Starting phenix.real_space_refine on Wed Nov 19 00:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bo9_7121/11_2025/6bo9_7121.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bo9_7121/11_2025/6bo9_7121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bo9_7121/11_2025/6bo9_7121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bo9_7121/11_2025/6bo9_7121.map" model { file = "/net/cci-nas-00/data/ceres_data/6bo9_7121/11_2025/6bo9_7121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bo9_7121/11_2025/6bo9_7121.cif" } resolution = 4.0 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 4.34, per 1000 atoms: 0.23 Number of scatterers: 19048 At special positions: 0 Unit cell: (140.14, 140.14, 125.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3368 8.00 N 3220 7.00 C 12304 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: 1.56 Conformation dependent library (CDL) restraints added in 860.3 milliseconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 63.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.753A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.175A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 4.105A pdb=" N ARG A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.860A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.717A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.725A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.846A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 removed outlier: 4.105A pdb=" N ARG B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.739A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.717A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.725A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.847A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.759A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.520A pdb=" N LEU B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.643A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.104A pdb=" N ARG C 224 " --> pdb=" O SER C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.716A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.726A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.847A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.643A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 4.373A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.587A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 removed outlier: 4.104A pdb=" N ARG D 224 " --> pdb=" O SER D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 224' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.716A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.726A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.031A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.847A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 960 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.09 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: 6070 1.34 - 1.46: 4285 1.46 - 1.58: 8865 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" C ILE A 565 " pdb=" N ALA A 566 " ideal model delta sigma weight residual 1.332 1.301 0.032 1.40e-02 5.10e+03 5.09e+00 bond pdb=" C ILE B 565 " pdb=" N ALA B 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C ILE C 565 " pdb=" N ALA C 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C ILE D 565 " pdb=" N ALA D 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" CA VAL D 404 " pdb=" CB VAL D 404 " ideal model delta sigma weight residual 1.534 1.548 -0.014 6.80e-03 2.16e+04 4.14e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 25987 3.65 - 7.30: 393 7.30 - 10.94: 56 10.94 - 14.59: 0 14.59 - 18.24: 4 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N SER B 112 " pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 108.79 117.21 -8.42 1.53e+00 4.27e-01 3.03e+01 angle pdb=" N SER C 112 " pdb=" CA SER C 112 " pdb=" C SER C 112 " ideal model delta sigma weight residual 108.79 117.17 -8.38 1.53e+00 4.27e-01 3.00e+01 angle pdb=" N SER A 112 " pdb=" CA SER A 112 " pdb=" C SER A 112 " ideal model delta sigma weight residual 108.79 117.16 -8.37 1.53e+00 4.27e-01 2.99e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.14 -8.35 1.53e+00 4.27e-01 2.98e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.17 -6.26 1.17e+00 7.31e-01 2.86e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 10904 15.36 - 30.73: 591 30.73 - 46.09: 177 46.09 - 61.45: 4 61.45 - 76.82: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 144.34 35.66 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ASN D 129 " pdb=" C ASN D 129 " pdb=" N MET D 130 " pdb=" CA MET D 130 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N MET B 130 " pdb=" CA MET B 130 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1969 0.049 - 0.097: 827 0.097 - 0.146: 168 0.146 - 0.195: 36 0.195 - 0.244: 12 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 323 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ARG D 323 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG D 323 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR D 324 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 323 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ARG A 323 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG A 323 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 324 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 323 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ARG B 323 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG B 323 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 324 " -0.013 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 4393 2.78 - 3.31: 19040 3.31 - 3.84: 31753 3.84 - 4.37: 38142 4.37 - 4.90: 61257 Nonbonded interactions: 154585 Sorted by model distance: nonbonded pdb=" O VAL A 427 " pdb=" OG1 THR A 431 " model vdw 2.245 3.040 nonbonded pdb=" O VAL C 427 " pdb=" OG1 THR C 431 " model vdw 2.245 3.040 nonbonded pdb=" O VAL D 427 " pdb=" OG1 THR D 431 " model vdw 2.245 3.040 nonbonded pdb=" O VAL B 427 " pdb=" OG1 THR B 431 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR C 339 " pdb=" O THR C 392 " model vdw 2.259 3.040 ... (remaining 154580 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: 0.05 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: 0.530 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.320 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 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 : 0.007 0.059 19484 Z= 0.334 Angle : 1.168 18.238 26440 Z= 0.658 Chirality : 0.055 0.244 3012 Planarity : 0.007 0.046 3336 Dihedral : 10.847 76.817 7184 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.97 % Allowed : 2.33 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.34 (0.14), residues: 2356 helix: -2.49 (0.10), residues: 1348 sheet: -5.71 (0.21), residues: 56 loop : -3.13 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.024 0.003 TYR C 524 PHE 0.026 0.003 PHE B 425 TRP 0.030 0.004 TRP C 593 HIS 0.017 0.002 