Starting phenix.real_space_refine on Thu Mar 5 07:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uw6_20918/03_2026/6uw6_20918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uw6_20918/03_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_20918/03_2026/6uw6_20918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uw6_20918/03_2026/6uw6_20918.map" model { file = "/net/cci-nas-00/data/ceres_data/6uw6_20918/03_2026/6uw6_20918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uw6_20918/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 137 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: 4.11, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 706.2 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: 0.41 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: 2.55 Time building geometry restraints manager: 1.93 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 - 27.41: 11502 27.41 - 54.81: 654 54.81 - 82.22: 96 82.22 - 109.63: 28 109.63 - 137.04: 4 Dihedral angle restraints: 12284 sinusoidal: 5200 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 12281 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: 0.03 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 18.262 137.037 7684 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 covalent geometry : bond 0.01462 (20472) covalent geometry : angle 1.23629 (27588) hydrogen bonds : bond 0.14945 ( 1040) hydrogen bonds : angle 5.85154 ( 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 : 0.767 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: 0.1399 time to fit residues: 75.6343 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 : 0.599 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3825 r_free = 0.3825 target = 0.163051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127288 restraints weight = 25876.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130153 restraints weight = 19202.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132052 restraints weight = 15695.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133390 restraints weight = 13653.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134112 restraints weight = 12401.378| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1878 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= 0.145 Angle : 0.587 5.975 27588 Z= 0.307 Chirality : 0.039 0.184 3112 Planarity : 0.004 0.053 3392 Dihedral : 13.724 137.583 2988 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.64 % Allowed : 15.93 % Favored : 82.42 % 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: -2.27 (0.16), residues: 2376 helix: -0.77 (0.12), residues: 1572 sheet: -1.89 (0.54), 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 covalent geometry : bond 0.00340 (20472) covalent geometry : angle 0.58697 (27588) hydrogen bonds : bond 0.03865 ( 1040) hydrogen bonds : angle 3.79933 ( 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 303 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8626 (pp) REVERT: A 590 PHE cc_start: 0.8438 (t80) cc_final: 0.8090 (t80) REVERT: A 702 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7164 (tt0) REVERT: B 193 PHE cc_start: 0.7942 (t80) cc_final: 0.7719 (t80) REVERT: B 422 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 430 HIS cc_start: 0.7738 (m-70) cc_final: 0.7439 (m-70) REVERT: B 575 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: C 369 ARG cc_start: 0.7295 (ttp80) cc_final: 0.7046 (ttp80) REVERT: C 422 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (pp) REVERT: C 575 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: C 590 PHE cc_start: 0.8540 (t80) cc_final: 0.8177 (t80) REVERT: D 368 LYS cc_start: 0.8283 (tptp) cc_final: 0.7876 (pttm) REVERT: D 422 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8660 (pp) REVERT: D 430 HIS cc_start: 0.7617 (m-70) cc_final: 0.7313 (m-70) REVERT: D 626 SER cc_start: 0.8633 (m) cc_final: 0.8248 (p) REVERT: D 631 GLU cc_start: 0.8105 (tp30) cc_final: 0.7871 (tp30) outliers start: 35 outliers final: 10 residues processed: 292 average time/residue: 0.1284 time to fit residues: 60.0069 Evaluate side-chains 239 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 274 GLN B 160 HIS B 274 GLN C 143 GLN C 160 HIS C 274 GLN C 452 ASN D 274 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128313 restraints weight = 25757.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131114 restraints weight = 19081.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133056 restraints weight = 15545.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134391 restraints weight = 13508.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135161 restraints weight = 12263.383| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20472 Z= 0.119 Angle : 0.534 9.715 27588 Z= 0.275 Chirality : 0.037 0.137 3112 Planarity : 0.003 0.037 3392 Dihedral : 12.466 111.234 2988 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.77 % Allowed : 18.23 % Favored : 78.99 % 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: -1.21 (0.17), residues: 2376 helix: 0.13 (0.13), residues: 1572 sheet: -1.82 (0.55), residues: 84 loop : -2.70 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 712 TYR 0.012 0.001 TYR A 260 PHE 0.007 0.001 PHE C 715 TRP 0.009 0.001 TRP C 433 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00275 (20472) covalent geometry : angle 0.53429 (27588) hydrogen bonds : bond 0.03321 ( 1040) hydrogen bonds : angle 3.53919 ( 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 322 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: A 590 PHE cc_start: 0.8327 (t80) cc_final: 0.7988 (t80) REVERT: A 626 SER cc_start: 0.8670 (m) cc_final: 0.8290 (p) REVERT: A 702 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7202 (tt0) REVERT: B 422 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8775 (pp) REVERT: B 508 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7623 (tp) REVERT: B 575 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: C 422 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8800 (pp) REVERT: C 575 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: C 590 PHE cc_start: 0.8354 (t80) cc_final: 0.8000 (t80) REVERT: C 626 SER cc_start: 0.8658 (m) cc_final: 0.8262 (p) REVERT: D 368 LYS cc_start: 0.8181 (tptp) cc_final: 0.7610 (pttm) REVERT: D 369 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7070 (ttp80) REVERT: D 422 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8795 (pp) REVERT: D 430 HIS cc_start: 0.7668 (m-70) cc_final: 0.7458 (m170) REVERT: D 575 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: D 626 SER cc_start: 0.8604 (m) cc_final: 0.8287 (p) REVERT: D 631 GLU cc_start: 0.8054 (tp30) cc_final: 0.7811 (tp30) outliers start: 59 outliers final: 21 residues processed: 304 average time/residue: 0.1278 time to fit residues: 61.3188 Evaluate side-chains 254 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 591 LEU 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 422 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU 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 575 TYR 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: 6.9990 chunk 130 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 160 HIS B 143 GLN C 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125500 restraints weight = 25947.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128102 restraints weight = 19472.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129942 restraints weight = 16090.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130809 restraints weight = 14109.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131891 restraints weight = 13041.357| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20472 Z= 0.158 Angle : 0.567 7.589 27588 Z= 0.291 Chirality : 0.039 0.137 3112 Planarity : 0.003 0.037 3392 Dihedral : 12.370 99.182 2988 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.68 % Allowed : 19.50 % Favored : 77.82 % 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: -0.79 (0.17), residues: 2376 helix: 0.43 (0.13), residues: 1576 sheet: -1.89 (0.52), residues: 84 loop : -2.45 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 716 TYR 0.015 0.001 TYR D 260 PHE 0.031 0.001 PHE B 193 TRP 0.013 0.001 TRP D 710 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00380 (20472) covalent geometry : angle 0.56719 (27588) hydrogen bonds : bond 0.03637 ( 1040) hydrogen bonds : angle 3.59863 ( 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 304 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: A 626 SER cc_start: 0.8623 (m) cc_final: 0.8291 (p) REVERT: B 368 LYS cc_start: 0.8177 (tptt) cc_final: 0.7929 (pttm) REVERT: B 422 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8802 (pp) REVERT: B 508 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7491 (tt) REVERT: B 575 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 626 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 422 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8820 (pp) REVERT: C 575 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: C 626 SER cc_start: 0.8610 (m) cc_final: 0.8284 (p) REVERT: C 710 TRP cc_start: 0.6957 (t60) cc_final: 0.6714 (t60) REVERT: D 368 LYS cc_start: 0.8248 (tptp) cc_final: 0.7992 (tptm) REVERT: D 422 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8831 (pp) REVERT: D 575 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: D 626 SER cc_start: 0.8577 (m) cc_final: 0.8264 (p) outliers start: 57 outliers final: 21 residues processed: 284 average time/residue: 0.1308 time to fit residues: 59.0912 Evaluate side-chains 253 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 422 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 636 THR 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 158 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 575 TYR 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: 6.9990 chunk 229 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127208 restraints weight = 25951.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129879 restraints weight = 19633.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131686 restraints weight = 16215.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132815 restraints weight = 14245.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133630 restraints weight = 13029.149| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20472 Z= 0.126 Angle : 0.532 10.339 27588 Z= 0.270 Chirality : 0.037 0.121 3112 Planarity : 0.003 0.036 3392 Dihedral : 11.832 94.373 2988 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.44 % Allowed : 20.35 % Favored : 77.21 % 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: -0.47 (0.17), residues: 2376 helix: 0.75 (0.13), residues: 1556 sheet: -1.86 (0.52), residues: 84 loop : -2.46 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 716 TYR 0.012 0.001 TYR A 594 PHE 0.023 0.001 PHE A 193 TRP 0.016 0.001 TRP B 710 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00300 (20472) covalent geometry : angle 0.53186 (27588) hydrogen bonds : bond 0.03197 ( 1040) hydrogen bonds : angle 3.48607 ( 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 293 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 575 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: A 578 MET cc_start: 0.6978 (mmt) cc_final: 0.6268 (mtt) REVERT: A 626 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 368 LYS cc_start: 0.8034 (tptt) cc_final: 0.7759 (pttm) REVERT: B 422 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8839 (pp) REVERT: B 508 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7443 (tt) REVERT: B 575 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 626 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8379 (p) REVERT: C 575 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: C 626 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8302 (p) REVERT: D 368 LYS cc_start: 0.8243 (tptp) cc_final: 0.8003 (tptm) REVERT: D 575 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: D 626 SER cc_start: 0.8475 (m) cc_final: 0.8219 (p) outliers start: 52 outliers final: 25 residues processed: 281 average time/residue: 0.1253 time to fit residues: 56.5873 Evaluate side-chains 252 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 217 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 626 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 716 ARG 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 422 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU 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 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 THR 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 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 636 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 212 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 223 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129725 restraints weight = 25543.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132399 restraints weight = 19175.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134268 restraints weight = 15801.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135558 restraints weight = 13823.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136259 restraints weight = 12596.283| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20472 Z= 0.102 Angle : 0.518 8.495 27588 Z= 0.262 Chirality : 0.037 0.138 3112 Planarity : 0.003 0.035 3392 Dihedral : 11.271 101.022 2988 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.63 % Allowed : 21.29 % Favored : 76.08 % 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: 0.98 (0.13), residues: 1556 sheet: -1.23 (0.55), residues: 76 loop : -2.37 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.011 0.001 TYR D 594 PHE 0.029 0.001 PHE D 193 TRP 0.020 0.001 TRP C 710 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00231 (20472) covalent geometry : angle 0.51766 (27588) hydrogen bonds : bond 0.02888 ( 1040) hydrogen bonds : angle 3.42187 ( 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 305 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5507 (tt0) REVERT: A 493 TRP cc_start: 0.7434 (t-100) cc_final: 0.6873 (t-100) REVERT: A 575 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: A 626 SER cc_start: 0.8479 (m) cc_final: 0.8190 (p) REVERT: B 368 LYS cc_start: 0.7959 (tptt) cc_final: 0.7706 (pttm) REVERT: B 508 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7420 (tt) REVERT: B 575 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: B 626 SER cc_start: 0.8447 (m) cc_final: 0.8192 (p) REVERT: C 145 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6987 (tp) REVERT: C 575 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: D 255 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.5483 (tt0) REVERT: D 575 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: D 626 SER cc_start: 0.8357 (m) cc_final: 0.8132 (p) outliers start: 56 outliers final: 33 residues processed: 293 average time/residue: 0.1322 time to fit residues: 62.0945 Evaluate side-chains 263 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 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 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 190 LEU 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 591 LEU 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 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128635 restraints weight = 25960.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131330 restraints weight = 19382.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133200 restraints weight = 15895.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134469 restraints weight = 13887.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135180 restraints weight = 12673.721| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20472 Z= 0.108 Angle : 0.517 7.720 27588 Z= 0.262 Chirality : 0.037 0.128 3112 Planarity : 0.003 0.035 3392 Dihedral : 10.857 103.736 2988 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.15 % Allowed : 22.04 % Favored : 74.81 % 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: 0.07 (0.17), residues: 2376 helix: 1.15 (0.13), residues: 1556 sheet: -1.12 (0.56), residues: 76 loop : -2.27 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.015 0.001 TYR A 213 PHE 0.029 0.001 PHE D 193 TRP 0.010 0.001 TRP C 710 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00248 (20472) covalent geometry : angle 0.51747 (27588) hydrogen bonds : bond 0.02956 ( 1040) hydrogen bonds : angle 3.41018 ( 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 307 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 255 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.5524 (tt0) REVERT: A 493 TRP cc_start: 0.7395 (t-100) cc_final: 0.6795 (t-100) REVERT: A 575 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: A 578 MET cc_start: 0.6831 (mmt) cc_final: 0.6187 (mtt) REVERT: A 584 LEU cc_start: 0.7877 (mm) cc_final: 0.7553 (mt) REVERT: A 626 SER cc_start: 0.8350 (m) cc_final: 0.8057 (p) REVERT: B 255 GLN cc_start: 0.6173 (OUTLIER) cc_final: 0.5632 (tt0) REVERT: B 508 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7445 (tt) REVERT: B 575 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: B 626 SER cc_start: 0.8420 (m) cc_final: 0.8182 (p) REVERT: C 145 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7025 (tp) REVERT: C 255 GLN cc_start: 0.6156 (OUTLIER) cc_final: 0.5619 (tt0) REVERT: C 575 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: D 255 GLN cc_start: 0.6041 (OUTLIER) cc_final: 0.5560 (tt0) REVERT: D 575 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: D 626 SER cc_start: 0.8318 (m) cc_final: 0.8109 (p) outliers start: 67 outliers final: 44 residues processed: 294 average time/residue: 0.1265 time to fit residues: 59.8350 Evaluate side-chains 273 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 255 GLN Chi-restraints excluded: chain A residue 272 THR 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 255 GLN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 397 THR 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 734 ILE Chi-restraints excluded: chain C residue 145 LEU 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 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 591 LEU 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 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR 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: 8.