Starting phenix.real_space_refine on Mon Jun 16 15:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bo9_7121/06_2025/6bo9_7121.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bo9_7121/06_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_7121/06_2025/6bo9_7121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bo9_7121/06_2025/6bo9_7121.map" model { file = "/net/cci-nas-00/data/ceres_data/6bo9_7121/06_2025/6bo9_7121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bo9_7121/06_2025/6bo9_7121.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 10.97, per 1000 atoms: 0.58 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: 4.45 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.73 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: 5.64 Time building geometry restraints manager: 5.35 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.620 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: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.160 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.590 ------------------------------------------------------------------------------- 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 : 8.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.004 TRP C 593 HIS 0.017 0.002 HIS C 522 PHE 0.026 0.003 PHE B 425 TYR 0.024 0.003 TYR C 524 ARG 0.005 0.001 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.17592 ( 960) hydrogen bonds : angle 9.52423 ( 2760) covalent geometry : bond 0.00664 (19484) covalent geometry : angle 1.16835 (26440) *********************** 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 : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.8537 (mt) REVERT: A 279 ASP cc_start: 0.6636 (t70) cc_final: 0.6218 (t70) REVERT: A 281 THR cc_start: 0.7710 (m) cc_final: 0.7375 (p) REVERT: A 284 ASP cc_start: 0.7773 (t0) cc_final: 0.6751 (t0) REVERT: A 328 TYR cc_start: 0.6983 (m-10) cc_final: 0.6564 (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: 0.7114 (t80) REVERT: A 442 MET cc_start: 0.8034 (tpp) cc_final: 0.7707 (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: 0.6793 (t80) REVERT: A 510 ILE cc_start: 0.6949 (mt) cc_final: 0.6533 (mt) REVERT: A 546 ASN cc_start: 0.8025 (t0) cc_final: 0.7712 (t0) REVERT: A 565 ILE cc_start: 0.6733 (tp) cc_final: 0.6144 (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: 0.7579 (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: 0.6187 (mtp) REVERT: B 202 ILE cc_start: 0.8730 (mm) cc_final: 0.8463 (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: 0.7961 (m-80) REVERT: B 281 THR cc_start: 0.7751 (m) cc_final: 0.7356 (p) REVERT: B 294 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 354 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7272 (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: 0.7516 (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: 0.6429 (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: 0.6242 (tp) REVERT: B 569 LEU cc_start: 0.5766 (tt) cc_final: 0.5316 (tt) REVERT: B 583 TRP cc_start: 0.6947 (t60) cc_final: 0.6491 (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: 0.8184 (mm-40) REVERT: C 222 TYR cc_start: 0.8431 (m-80) cc_final: 0.7894 (m-80) REVERT: C 242 THR cc_start: 0.7176 (p) cc_final: 0.6952 (t) REVERT: C 246 LEU cc_start: 0.7633 (tp) cc_final: 0.7224 (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: 0.7433 (t0) REVERT: C 352 LEU cc_start: 0.7812 (mp) cc_final: 0.7265 (mm) REVERT: C 354 PRO cc_start: 0.8404 (Cg_exo) cc_final: 0.8165 (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: 0.7958 (mp) REVERT: C 434 PHE cc_start: 0.7830 (m-80) cc_final: 0.7231 (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: 0.6123 (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: 0.6661 (t) REVERT: C 546 ASN cc_start: 0.8170 (t0) cc_final: 0.7688 (t0) REVERT: C 565 ILE cc_start: 0.7008 (tp) cc_final: 0.6795 (tp) REVERT: C 569 LEU cc_start: 0.5979 (tt) cc_final: 0.5686 (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: 0.7618 (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: 0.5609 (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: 0.7168 (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: 0.7693 (ptpp) REVERT: D 279 ASP cc_start: 0.6799 (t70) cc_final: 0.6153 (t70) REVERT: D 284 ASP cc_start: 0.7912 (t0) cc_final: 0.7178 (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: 0.7600 (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: 0.5965 (ttp) REVERT: D 352 LEU cc_start: 0.7886 (mp) cc_final: 0.7512 (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: 0.7268 (Cg_endo) REVERT: D 491 MET cc_start: 0.7094 (mmm) cc_final: 0.6858 (ttp) REVERT: D 514 THR cc_start: 0.7948 (m) cc_final: 0.7642 (p) REVERT: D 522 HIS cc_start: 0.6402 (m-70) cc_final: 0.6011 (m170) REVERT: D 532 SER cc_start: 0.7199 (t) cc_final: 0.6864 (t) REVERT: D 534 PHE cc_start: 0.5598 (t80) cc_final: 0.5386 (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: 0.6771 (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: 0.3150 time to fit residues: 440.1479 Evaluate side-chains 573 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 570 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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 199 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 214 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 257 GLN B 365 ASN B 522 HIS B 546 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 206 GLN C 257 GLN C 265 HIS 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.162122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137677 restraints weight = 37862.