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00664 (19484) covalent geometry : angle 1.16835 (26440) hydrogen bonds : bond 0.17592 ( 960) hydrogen bonds : angle 9.52423 ( 2760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 930 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7172 (ptpt) cc_final: 0.6900 (tppt) REVERT: A 160 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6449 (pp) REVERT: A 174 ASN cc_start: 0.6809 (t0) cc_final: 0.6135 (t0) REVERT: A 222 TYR cc_start: 0.8400 (m-80) cc_final: 0.7995 (m-80) REVERT: A 242 THR cc_start: 0.7231 (p) cc_final: 0.7027 (p) REVERT: A 246 LEU cc_start: 0.7454 (tp) cc_final: 0.6905 (tp) REVERT: A 259 LEU cc_start: 0.9054 (mp) cc_final: 0.8538 (mt) REVERT: A 279 ASP cc_start: 0.6636 (t70) cc_final: 0.6219 (t70) REVERT: A 281 THR cc_start: 0.7710 (m) cc_final: 0.7378 (p) REVERT: A 284 ASP cc_start: 0.7773 (t0) cc_final: 0.6739 (t0) REVERT: A 328 TYR cc_start: 0.6983 (m-10) cc_final: 0.6563 (m-10) REVERT: A 345 MET cc_start: 0.6098 (ttm) cc_final: 0.5610 (ttp) REVERT: A 382 ASP cc_start: 0.7672 (m-30) cc_final: 0.7206 (t0) REVERT: A 434 PHE cc_start: 0.7675 (m-80) cc_final: 0.7115 (t80) REVERT: A 440 MET cc_start: 0.7685 (tmm) cc_final: 0.7085 (tpp) REVERT: A 442 MET cc_start: 0.8034 (tpp) cc_final: 0.7696 (ttp) REVERT: A 487 PHE cc_start: 0.7799 (m-80) cc_final: 0.7219 (m-10) REVERT: A 509 TYR cc_start: 0.7154 (t80) cc_final: 0.6797 (t80) REVERT: A 510 ILE cc_start: 0.6949 (mt) cc_final: 0.6553 (mt) REVERT: A 546 ASN cc_start: 0.8025 (t0) cc_final: 0.7711 (t0) REVERT: A 565 ILE cc_start: 0.6733 (tp) cc_final: 0.6367 (tp) REVERT: A 594 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6879 (mtp-110) REVERT: A 630 PHE cc_start: 0.7926 (m-80) cc_final: 0.7580 (m-10) REVERT: B 71 LYS cc_start: 0.6775 (ptpt) cc_final: 0.6467 (tptm) REVERT: B 78 MET cc_start: 0.4439 (pmt) cc_final: 0.4206 (pmm) REVERT: B 110 MET cc_start: 0.6834 (mtp) cc_final: 0.6186 (mtp) REVERT: B 202 ILE cc_start: 0.8730 (mm) cc_final: 0.8462 (mm) REVERT: B 204 ILE cc_start: 0.8803 (mt) cc_final: 0.8599 (mt) REVERT: B 222 TYR cc_start: 0.8429 (m-80) cc_final: 0.7962 (m-80) REVERT: B 281 THR cc_start: 0.7751 (m) cc_final: 0.7355 (p) REVERT: B 354 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7273 (Cg_endo) REVERT: B 440 MET cc_start: 0.7851 (tmm) cc_final: 0.7406 (tpp) REVERT: B 442 MET cc_start: 0.7843 (tpp) cc_final: 0.7517 (ttp) REVERT: B 450 GLU cc_start: 0.6742 (pt0) cc_final: 0.6214 (pt0) REVERT: B 460 LEU cc_start: 0.5272 (mp) cc_final: 0.4909 (mp) REVERT: B 491 MET cc_start: 0.6825 (mmm) cc_final: 0.6241 (ttp) REVERT: B 509 TYR cc_start: 0.6889 (t80) cc_final: 0.6430 (t80) REVERT: B 546 ASN cc_start: 0.8385 (t0) cc_final: 0.8012 (t0) REVERT: B 565 ILE cc_start: 0.6845 (tp) cc_final: 0.6591 (tp) REVERT: B 569 LEU cc_start: 0.5766 (tt) cc_final: 0.5489 (tt) REVERT: B 583 TRP cc_start: 0.6947 (t60) cc_final: 0.6492 (t60) REVERT: B 594 ARG cc_start: 0.7365 (ttm110) cc_final: 0.6829 (mtp-110) REVERT: B 630 PHE cc_start: 0.7855 (m-80) cc_final: 0.7302 (m-10) REVERT: C 71 LYS cc_start: 0.6985 (ptpt) cc_final: 0.6753 (tppt) REVERT: C 206 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8185 (mm-40) REVERT: C 222 TYR cc_start: 0.8431 (m-80) cc_final: 0.7895 (m-80) REVERT: C 242 THR cc_start: 0.7176 (p) cc_final: 0.6934 (t) REVERT: C 246 LEU cc_start: 0.7633 (tp) cc_final: 0.7227 (tp) REVERT: C 259 LEU cc_start: 0.9095 (mp) cc_final: 0.8832 (mt) REVERT: C 284 ASP cc_start: 0.7835 (t0) cc_final: 0.7431 (t0) REVERT: C 352 LEU cc_start: 0.7812 (mp) cc_final: 0.7264 (mm) REVERT: C 354 PRO cc_start: 0.8404 (Cg_exo) cc_final: 0.8164 (Cg_endo) REVERT: C 358 ASN cc_start: 0.7273 (p0) cc_final: 0.6938 (p0) REVERT: C 384 ILE cc_start: 0.8217 (mt) cc_final: 0.7959 (mp) REVERT: C 434 PHE cc_start: 0.7830 (m-80) cc_final: 0.7233 (t80) REVERT: C 487 PHE cc_start: 0.7909 (m-80) cc_final: 0.7630 (m-10) REVERT: C 491 MET cc_start: 0.6758 (mmm) cc_final: 0.6129 (ttp) REVERT: C 508 PHE cc_start: 0.6401 (m-10) cc_final: 0.6122 (m-10) REVERT: C 509 TYR cc_start: 0.6967 (t80) cc_final: 0.6525 (t80) REVERT: C 526 TYR cc_start: 0.7393 (t80) cc_final: 0.7013 (t80) REVERT: C 532 SER cc_start: 0.6967 (t) cc_final: 0.6662 (t) REVERT: C 546 ASN cc_start: 0.8170 (t0) cc_final: 0.7689 (t0) REVERT: C 565 ILE cc_start: 0.7008 (tp) cc_final: 0.6794 (tp) REVERT: C 569 LEU cc_start: 0.5979 (tt) cc_final: 0.5660 (tt) REVERT: C 583 TRP cc_start: 0.7082 (t60) cc_final: 0.6784 (t60) REVERT: C 594 ARG cc_start: 0.7353 (ttm110) cc_final: 0.6926 (mtp-110) REVERT: C 615 ARG cc_start: 0.6910 (mtm110) cc_final: 0.6568 (mtm110) REVERT: C 630 PHE cc_start: 0.8032 (m-80) cc_final: 0.7619 (m-80) REVERT: D 71 LYS cc_start: 0.6939 (ptpt) cc_final: 0.6607 (tptt) REVERT: D 110 MET cc_start: 0.6227 (mtp) cc_final: 0.5848 (mtp) REVERT: D 174 ASN cc_start: 0.6899 (t0) cc_final: 0.5610 (t0) REVERT: D 202 ILE cc_start: 0.8797 (mm) cc_final: 0.8519 (mm) REVERT: D 222 TYR cc_start: 0.8493 (m-80) cc_final: 0.7989 (m-80) REVERT: D 242 THR cc_start: 0.7084 (p) cc_final: 0.6869 (t) REVERT: D 246 LEU cc_start: 0.7459 (tp) cc_final: 0.7167 (tp) REVERT: D 259 LEU cc_start: 0.9077 (mp) cc_final: 0.8846 (tp) REVERT: D 264 LYS cc_start: 0.7971 (pttt) cc_final: 0.7692 (ptpp) REVERT: D 279 ASP cc_start: 0.6799 (t70) cc_final: 0.6152 (t70) REVERT: D 284 ASP cc_start: 0.7912 (t0) cc_final: 0.7177 (t0) REVERT: D 285 SER cc_start: 0.6453 (p) cc_final: 0.5994 (m) REVERT: D 323 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7599 (mtp180) REVERT: D 342 CYS cc_start: 0.8127 (t) cc_final: 0.7873 (t) REVERT: D 345 MET cc_start: 0.6383 (ttm) cc_final: 0.5964 (ttp) REVERT: D 352 LEU cc_start: 0.7886 (mp) cc_final: 0.7492 (mm) REVERT: D 390 LEU cc_start: 0.8877 (mt) cc_final: 0.8621 (tp) REVERT: D 434 PHE cc_start: 0.7753 (m-80) cc_final: 0.7100 (t80) REVERT: D 436 VAL cc_start: 0.7052 (t) cc_final: 0.6797 (m) REVERT: D 440 MET cc_start: 0.7989 (tmm) cc_final: 0.7241 (tpp) REVERT: D 453 PRO cc_start: 0.7524 (Cg_exo) cc_final: 0.7269 (Cg_endo) REVERT: D 491 MET cc_start: 0.7094 (mmm) cc_final: 0.6856 (ttp) REVERT: D 492 ARG cc_start: 0.6705 (ptt90) cc_final: 0.6501 (ptt90) REVERT: D 514 THR cc_start: 0.7948 (m) cc_final: 0.7643 (p) REVERT: D 522 HIS cc_start: 0.6402 (m-70) cc_final: 0.6012 (m170) REVERT: D 532 SER cc_start: 0.7199 (t) cc_final: 0.6862 (t) REVERT: D 534 PHE cc_start: 0.5598 (t80) cc_final: 0.5383 (t80) REVERT: D 546 ASN cc_start: 0.7900 (t0) cc_final: 0.7045 (t0) REVERT: D 594 ARG cc_start: 0.7246 (ttm110) cc_final: 0.6772 (mtp-110) REVERT: D 630 PHE cc_start: 0.8158 (m-80) cc_final: 0.7799 (m-10) outliers start: 20 outliers final: 2 residues processed: 942 average time/residue: 0.1431 time to fit residues: 201.1441 Evaluate side-chains 572 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 569 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 HIS A 257 GLN A 357 ASN A 365 ASN A 464 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 174 ASN B 257 GLN B 365 ASN B 522 HIS B 546 ASN C 41 GLN C 174 ASN C 206 GLN C 257 GLN C 267 GLN C 357 ASN C 365 ASN C 464 ASN C 522 HIS C 546 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 267 GLN D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.160395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135901 restraints weight = 38088.