276 average time/residue: 0.1390 time to fit residues: 60.9770 Evaluate side-chains 261 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN A 160 HIS ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.159302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123115 restraints weight = 26201.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125631 restraints weight = 19843.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127343 restraints weight = 16463.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128334 restraints weight = 14534.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129181 restraints weight = 13382.295| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20472 Z= 0.198 Angle : 0.597 11.214 27588 Z= 0.302 Chirality : 0.040 0.133 3112 Planarity : 0.003 0.036 3392 Dihedral : 8.410 85.574 2840 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.57 % Allowed : 21.57 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2376 helix: 0.89 (0.13), residues: 1548 sheet: -1.92 (0.51), residues: 84 loop : -2.38 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.016 0.002 TYR B 260 PHE 0.027 0.001 PHE D 193 TRP 0.010 0.001 TRP C 433 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (20472) covalent geometry : angle 0.59692 / 0.30 (27588) hydrogen bonds : bond 0.03872 / 2.53 ( 1040) hydrogen bonds : angle 3.66016 / 2.53 ( 3060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 233 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6015 (OUTLIER) cc_final: 0.5524 (tt0) REVERT: A 570 GLN cc_start: 0.8404 (tt0) cc_final: 0.8156 (tm-30) REVERT: A 575 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: B 122 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7744 (ptp-110) REVERT: B 255 GLN cc_start: 0.6033 (OUTLIER) cc_final: 0.5559 (tt0) REVERT: B 368 LYS cc_start: 0.8181 (tptt) cc_final: 0.7887 (pttm) REVERT: B 508 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 575 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: C 255 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.5540 (tt0) REVERT: C 575 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: C 578 MET cc_start: 0.6967 (mmt) cc_final: 0.6303 (mtt) REVERT: D 255 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.5542 (tt0) REVERT: D 570 GLN cc_start: 0.8369 (tt0) cc_final: 0.8134 (tm-30) outliers start: 76 outliers final: 53 residues processed: 294 average time/residue: 0.1256 time to fit residues: 59.9477 Evaluate side-chains 286 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 138 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128411 restraints weight = 25952.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131067 restraints weight = 19415.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132943 restraints weight = 15973.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133947 restraints weight = 13961.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134995 restraints weight = 12801.396| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20472 Z= 0.105 Angle : 0.521 10.749 27588 Z= 0.264 Chirality : 0.037 0.125 3112 Planarity : 0.003 0.038 3392 Dihedral : 7.586 76.748 2840 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.54 % Allowed : 23.17 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2376 helix: 1.12 (0.13), residues: 1548 sheet: -1.30 (0.55), residues: 76 loop : -2.29 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.015 0.001 TYR A 213 PHE 0.027 0.001 PHE D 193 TRP 0.026 0.001 TRP C 710 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20472) covalent geometry : angle 0.52051 / 0.26 (27588) hydrogen bonds : bond 0.02940 / 1.93 ( 1040) hydrogen bonds : angle 3.48881 / 2.41 ( 3060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 TRP cc_start: 0.7417 (t-100) cc_final: 0.6837 (t-100) REVERT: A 575 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: A 578 MET cc_start: 0.6843 (mmt) cc_final: 0.6179 (mtt) REVERT: B 368 LYS cc_start: 0.7924 (tptt) cc_final: 0.7713 (pttm) REVERT: B 508 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7482 (tt) REVERT: B 575 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: C 255 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5532 (tt0) REVERT: C 368 LYS cc_start: 0.8121 (tptm) cc_final: 0.7744 (pttm) REVERT: C 575 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: C 578 MET cc_start: 0.6853 (mmt) cc_final: 0.6221 (mtt) REVERT: D 255 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5509 (tt0) outliers start: 54 outliers final: 40 residues processed: 287 average time/residue: 0.1221 time to fit residues: 57.1260 Evaluate side-chains 264 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 186 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.161283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125337 restraints weight = 25678.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128081 restraints weight = 18877.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129955 restraints weight = 15411.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131232 restraints weight = 13417.