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130369 restraints weight = 25897.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133164 restraints weight = 19389.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134979 restraints weight = 15905.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136285 restraints weight = 13877.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137196 restraints weight = 12615.120| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20472 Z= 0.098 Angle : 0.513 7.527 27588 Z= 0.258 Chirality : 0.037 0.123 3112 Planarity : 0.003 0.035 3392 Dihedral : 10.400 97.929 2988 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.10 % Allowed : 22.42 % Favored : 74.48 % 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: 0.27 (0.18), residues: 2376 helix: 1.31 (0.13), residues: 1552 sheet: -1.01 (0.59), residues: 76 loop : -2.17 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.015 0.001 TYR A 213 PHE 0.029 0.001 PHE D 193 TRP 0.009 0.001 TRP C 710 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00219 (20472) covalent geometry : angle 0.51328 (27588) hydrogen bonds : bond 0.02741 ( 1040) hydrogen bonds : angle 3.35468 ( 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 308 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 242 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 TRP cc_start: 0.7411 (t-100) cc_final: 0.6855 (t-100) REVERT: A 578 MET cc_start: 0.6809 (mmt) cc_final: 0.6100 (mtt) REVERT: A 626 SER cc_start: 0.8360 (m) cc_final: 0.7985 (p) REVERT: B 255 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5620 (tt0) REVERT: B 508 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7417 (tt) REVERT: B 575 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: B 626 SER cc_start: 0.8485 (m) cc_final: 0.8143 (p) REVERT: C 145 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7080 (tp) REVERT: C 255 GLN cc_start: 0.6121 (OUTLIER) cc_final: 0.5597 (tt0) REVERT: C 575 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: C 741 GLU cc_start: 0.7736 (mp0) cc_final: 0.7523 (mp0) REVERT: D 255 GLN cc_start: 0.6007 (OUTLIER) cc_final: 0.5533 (tt0) REVERT: D 368 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7610 (tptm) REVERT: D 575 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: D 626 SER cc_start: 0.8379 (m) cc_final: 0.8087 (p) outliers start: 66 outliers final: 42 residues processed: 298 average time/residue: 0.1249 time to fit residues: 60.6163 Evaluate side-chains 274 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 272 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 508 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 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 299 ILE Chi-restraints excluded: chain B residue 397 THR 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 145 LEU Chi-restraints excluded: chain C residue 153 ASP 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 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 636 THR 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 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 186 optimal weight: 0.0570 chunk 235 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 30 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132171 restraints weight = 25689.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134860 restraints weight = 19230.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136720 restraints weight = 15785.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137772 restraints weight = 13801.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138830 restraints weight = 12626.818| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20472 Z= 0.094 Angle : 0.522 8.172 27588 Z= 0.259 Chirality : 0.037 0.158 3112 Planarity : 0.003 0.035 3392 Dihedral : 9.927 94.291 2988 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.40 % Allowed : 23.59 % 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: 0.37 (0.18), residues: 2376 helix: 1.36 (0.13), residues: 1576 sheet: -0.99 (0.60), residues: 76 loop : -2.18 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 714 TYR 0.015 0.001 TYR A 213 PHE 0.028 0.001 PHE D 193 TRP 0.008 0.001 TRP C 710 HIS 0.003 0.000 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00205 (20472) covalent geometry : angle 0.52169 (27588) hydrogen bonds : bond 0.02589 ( 1040) hydrogen bonds : angle 3.29893 ( 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 295 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6122 (OUTLIER) cc_final: 0.5566 (tt0) REVERT: A 368 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7437 (pttm) REVERT: A 493 TRP cc_start: 0.7383 (t-100) cc_final: 0.6830 (t-100) REVERT: A 626 SER cc_start: 0.8301 (m) cc_final: 0.7962 (p) REVERT: B 255 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.5707 (tt0) REVERT: B 286 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7491 (tp40) REVERT: B 368 LYS cc_start: 0.7828 (tptm) cc_final: 0.7318 (pttm) REVERT: B 508 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7440 (tt) REVERT: B 575 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: B 626 SER cc_start: 0.8416 (m) cc_final: 0.8077 (p) REVERT: B 741 GLU cc_start: 0.7556 (mp0) cc_final: 0.7343 (mp0) REVERT: C 145 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7070 (tp) REVERT: C 255 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5677 (tt0) REVERT: C 286 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7542 (tp40) REVERT: C 575 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 575 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: D 626 SER cc_start: 0.8294 (m) cc_final: 0.7963 (p) outliers start: 51 outliers final: 36 residues processed: 289 average time/residue: 0.1233 time to fit residues: 57.9867 Evaluate side-chains 271 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 255 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 508 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 255 GLN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 ASP 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 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 584 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 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 575 TYR Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 642 LEU 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: 2.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 chunk 187 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127220 restraints weight = 25910.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130027 restraints weight = 19126.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131894 restraints weight = 15550.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133193 restraints weight = 13519.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133974 restraints weight = 12262.168| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20472 Z= 0.115 Angle : 0.551 13.096 27588 Z= 0.272 Chirality : 0.038 0.161 3112 Planarity : 0.003 0.035 3392 Dihedral : 9.858 92.386 2988 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.49 % Allowed : 24.15 % Favored : 73.36 % 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: 0.49 (0.18), residues: 2376 helix: 1.45 (0.13), residues: 1552 sheet: -1.04 (0.59), residues: 76 loop : -2.00 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 714 TYR 0.015 0.001 TYR A 213 PHE 0.029 0.001 PHE D 193 TRP 0.009 0.001 TRP C 433 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00266 (20472) covalent geometry : angle 0.55149 (27588) hydrogen bonds : bond 0.02918 ( 1040) hydrogen bonds : angle 3.36255 ( 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 284 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: A 493 TRP cc_start: 0.7392 (t-100) cc_final: 0.6851 (t-100) REVERT: A 584 LEU cc_start: 0.7722 (mm) cc_final: 0.7487 (mt) REVERT: A 626 SER cc_start: 0.8332 (m) cc_final: 0.7977 (p) REVERT: B 255 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5744 (tt0) REVERT: B 261 PHE cc_start: 0.8422 (p90) cc_final: 0.8113 (p90) REVERT: B 286 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7511 (tp40) REVERT: B 508 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7403 (tt) REVERT: B 575 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 626 SER cc_start: 0.8283 (m) cc_final: 0.7968 (p) REVERT: B 741 GLU cc_start: 0.7530 (mp0) cc_final: 0.7299 (mp0) REVERT: C 145 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7115 (tp) REVERT: C 255 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5730 (tt0) REVERT: C 286 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7534 (tp40) REVERT: C 575 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: D 255 GLN cc_start: 0.6170 (OUTLIER) cc_final: 0.5619 (tt0) REVERT: D 368 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7529 (tptm) REVERT: D 575 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: D 626 SER cc_start: 0.8405 (m) cc_final: 0.8113 (p) outliers start: 53 outliers final: 42 residues processed: 279 average time/residue: 0.1266 time to fit residues: 56.9779 Evaluate side-chains 281 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 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 508 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 145 LEU 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 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 584 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 255 GLN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 584 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: 0.9980 chunk 40 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127139 restraints weight = 25774.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129885 restraints weight = 19049.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131768 restraints weight = 15569.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132877 restraints weight = 13561.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133814 restraints weight = 12379.154| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20472 Z= 0.112 Angle : 0.553 13.664 27588 Z= 0.273 Chirality : 0.038 0.159 3112 Planarity : 0.003 0.035 3392 Dihedral : 9.639 90.755 2988 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.87 % Allowed : 24.01 % Favored : 73.12 % 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: 0.44 (0.18), residues: 2376 helix: 1.38 (0.13), residues: 1576 sheet: -1.05 (0.59), residues: 76 loop : -2.06 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 716 TYR 0.016 0.001 TYR A 213 PHE 0.030 0.001 PHE D 193 TRP 0.008 0.001 TRP A 433 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00261 (20472) covalent geometry : angle 0.55264 (27588) hydrogen bonds : bond 0.02878 ( 1040) hydrogen bonds : angle 3.37444 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.74 seconds wall clock time: 52 minutes 26.21 seconds (3146.21 seconds total)