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136961 restraints weight = 27618.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.137564 restraints weight = 20814.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137983 restraints weight = 19803.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138325 restraints weight = 17194.056| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19484 Z= 0.163 Angle : 0.810 12.530 26440 Z= 0.397 Chirality : 0.045 0.245 3012 Planarity : 0.005 0.039 3336 Dihedral : 5.964 49.222 2600 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.55 % Favored : 90.41 % Rotamer: Outliers : 4.02 % Allowed : 15.89 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2356 helix: -0.47 (0.13), residues: 1380 sheet: -4.79 (0.30), residues: 56 loop : -2.61 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 180 TYR 0.024 0.002 TYR A 270 PHE 0.032 0.002 PHE C 531 TRP 0.018 0.002 TRP D 29 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00365 (19484) covalent geometry : angle 0.81025 (26440) hydrogen bonds : bond 0.04435 ( 960) hydrogen bonds : angle 5.05545 ( 2760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 636 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.6626 (m-30) cc_final: 0.6275 (m-30) REVERT: A 279 ASP cc_start: 0.7411 (t70) cc_final: 0.7043 (t70) REVERT: A 281 THR cc_start: 0.8157 (m) cc_final: 0.7731 (p) REVERT: A 440 MET cc_start: 0.7683 (tmm) cc_final: 0.7327 (tpp) REVERT: A 456 PHE cc_start: 0.8349 (m-10) cc_final: 0.8142 (m-80) REVERT: A 464 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7464 (t0) REVERT: A 467 TYR cc_start: 0.7761 (t80) cc_final: 0.7467 (t80) REVERT: A 565 ILE cc_start: 0.9263 (tp) cc_final: 0.9024 (tp) REVERT: A 583 TRP cc_start: 0.7480 (t60) cc_final: 0.7066 (t60) REVERT: B 44 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6496 (mp) REVERT: B 107 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: B 281 THR cc_start: 0.8218 (m) cc_final: 0.7767 (p) REVERT: B 339 TYR cc_start: 0.8293 (t80) cc_final: 0.8065 (t80) REVERT: B 429 ILE cc_start: 0.8560 (mt) cc_final: 0.8234 (mt) REVERT: B 464 ASN cc_start: 0.7936 (t160) cc_final: 0.7640 (t0) REVERT: B 565 ILE cc_start: 0.9052 (tp) cc_final: 0.8728 (tp) REVERT: B 583 TRP cc_start: 0.7549 (t60) cc_final: 0.7340 (t60) REVERT: C 339 TYR cc_start: 0.8627 (t80) cc_final: 0.8319 (t80) REVERT: C 464 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7358 (t0) REVERT: C 502 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9062 (mm) REVERT: C 565 ILE cc_start: 0.9100 (tp) cc_final: 0.8876 (tp) REVERT: C 578 MET cc_start: 0.8086 (mtm) cc_final: 0.7885 (mtm) REVERT: C 583 TRP cc_start: 0.7735 (t60) cc_final: 0.7301 (t60) REVERT: C 616 SER cc_start: 0.8269 (t) cc_final: 0.7982 (p) REVERT: D 40 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8556 (tm-30) REVERT: D 44 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7309 (mp) REVERT: D 260 MET cc_start: 0.8280 (tpp) cc_final: 0.8019 (tpp) REVERT: D 277 LEU cc_start: 0.8098 (tp) cc_final: 0.7831 (mt) REVERT: D 321 TRP cc_start: 0.8150 (t-100) cc_final: 0.7800 (t-100) REVERT: D 440 MET cc_start: 0.7823 (tmm) cc_final: 0.7351 (tpp) REVERT: D 464 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7613 (t0) REVERT: D 467 TYR cc_start: 0.7836 (t80) cc_final: 0.7567 (t80) REVERT: D 536 LEU cc_start: 0.9235 (mt) cc_final: 0.9013 (mt) REVERT: D 583 TRP cc_start: 0.7591 (t60) cc_final: 0.7270 (t60) outliers start: 83 outliers final: 37 residues processed: 688 average time/residue: 0.1267 time to fit residues: 136.3705 Evaluate side-chains 561 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 517 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 ASN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 17 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 267 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 572 ASN B 31 GLN B 73 HIS B 118 GLN B 257 GLN B 267 GLN B 357 ASN C 31 GLN C 73 HIS C 118 GLN C 257 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.155742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128844 restraints weight = 37431.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130294 restraints weight = 24511.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131077 restraints weight = 18830.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131410 restraints weight = 17556.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131557 restraints weight = 15992.693| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19484 Z= 0.153 Angle : 0.770 12.430 26440 Z= 0.374 Chirality : 0.045 0.264 3012 Planarity : 0.004 0.043 3336 Dihedral : 5.505 46.108 2598 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.60 % Allowed : 19.14 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2356 helix: 0.42 (0.14), residues: 1376 sheet: -3.46 (0.47), residues: 56 loop : -2.38 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 615 TYR 0.021 0.002 TYR B 270 PHE 0.031 0.002 PHE C 531 TRP 0.020 0.002 TRP D 613 HIS 0.005 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00345 (19484) covalent geometry : angle 0.76986 (26440) hydrogen bonds : bond 0.04003 ( 960) hydrogen bonds : angle 4.56753 ( 2760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 543 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 THR cc_start: 0.8079 (m) cc_final: 0.7787 (p) REVERT: A 311 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 339 TYR cc_start: 0.8480 (t80) cc_final: 0.8096 (t80) REVERT: A 440 MET cc_start: 0.7863 (tmm) cc_final: 0.7441 (tpp) REVERT: A 456 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: A 492 ARG cc_start: 0.7506 (ptt90) cc_final: 0.7268 (ptt90) REVERT: A 583 TRP cc_start: 0.7604 (t60) cc_final: 0.7256 (t60) REVERT: B 44 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6610 (mp) REVERT: B 45 TRP cc_start: 0.7028 (t-100) cc_final: 0.6754 (m100) REVERT: B 107 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: B 214 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: B 281 THR cc_start: 0.8198 (m) cc_final: 0.7907 (p) REVERT: B 339 TYR cc_start: 0.8489 (t80) cc_final: 0.8107 (t80) REVERT: B 341 ILE cc_start: 0.8636 (mm) cc_final: 0.8397 (mm) REVERT: B 464 ASN cc_start: 0.8068 (t160) cc_final: 0.7682 (t0) REVERT: B 530 LEU cc_start: 0.9283 (mm) cc_final: 0.9047 (mt) REVERT: B 565 ILE cc_start: 0.9351 (tp) cc_final: 0.9144 (tp) REVERT: B 603 MET cc_start: 0.7090 (tmm) cc_final: 0.6832 (tmm) REVERT: C 222 TYR cc_start: 0.7501 (m-10) cc_final: 0.7281 (m-10) REVERT: C 260 MET cc_start: 0.8320 (tpp) cc_final: 0.8116 (tpp) REVERT: C 311 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8086 (p) REVERT: C 339 TYR cc_start: 0.8742 (t80) cc_final: 0.8217 (t80) REVERT: C 502 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9053 (mm) REVERT: C 565 ILE cc_start: 0.9331 (tp) cc_final: 0.9091 (tp) REVERT: C 583 TRP cc_start: 0.7723 (t60) cc_final: 0.7242 (t60) REVERT: C 616 SER cc_start: 0.8409 (t) cc_final: 0.8087 (p) REVERT: D 34 ASP cc_start: 0.7044 (m-30) cc_final: 0.6833 (m-30) REVERT: D 40 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8752 (tm-30) REVERT: D 44 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7323 (mp) REVERT: D 118 GLN cc_start: 0.6403 (tm-30) cc_final: 0.6179 (tm-30) REVERT: D 164 GLU cc_start: 0.6359 (pt0) cc_final: 0.6146 (pt0) REVERT: D 259 LEU cc_start: 0.8751 (mt) cc_final: 0.8161 (tp) REVERT: D 260 MET cc_start: 0.8372 (tpp) cc_final: 0.8169 (tpp) REVERT: D 440 MET cc_start: 0.7756 (tmm) cc_final: 0.7439 (tpp) REVERT: D 472 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: D 526 TYR cc_start: 0.9012 (t80) cc_final: 0.8797 (t80) REVERT: D 528 MET cc_start: 0.8166 (tmm) cc_final: 0.7823 (tmm) REVERT: D 583 TRP cc_start: 0.7767 (t60) cc_final: 0.7376 (t60) outliers start: 95 outliers final: 44 residues processed: 595 average time/residue: 0.1222 time to fit residues: 115.6123 Evaluate side-chains 550 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 497 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 151 optimal weight: 0.0050 chunk 50 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 464 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 41 GLN B 596 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN C 546 ASN C 596 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126154 restraints weight = 37834.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128248 restraints weight = 24747.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129758 restraints weight = 18593.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130500 restraints weight = 15166.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131040 restraints weight = 13464.799| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19484 Z= 0.141 Angle : 0.744 13.323 26440 Z= 0.359 Chirality : 0.044 0.247 3012 Planarity : 0.004 0.043 3336 Dihedral : 5.296 46.822 2598 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.84 % Allowed : 19.82 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2356 helix: 0.70 (0.14), residues: 1384 sheet: -2.58 (0.60), residues: 56 loop : -2.28 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 492 TYR 0.017 0.001 TYR B 270 PHE 0.027 0.002 PHE B 531 TRP 0.015 0.002 TRP C 629 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00316 (19484) covalent geometry : angle 0.74387 (26440) hydrogen bonds : bond 0.03712 ( 960) hydrogen bonds : angle 4.35787 ( 2760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 521 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6855 (mp) REVERT: A 107 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: A 218 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 250 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7044 (tp30) REVERT: A 281 THR cc_start: 0.8193 (m) cc_final: 0.7952 (p) REVERT: A 339 TYR cc_start: 0.8559 (t80) cc_final: 0.8029 (t80) REVERT: A 440 MET cc_start: 0.7820 (tmm) cc_final: 0.7445 (tpp) REVERT: A 492 ARG cc_start: 0.7499 (ptt90) cc_final: 0.7257 (ptt90) REVERT: A 583 TRP cc_start: 0.7617 (t60) cc_final: 0.7345 (t60) REVERT: B 44 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6785 (mp) REVERT: B 45 TRP cc_start: 0.7158 (t-100) cc_final: 0.6839 (m100) REVERT: B 107 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: B 281 THR cc_start: 0.8277 (m) cc_final: 0.7936 (p) REVERT: B 307 ILE cc_start: 0.8923 (mm) cc_final: 0.8708 (mm) REVERT: B 339 TYR cc_start: 0.8589 (t80) cc_final: 0.8148 (t80) REVERT: B 364 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: B 464 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7554 (t0) REVERT: B 565 ILE cc_start: 0.9469 (tp) cc_final: 0.9206 (tp) REVERT: B 619 CYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7515 (t) REVERT: B 629 TRP cc_start: 0.6916 (m-10) cc_final: 0.6311 (m100) REVERT: C 96 MET cc_start: 0.7966 (tmm) cc_final: 0.7760 (tmm) REVERT: C 107 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: C 228 HIS cc_start: 0.5068 (m-70) cc_final: 0.4540 (p-80) REVERT: C 339 TYR cc_start: 0.8809 (t80) cc_final: 0.8184 (t80) REVERT: C 353 LYS cc_start: 0.7163 (pttp) cc_final: 0.6905 (pttt) REVERT: C 464 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7476 (t0) REVERT: C 528 MET cc_start: 0.7743 (tmm) cc_final: 0.7533 (tmm) REVERT: C 538 LEU cc_start: 0.8464 (mp) cc_final: 0.8193 (mp) REVERT: C 565 ILE cc_start: 0.9421 (tp) cc_final: 0.9214 (tp) REVERT: C 583 TRP cc_start: 0.7740 (t60) cc_final: 0.7365 (t60) REVERT: C 629 TRP cc_start: 0.7966 (m100) cc_final: 0.7701 (m100) REVERT: D 34 ASP cc_start: 0.7168 (m-30) cc_final: 0.6868 (m-30) REVERT: D 44 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7370 (mp) REVERT: D 164 GLU cc_start: 0.6348 (pt0) cc_final: 0.6115 (pt0) REVERT: D 260 MET cc_start: 0.8397 (tpp) cc_final: 0.8161 (tpp) REVERT: D 440 MET cc_start: 0.7829 (tmm) cc_final: 0.7523 (tpp) REVERT: D 464 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7842 (t0) REVERT: D 583 TRP cc_start: 0.7870 (t60) cc_final: 0.7466 (t60) outliers start: 100 outliers final: 46 residues processed: 580 average time/residue: 0.1198 time to fit residues: 110.9129 Evaluate side-chains 535 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 477 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 464 ASN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 464 ASN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 38 optimal weight: 3.9990 chunk 193 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 257 GLN D 265 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127791 restraints weight = 37792.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128593 restraints weight = 26638.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128985 restraints weight = 20198.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129766 restraints weight = 19941.