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132108 restraints weight = 12195.422| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20472 Z= 0.116 Angle : 0.544 11.157 27588 Z= 0.271 Chirality : 0.038 0.129 3112 Planarity : 0.003 0.037 3392 Dihedral : 7.323 75.531 2840 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.10 % Allowed : 23.17 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2376 helix: 1.22 (0.13), residues: 1548 sheet: -1.69 (0.53), residues: 84 loop : -2.11 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 122 TYR 0.016 0.001 TYR B 260 PHE 0.028 0.001 PHE D 193 TRP 0.017 0.001 TRP B 710 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (20472) covalent geometry : angle 0.54369 / 0.27 (27588) hydrogen bonds : bond 0.03080 / 2.02 ( 1040) hydrogen bonds : angle 3.48956 / 2.40 ( 3060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6019 (OUTLIER) cc_final: 0.5551 (tt0) REVERT: A 493 TRP cc_start: 0.7384 (t-100) cc_final: 0.6782 (t-100) REVERT: A 578 MET cc_start: 0.6769 (mmt) cc_final: 0.6094 (mtt) REVERT: B 255 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5642 (tt0) REVERT: B 286 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7580 (tp40) REVERT: B 508 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7483 (tt) REVERT: B 575 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: C 255 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5614 (tt0) REVERT: C 368 LYS cc_start: 0.8028 (tptm) cc_final: 0.7440 (pttm) REVERT: C 555 MET cc_start: 0.7085 (ttp) cc_final: 0.6620 (ttm) REVERT: D 255 GLN cc_start: 0.6019 (OUTLIER) cc_final: 0.5559 (tt0) REVERT: D 368 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7780 (tptm) outliers start: 66 outliers final: 47 residues processed: 291 average time/residue: 0.1280 time to fit residues: 60.7056 Evaluate side-chains 276 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.161916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126031 restraints weight = 26048.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128605 restraints weight = 19637.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130395 restraints weight = 16254.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131453 restraints weight = 14284.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132429 restraints weight = 13106.266| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20472 Z= 0.144 Angle : 0.581 13.299 27588 Z= 0.289 Chirality : 0.039 0.140 3112 Planarity : 0.003 0.038 3392 Dihedral : 7.422 77.630 2840 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.68 % Allowed : 23.31 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2376 helix: 1.17 (0.13), residues: 1548 sheet: -1.70 (0.54), residues: 84 loop : -2.06 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 716 TYR 0.015 0.001 TYR A 213 PHE 0.028 0.001 PHE D 193 TRP 0.014 0.001 TRP B 710 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (20472) covalent geometry : angle 0.58133 / 0.29 (27588) hydrogen bonds : bond 0.03367 / 2.21 ( 1040) hydrogen bonds : angle 3.57161 / 2.46 ( 3060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.5579 (tt0) REVERT: A 493 TRP cc_start: 0.7374 (t-100) cc_final: 0.6828 (t-100) REVERT: B 255 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5692 (tt0) REVERT: B 261 PHE cc_start: 0.8448 (p90) cc_final: 0.8214 (p90) REVERT: B 286 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7724 (tp40) REVERT: B 508 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7522 (tt) REVERT: B 575 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: C 255 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5661 (tt0) REVERT: C 286 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7590 (tp40) REVERT: C 555 MET cc_start: 0.7242 (ttp) cc_final: 0.6826 (ttm) REVERT: D 255 GLN cc_start: 0.6198 (OUTLIER) cc_final: 0.5626 (tt0) REVERT: D 368 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7763 (tptm) outliers start: 57 outliers final: 48 residues processed: 282 average time/residue: 0.1314 time to fit residues: 59.5076 Evaluate side-chains 279 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.158259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122121 restraints weight = 25949.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124761 restraints weight = 19281.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126550 restraints weight = 15825.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127631 restraints weight = 13841.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128600 restraints weight = 12658.246| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20472 Z= 0.163 Angle : 0.594 13.390 27588 Z= 0.296 Chirality : 0.039 0.141 3112 Planarity : 0.003 0.039 3392 Dihedral : 7.606 80.209 2840 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.01 % Allowed : 23.26 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2376 helix: 1.07 (0.13), residues: 1556 sheet: -1.81 (0.54), residues: 84 loop : -2.01 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.015 0.002 TYR B 260 PHE 0.029 0.001 PHE D 193 TRP 0.011 0.001 TRP B 710 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (20472) covalent geometry : angle 0.59404 / 0.30 (27588) hydrogen bonds : bond 0.03571 / 2.35 ( 1040) hydrogen bonds : angle 3.63494 / 2.51 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.93 seconds wall clock time: 56 minutes 2.29 seconds (3362.29 seconds total)