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129850 restraints weight = 16897.485| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19484 Z= 0.135 Angle : 0.751 13.760 26440 Z= 0.359 Chirality : 0.043 0.256 3012 Planarity : 0.004 0.035 3336 Dihedral : 5.153 46.598 2598 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.31 % Allowed : 21.37 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2356 helix: 0.76 (0.14), residues: 1412 sheet: -2.02 (0.61), residues: 56 loop : -2.32 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 492 TYR 0.021 0.002 TYR C 222 PHE 0.026 0.002 PHE A 553 TRP 0.014 0.001 TRP C 629 HIS 0.004 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00307 (19484) covalent geometry : angle 0.75093 (26440) hydrogen bonds : bond 0.03632 ( 960) hydrogen bonds : angle 4.25093 ( 2760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 494 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6950 (mp) REVERT: A 107 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6381 (m-80) REVERT: A 222 TYR cc_start: 0.6851 (m-80) cc_final: 0.6594 (m-80) REVERT: A 281 THR cc_start: 0.8280 (m) cc_final: 0.7968 (p) REVERT: A 339 TYR cc_start: 0.8612 (t80) cc_final: 0.8077 (t80) REVERT: A 440 MET cc_start: 0.7904 (tmm) cc_final: 0.7512 (tpp) REVERT: A 583 TRP cc_start: 0.7679 (t60) cc_final: 0.7388 (t60) REVERT: B 44 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6777 (mp) REVERT: B 45 TRP cc_start: 0.7087 (t-100) cc_final: 0.6777 (m100) REVERT: B 107 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: B 218 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7894 (tp) REVERT: B 241 LEU cc_start: 0.7750 (mm) cc_final: 0.7481 (mm) REVERT: B 281 THR cc_start: 0.8358 (m) cc_final: 0.7995 (p) REVERT: B 307 ILE cc_start: 0.8863 (mm) cc_final: 0.8660 (mm) REVERT: B 315 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: B 339 TYR cc_start: 0.8629 (t80) cc_final: 0.8132 (t80) REVERT: B 464 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7665 (t0) REVERT: B 565 ILE cc_start: 0.9428 (tp) cc_final: 0.9096 (tp) REVERT: C 96 MET cc_start: 0.7965 (tmm) cc_final: 0.7735 (tmm) REVERT: C 107 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: C 228 HIS cc_start: 0.5303 (m-70) cc_final: 0.4660 (p-80) REVERT: C 292 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8645 (tt) REVERT: C 339 TYR cc_start: 0.8786 (t80) cc_final: 0.8167 (t80) REVERT: C 353 LYS cc_start: 0.7041 (pttp) cc_final: 0.6626 (pttt) REVERT: C 454 MET cc_start: 0.8572 (ttm) cc_final: 0.7840 (ttm) REVERT: C 528 MET cc_start: 0.7656 (tmm) cc_final: 0.7435 (tmm) REVERT: C 542 ASP cc_start: 0.7272 (m-30) cc_final: 0.7044 (m-30) REVERT: C 565 ILE cc_start: 0.9355 (tp) cc_final: 0.9053 (tp) REVERT: C 583 TRP cc_start: 0.7806 (t60) cc_final: 0.7362 (t60) REVERT: C 629 TRP cc_start: 0.7978 (m100) cc_final: 0.7689 (m100) REVERT: D 34 ASP cc_start: 0.7218 (m-30) cc_final: 0.6966 (m-30) REVERT: D 44 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7400 (mp) REVERT: D 164 GLU cc_start: 0.6350 (pt0) cc_final: 0.5616 (pt0) REVERT: D 260 MET cc_start: 0.8327 (tpp) cc_final: 0.7947 (tpp) REVERT: D 261 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7962 (tm-30) REVERT: D 294 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 301 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6681 (mmtt) REVERT: D 440 MET cc_start: 0.7801 (tmm) cc_final: 0.7481 (mmm) REVERT: D 474 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5953 (ptt) REVERT: D 481 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7101 (ttm) REVERT: D 583 TRP cc_start: 0.7924 (t60) cc_final: 0.7541 (t60) outliers start: 89 outliers final: 33 residues processed: 543 average time/residue: 0.1234 time to fit residues: 106.4068 Evaluate side-chains 512 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 467 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 169 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 192 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 125 optimal weight: 0.0060 chunk 29 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 258 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127635 restraints weight = 37577.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129148 restraints weight = 26242.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129625 restraints weight = 20097.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129882 restraints weight = 17834.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130171 restraints weight = 17388.010| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19484 Z= 0.128 Angle : 0.747 14.745 26440 Z= 0.354 Chirality : 0.043 0.210 3012 Planarity : 0.004 0.034 3336 Dihedral : 5.090 47.424 2598 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.92 % Allowed : 22.97 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2356 helix: 0.81 (0.14), residues: 1424 sheet: -1.55 (0.61), residues: 56 loop : -2.34 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 492 TYR 0.030 0.002 TYR A 526 PHE 0.022 0.001 PHE D 434 TRP 0.012 0.001 TRP D 613 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00282 (19484) covalent geometry : angle 0.74693 (26440) hydrogen bonds : bond 0.03506 ( 960) hydrogen bonds : angle 4.24197 ( 2760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 497 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 107 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: A 281 THR cc_start: 0.8421 (m) cc_final: 0.8217 (p) REVERT: A 315 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: A 339 TYR cc_start: 0.8648 (t80) cc_final: 0.8067 (t80) REVERT: A 440 MET cc_start: 0.7834 (tmm) cc_final: 0.7451 (tpp) REVERT: A 583 TRP cc_start: 0.7676 (t60) cc_final: 0.7408 (t60) REVERT: B 44 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6794 (mp) REVERT: B 45 TRP cc_start: 0.7095 (t-100) cc_final: 0.6754 (m100) REVERT: B 107 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: B 281 THR cc_start: 0.8377 (m) cc_final: 0.7761 (p) REVERT: B 282 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6860 (mm-30) REVERT: B 307 ILE cc_start: 0.8840 (mm) cc_final: 0.8625 (mm) REVERT: B 315 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: B 339 TYR cc_start: 0.8651 (t80) cc_final: 0.7986 (t80) REVERT: B 464 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7629 (t0) REVERT: B 565 ILE cc_start: 0.9505 (tp) cc_final: 0.9255 (tp) REVERT: C 34 ASP cc_start: 0.7090 (m-30) cc_final: 0.6741 (m-30) REVERT: C 96 MET cc_start: 0.7991 (tmm) cc_final: 0.7737 (tmm) REVERT: C 107 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: C 228 HIS cc_start: 0.5467 (m-70) cc_final: 0.4729 (p-80) REVERT: C 261 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8156 (tm-30) REVERT: C 301 LYS cc_start: 0.7253 (mtmt) cc_final: 0.7037 (mmtt) REVERT: C 307 ILE cc_start: 0.8823 (mm) cc_final: 0.8569 (mm) REVERT: C 339 TYR cc_start: 0.8787 (t80) cc_final: 0.8049 (t80) REVERT: C 440 MET cc_start: 0.6872 (tpp) cc_final: 0.6600 (tpp) REVERT: C 515 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6919 (mm-30) REVERT: C 565 ILE cc_start: 0.9375 (tp) cc_final: 0.9102 (tp) REVERT: C 583 TRP cc_start: 0.7708 (t60) cc_final: 0.7414 (t60) REVERT: C 629 TRP cc_start: 0.7940 (m100) cc_final: 0.7331 (m100) REVERT: D 34 ASP cc_start: 0.7311 (m-30) cc_final: 0.7024 (m-30) REVERT: D 164 GLU cc_start: 0.6165 (pt0) cc_final: 0.5502 (pt0) REVERT: D 220 LEU cc_start: 0.8368 (mm) cc_final: 0.8126 (mm) REVERT: D 222 TYR cc_start: 0.6901 (m-80) cc_final: 0.6633 (m-80) REVERT: D 260 MET cc_start: 0.8277 (tpp) cc_final: 0.7890 (tpp) REVERT: D 261 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7955 (tm-30) REVERT: D 294 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7499 (mm-30) REVERT: D 301 LYS cc_start: 0.7224 (mtmt) cc_final: 0.6654 (mmtt) REVERT: D 436 VAL cc_start: 0.9409 (m) cc_final: 0.9051 (p) REVERT: D 440 MET cc_start: 0.7818 (tmm) cc_final: 0.7493 (mmm) REVERT: D 481 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7093 (ttm) REVERT: D 583 TRP cc_start: 0.7884 (t60) cc_final: 0.7507 (t60) outliers start: 81 outliers final: 35 residues processed: 541 average time/residue: 0.1263 time to fit residues: 107.6195 Evaluate side-chains 503 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 459 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 227 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.154024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127046 restraints weight = 37575.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127896 restraints weight = 23254.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128411 restraints weight = 19268.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128453 restraints weight = 17600.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128570 restraints weight = 17053.219| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19484 Z= 0.131 Angle : 0.765 16.757 26440 Z= 0.359 Chirality : 0.043 0.287 3012 Planarity : 0.004 0.051 3336 Dihedral : 5.046 48.830 2598 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.20 % Allowed : 24.22 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.18), residues: 2356 helix: 0.89 (0.14), residues: 1404 sheet: -1.25 (0.62), residues: 56 loop : -2.28 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 139 TYR 0.023 0.001 TYR A 526 PHE 0.030 0.002 PHE B 553 TRP 0.011 0.001 TRP A 613 HIS 0.004 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00298 (19484) covalent geometry : angle 0.76478 (26440) hydrogen bonds : bond 0.03468 ( 960) hydrogen bonds : angle 4.25721 ( 2760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 481 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6900 (mp) REVERT: A 107 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: A 281 THR cc_start: 0.8556 (m) cc_final: 0.8154 (p) REVERT: A 315 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 339 TYR cc_start: 0.8678 (t80) cc_final: 0.8133 (t80) REVERT: A 434 PHE cc_start: 0.7633 (t80) cc_final: 0.7420 (t80) REVERT: A 440 MET cc_start: 0.7895 (tmm) cc_final: 0.7433 (tpp) REVERT: A 456 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 497 MET cc_start: 0.6691 (ttp) cc_final: 0.6444 (ttp) REVERT: A 583 TRP cc_start: 0.7691 (t60) cc_final: 0.7382 (t60) REVERT: B 44 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6851 (mp) REVERT: B 45 TRP cc_start: 0.7207 (t-100) cc_final: 0.6868 (m100) REVERT: B 107 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: B 139 ARG cc_start: 0.7242 (mmt-90) cc_final: 0.7020 (mmm-85) REVERT: B 228 HIS cc_start: 0.5172 (m-70) cc_final: 0.4798 (p-80) REVERT: B 241 LEU cc_start: 0.7747 (mm) cc_final: 0.7385 (mm) REVERT: B 261 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8014 (tm-30) REVERT: B 281 THR cc_start: 0.8358 (m) cc_final: 0.7724 (p) REVERT: B 282 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 307 ILE cc_start: 0.8833 (mm) cc_final: 0.8620 (mm) REVERT: B 315 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 339 TYR cc_start: 0.8661 (t80) cc_final: 0.7972 (t80) REVERT: B 464 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7594 (t0) REVERT: B 565 ILE cc_start: 0.9504 (tp) cc_final: 0.9218 (tp) REVERT: C 34 ASP cc_start: 0.7057 (m-30) cc_final: 0.6631 (m-30) REVERT: C 44 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7183 (mp) REVERT: C 96 MET cc_start: 0.8018 (tmm) cc_final: 0.7778 (tmm) REVERT: C 107 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: C 220 LEU cc_start: 0.8409 (mm) cc_final: 0.8187 (mm) REVERT: C 228 HIS cc_start: 0.5464 (m-70) cc_final: 0.4685 (p-80) REVERT: C 261 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8206 (tm-30) REVERT: C 301 LYS cc_start: 0.7375 (mtmt) cc_final: 0.7105 (mmtt) REVERT: C 307 ILE cc_start: 0.8888 (mm) cc_final: 0.8684 (mm) REVERT: C 315 GLU cc_start: 0.8108 (mp0) cc_final: 0.7818 (mp0) REVERT: C 339 TYR cc_start: 0.8830 (t80) cc_final: 0.8266 (t80) REVERT: C 390 LEU cc_start: 0.8394 (mp) cc_final: 0.8041 (tp) REVERT: C 440 MET cc_start: 0.7018 (tpp) cc_final: 0.6760 (tpp) REVERT: C 515 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6900 (mm-30) REVERT: C 565 ILE cc_start: 0.9459 (tp) cc_final: 0.9223 (tp) REVERT: C 583 TRP cc_start: 0.7733 (t60) cc_final: 0.7439 (t60) REVERT: C 629 TRP cc_start: 0.7960 (m100) cc_final: 0.7513 (m100) REVERT: D 34 ASP cc_start: 0.7291 (m-30) cc_final: 0.7038 (m-30) REVERT: D 164 GLU cc_start: 0.6283 (pt0) cc_final: 0.5578 (pt0) REVERT: D 260 MET cc_start: 0.8265 (tpp) cc_final: 0.7875 (tpp) REVERT: D 261 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7921 (tm-30) REVERT: D 294 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7497 (mm-30) REVERT: D 339 TYR cc_start: 0.8821 (t80) cc_final: 0.8259 (t80) REVERT: D 436 VAL cc_start: 0.9406 (m) cc_final: 0.9076 (p) REVERT: D 440 MET cc_start: 0.7850 (tmm) cc_final: 0.7522 (mmm) REVERT: D 474 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5887 (ptt) REVERT: D 481 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7123 (ttm) REVERT: D 583 TRP cc_start: 0.7898 (t60) cc_final: 0.7533 (t60) outliers start: 66 outliers final: 37 residues processed: 516 average time/residue: 0.1225 time to fit residues: 100.1381 Evaluate side-chains 511 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 462 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 132 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 99 optimal weight: 0.0980 chunk 210 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119650 restraints weight = 37950.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121694 restraints weight = 24743.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123138 restraints weight = 18452.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123723 restraints weight = 15065.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124636 restraints weight = 13464.654| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19484 Z= 0.177 Angle : 0.808 15.794 26440 Z= 0.387 Chirality : 0.046 0.256 3012 Planarity : 0.004 0.049 3336 Dihedral : 5.139 49.027 2598 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.42 % Favored : 90.53 % Rotamer: Outliers : 3.92 % Allowed : 23.79 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2356 helix: 0.83 (0.14), residues: 1384 sheet: -0.99 (0.63), residues: 56 loop : -2.05 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 492 TYR 0.021 0.002 TYR B 467 PHE 0.035 0.002 PHE B 553 TRP 0.017 0.002 TRP A 29 HIS 0.004 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00410 (19484) covalent geometry : angle 0.80847 (26440) hydrogen bonds : bond 0.03763 ( 960) hydrogen bonds : angle 4.48592 ( 2760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 496 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.7008 (m-30) cc_final: 0.6456 (m-30) REVERT: A 107 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: A 228 HIS cc_start: 0.5220 (m-70) cc_final: 0.4651 (p-80) REVERT: A 261 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7962 (tm-30) REVERT: A 281 THR cc_start: 0.8463 (m) cc_final: 0.8090 (p) REVERT: A 297 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7463 (tp) REVERT: A 301 LYS cc_start: 0.6894 (mtmt) cc_final: 0.6662 (mmtt) REVERT: A 339 TYR cc_start: 0.8911 (t80) cc_final: 0.8649 (t80) REVERT: A 436 VAL cc_start: 0.9324 (m) cc_final: 0.8939 (p) REVERT: A 497 MET cc_start: 0.6951 (ttp) cc_final: 0.6642 (ttp) REVERT: A 515 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6733 (mm-30) REVERT: A 542 ASP cc_start: 0.7502 (t0) cc_final: 0.5919 (t0) REVERT: A 583 TRP cc_start: 0.7964 (t60) cc_final: 0.7746 (t60) REVERT: A 632 ARG cc_start: 0.8447 (ptm-80) cc_final: 0.8144 (ptt90) REVERT: B 107 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: B 228 HIS cc_start: 0.5123 (m-70) cc_final: 0.4656 (p-80) REVERT: B 281 THR cc_start: 0.8318 (m) cc_final: 0.7669 (p) REVERT: B 282 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 297 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7050 (tp) REVERT: B 307 ILE cc_start: 0.8851 (mm) cc_final: 0.8641 (mm) REVERT: B 315 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: B 339 TYR cc_start: 0.8863 (t80) cc_final: 0.8349 (t80) REVERT: B 464 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 474 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.6054 (ptt) REVERT: B 565 ILE cc_start: 0.9568 (tp) cc_final: 0.9359 (tp) REVERT: C 34 ASP cc_start: 0.6952 (m-30) cc_final: 0.6549 (m-30) REVERT: C 44 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7120 (mp) REVERT: C 107 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: C 220 LEU cc_start: 0.8303 (mm) cc_final: 0.8083 (mm) REVERT: C 228 HIS cc_start: 0.5301 (m-70) cc_final: 0.4556 (p-80) REVERT: C 261 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8122 (tm-30) REVERT: C 297 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7580 (tp) REVERT: C 307 ILE cc_start: 0.8942 (mm) cc_final: 0.8704 (mm) REVERT: C 315 GLU cc_start: 0.8107 (mp0) cc_final: 0.7859 (mp0) REVERT: C 339 TYR cc_start: 0.8967 (t80) cc_final: 0.8722 (t80) REVERT: C 346 CYS cc_start: 0.8027 (m) cc_final: 0.7734 (p) REVERT: C 390 LEU cc_start: 0.8405 (mp) cc_final: 0.8023 (tp) REVERT: C 515 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6922 (mm-30) REVERT: C 583 TRP cc_start: 0.7788 (t60) cc_final: 0.7509 (t60) REVERT: C 629 TRP cc_start: 0.8138 (m100) cc_final: 0.7175 (m100) REVERT: D 34 ASP cc_start: 0.7277 (m-30) cc_final: 0.6957 (m-30) REVERT: D 99 MET cc_start: 0.5783 (mmt) cc_final: 0.5564 (mmt) REVERT: D 164 GLU cc_start: 0.6978 (pt0) cc_final: 0.6535 (pt0) REVERT: D 228 HIS cc_start: 0.5269 (m-70) cc_final: 0.4586 (p-80) REVERT: D 261 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8074 (tm-30) REVERT: D 294 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7541 (mm-30) REVERT: D 301 LYS cc_start: 0.7520 (mtmt) cc_final: 0.7202 (mptt) REVERT: D 339 TYR cc_start: 0.8893 (t80) cc_final: 0.8435 (t80) REVERT: D 346 CYS cc_start: 0.7989 (m) cc_final: 0.7720 (p) REVERT: D 436 VAL cc_start: 0.9423 (m) cc_final: 0.9191 (p) REVERT: D 440 MET cc_start: 0.7903 (tmm) cc_final: 0.7639 (mmm) REVERT: D 474 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5913 (ptt) REVERT: D 481 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7423 (ttm) REVERT: D 483 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6203 (tp40) outliers start: 81 outliers final: 46 residues processed: 539 average time/residue: 0.1216 time to fit residues: 104.6730 Evaluate side-chains 522 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 463 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 208 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS C 572 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113319 restraints weight = 38213.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115175 restraints weight = 25703.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116420 restraints weight = 19433.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117182 restraints weight = 16077.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117188 restraints weight = 14332.668| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.8203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 19484 Z= 0.293 Angle : 0.972 15.233 26440 Z= 0.471 Chirality : 0.052 0.252 3012 Planarity : 0.005 0.049 3336 Dihedral : 5.633 50.808 2598 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.02 % Allowed : 25.48 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 2356 helix: 0.31 (0.14), residues: 1380 sheet: -0.93 (0.65), residues: 56 loop : -2.18 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 305 TYR 0.025 0.002 TYR B 216 PHE 0.038 0.003 PHE C 478 TRP 0.028 0.003 TRP D 29 HIS 0.007 0.002 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00682 (19484) covalent geometry : angle 0.97224 (26440) hydrogen bonds : bond 0.04410 ( 960) hydrogen bonds : angle 4.93174 ( 2760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 477 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.7219 (m-30) cc_final: 0.6756 (m-30) REVERT: A 107 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: A 497 MET cc_start: 0.7158 (ttp) cc_final: 0.6763 (ttp) REVERT: A 583 TRP cc_start: 0.8228 (t60) cc_final: 0.7889 (t60) REVERT: A 629 TRP cc_start: 0.7807 (m-10) cc_final: 0.7442 (m-10) REVERT: B 107 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: B 228 HIS cc_start: 0.5840 (m-70) cc_final: 0.4854 (p-80) REVERT: B 281 THR cc_start: 0.8409 (m) cc_final: 0.7992 (p) REVERT: B 301 LYS cc_start: 0.7214 (mtmt) cc_final: 0.6995 (mmtm) REVERT: B 315 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: B 390 LEU cc_start: 0.8679 (mt) cc_final: 0.8272 (tp) REVERT: B 464 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8029 (t0) REVERT: B 474 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.6027 (ptt) REVERT: B 629 TRP cc_start: 0.7945 (m-10) cc_final: 0.7634 (m-10) REVERT: C 34 ASP cc_start: 0.7009 (m-30) cc_final: 0.6694 (m-30) REVERT: C 44 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7318 (mp) REVERT: C 107 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: C 261 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8332 (tm-30) REVERT: C 297 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7874 (tp) REVERT: C 390 LEU cc_start: 0.8362 (mp) cc_final: 0.8011 (tp) REVERT: C 454 MET cc_start: 0.8543 (tpp) cc_final: 0.8144 (tpp) REVERT: C 483 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6381 (tp40) REVERT: C 583 TRP cc_start: 0.7986 (t60) cc_final: 0.7674 (t60) REVERT: C 629 TRP cc_start: 0.8299 (m100) cc_final: 0.7160 (m100) REVERT: D 34 ASP cc_start: 0.7292 (m-30) cc_final: 0.7083 (m-30) REVERT: D 228 HIS cc_start: 0.5420 (m-70) cc_final: 0.4438 (p-80) REVERT: D 260 MET cc_start: 0.8265 (tpp) cc_final: 0.7994 (tpp) REVERT: D 261 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8130 (tm-30) REVERT: D 294 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 301 LYS cc_start: 0.7606 (mtmt) cc_final: 0.7287 (mmtt) REVERT: D 440 MET cc_start: 0.8014 (tmm) cc_final: 0.7756 (mmm) REVERT: D 474 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6383 (ptt) REVERT: D 481 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (ttm) REVERT: D 483 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6194 (tp40) outliers start: 83 outliers final: 43 residues processed: 525 average time/residue: 0.1283 time to fit residues: 105.2045 Evaluate side-chains 479 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 424 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 4 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 464 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119989 restraints weight = 37316.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120944 restraints weight = 24249.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121642 restraints weight = 19196.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122483 restraints weight = 15476.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122593 restraints weight = 15362.654| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.8286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 19484 Z= 0.163 Angle : 0.892 16.054 26440 Z= 0.420 Chirality : 0.046 0.241 3012 Planarity : 0.004 0.047 3336 Dihedral : 5.371 50.470 2598 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.86 % Allowed : 28.34 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2356 helix: 0.40 (0.14), residues: 1404 sheet: -1.11 (0.62), residues: 56 loop : -2.25 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 615 TYR 0.022 0.002 TYR C 339 PHE 0.034 0.002 PHE B 553 TRP 0.021 0.002 TRP D 583 HIS 0.005 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00383 (19484) covalent geometry : angle 0.89242 (26440) hydrogen bonds : bond 0.03966 ( 960) hydrogen bonds : angle 4.63148 ( 2760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 464 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.7083 (m-30) cc_final: 0.6581 (m-30) REVERT: A 107 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: A 228 HIS cc_start: 0.5793 (m-70) cc_final: 0.4677 (p-80) REVERT: A 261 GLN cc_start: 0.8464 (mm-40) cc_final: 0.7940 (tm-30) REVERT: A 294 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 339 TYR cc_start: 0.8957 (t80) cc_final: 0.8727 (t80) REVERT: A 436 VAL cc_start: 0.9400 (m) cc_final: 0.9085 (p) REVERT: A 439 THR cc_start: 0.8934 (t) cc_final: 0.8556 (m) REVERT: A 464 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7658 (t0) REVERT: A 483 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6528 (tp40) REVERT: A 497 MET cc_start: 0.7307 (ttp) cc_final: 0.6909 (ttp) REVERT: A 583 TRP cc_start: 0.8102 (t60) cc_final: 0.7865 (t60) REVERT: B 34 ASP cc_start: 0.6974 (m-30) cc_final: 0.6490 (m-30) REVERT: B 45 TRP cc_start: 0.7414 (t-100) cc_final: 0.6766 (m100) REVERT: B 107 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: B 228 HIS cc_start: 0.5817 (m-70) cc_final: 0.4754 (p-80) REVERT: B 261 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8120 (tm-30) REVERT: B 281 THR cc_start: 0.8358 (m) cc_final: 0.8038 (p) REVERT: B 301 LYS cc_start: 0.7239 (mtmt) cc_final: 0.6980 (mmtt) REVERT: B 315 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: B 390 LEU cc_start: 0.8644 (mt) cc_final: 0.8226 (tp) REVERT: B 464 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8017 (t0) REVERT: B 474 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.6014 (ptt) REVERT: B 483 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6453 (tp40) REVERT: B 583 TRP cc_start: 0.8159 (t60) cc_final: 0.7828 (t60) REVERT: C 34 ASP cc_start: 0.7078 (m-30) cc_final: 0.6775 (m-30) REVERT: C 44 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7162 (mp) REVERT: C 96 MET cc_start: 0.7888 (tmm) cc_final: 0.7638 (tmm) REVERT: C 107 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: C 250 GLU cc_start: 0.7848 (mm-30) cc_final: 0.6482 (tm-30) REVERT: C 297 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7922 (tp) REVERT: C 390 LEU cc_start: 0.8469 (mp) cc_final: 0.8114 (tp) REVERT: C 483 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6249 (tp40) REVERT: C 583 TRP cc_start: 0.7819 (t60) cc_final: 0.7394 (t60) REVERT: C 619 CYS cc_start: 0.8132 (t) cc_final: 0.7506 (p) REVERT: C 629 TRP cc_start: 0.8108 (m100) cc_final: 0.7740 (m100) REVERT: D 34 ASP cc_start: 0.7293 (m-30) cc_final: 0.7084 (m-30) REVERT: D 228 HIS cc_start: 0.5375 (m-70) cc_final: 0.4497 (p-80) REVERT: D 260 MET cc_start: 0.8216 (tpp) cc_final: 0.7926 (tpp) REVERT: D 261 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8127 (tm-30) REVERT: D 294 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 439 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8586 (m) REVERT: D 474 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6211 (ptt) REVERT: D 481 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: D 483 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6359 (tp40) REVERT: D 485 MET cc_start: 0.7703 (mtm) cc_final: 0.7471 (mtt) outliers start: 59 outliers final: 36 residues processed: 498 average time/residue: 0.1215 time to fit residues: 96.3609 Evaluate side-chains 482 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 430 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 58 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 188 optimal weight: 0.0000 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 0.0670 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 158 ASN D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123277 restraints weight = 37675.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123777 restraints weight = 23291.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124370 restraints weight = 19571.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124830 restraints weight = 16259.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124942 restraints weight = 16057.018| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.8380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19484 Z= 0.150 Angle : 0.886 15.630 26440 Z= 0.413 Chirality : 0.045 0.245 3012 Planarity : 0.004 0.041 3336 Dihedral : 5.254 51.854 2598 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.86 % Allowed : 29.36 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2356 helix: 0.60 (0.14), residues: 1400 sheet: -0.91 (0.61), residues: 56 loop : -2.22 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 492 TYR 0.040 0.002 TYR C 509 PHE 0.038 0.002 PHE A 553 TRP 0.021 0.002 TRP D 583 HIS 0.007 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00338 (19484) covalent geometry : angle 0.88590 (26440) hydrogen bonds : bond 0.03797 ( 960) hydrogen bonds : angle 4.54611 ( 2760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.34 seconds wall clock time: 58 minutes 52.11 seconds (3532.11 seconds total)