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139001 restraints weight = 27567.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139977 restraints weight = 19790.228| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19484 Z= 0.155 Angle : 0.805 12.319 26440 Z= 0.394 Chirality : 0.044 0.244 3012 Planarity : 0.005 0.037 3336 Dihedral : 5.974 48.639 2600 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.38 % Favored : 90.58 % Rotamer: Outliers : 3.73 % Allowed : 15.50 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 2356 helix: -0.50 (0.13), residues: 1380 sheet: -4.71 (0.30), residues: 56 loop : -2.62 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 629 HIS 0.006 0.001 HIS C 201 PHE 0.031 0.002 PHE C 531 TYR 0.025 0.002 TYR A 270 ARG 0.005 0.001 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 960) hydrogen bonds : angle 5.06421 ( 2760) covalent geometry : bond 0.00344 (19484) covalent geometry : angle 0.80451 (26440) *********************** 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 721 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 644 time to evaluate : 2.310 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: A 34 ASP cc_start: 0.6622 (m-30) cc_final: 0.6348 (m-30) REVERT: A 244 PHE cc_start: 0.7846 (t80) cc_final: 0.7635 (t80) REVERT: A 279 ASP cc_start: 0.7466 (t70) cc_final: 0.7080 (t70) REVERT: A 281 THR cc_start: 0.8120 (m) cc_final: 0.7740 (p) REVERT: A 456 PHE cc_start: 0.8172 (m-10) cc_final: 0.7896 (m-80) REVERT: A 464 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (t0) REVERT: A 534 PHE cc_start: 0.7630 (t80) cc_final: 0.7398 (t80) REVERT: A 565 ILE cc_start: 0.9339 (tp) cc_final: 0.9114 (tp) REVERT: A 583 TRP cc_start: 0.7427 (t60) cc_final: 0.7037 (t60) REVERT: B 44 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6494 (mp) REVERT: B 107 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: B 281 THR cc_start: 0.8186 (m) cc_final: 0.7856 (p) REVERT: B 328 TYR cc_start: 0.7681 (m-10) cc_final: 0.7382 (m-10) REVERT: B 429 ILE cc_start: 0.8435 (mt) cc_final: 0.8096 (mt) REVERT: B 464 ASN cc_start: 0.7779 (t160) cc_final: 0.7459 (t0) REVERT: B 565 ILE cc_start: 0.8973 (tp) cc_final: 0.8728 (tp) REVERT: C 339 TYR cc_start: 0.8601 (t80) cc_final: 0.8278 (t80) REVERT: C 464 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7281 (t0) REVERT: C 525 ASP cc_start: 0.7495 (p0) cc_final: 0.7282 (p0) REVERT: C 565 ILE cc_start: 0.9056 (tp) cc_final: 0.8836 (tp) REVERT: C 583 TRP cc_start: 0.7680 (t60) cc_final: 0.7248 (t60) REVERT: C 616 SER cc_start: 0.8241 (t) cc_final: 0.7939 (p) REVERT: D 40 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8558 (tm-30) REVERT: D 44 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7242 (mp) REVERT: D 180 ARG cc_start: 0.7377 (ptp90) cc_final: 0.7133 (ptp-170) REVERT: D 260 MET cc_start: 0.8262 (tpp) cc_final: 0.8038 (tpp) REVERT: D 277 LEU cc_start: 0.8026 (tp) cc_final: 0.7803 (mt) REVERT: D 321 TRP cc_start: 0.8129 (t-100) cc_final: 0.7737 (t-100) REVERT: D 440 MET cc_start: 0.7795 (tmm) cc_final: 0.7189 (tpp) REVERT: D 464 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7558 (t0) REVERT: D 467 TYR cc_start: 0.7740 (t80) cc_final: 0.7498 (t80) REVERT: D 583 TRP cc_start: 0.7575 (t60) cc_final: 0.7277 (t60) outliers start: 77 outliers final: 29 residues processed: 692 average time/residue: 0.2910 time to fit residues: 310.8012 Evaluate side-chains 556 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 521 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 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 368 LEU Chi-restraints excluded: chain B residue 379 THR 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 308 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 VAL 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 619 CYS Chi-restraints excluded: chain D residue 44 ILE 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 452 VAL 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 24 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 154 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 73 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS B 31 GLN B 73 HIS B 118 GLN B 357 ASN C 31 GLN C 73 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 572 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN D 572 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129852 restraints weight = 37452.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131091 restraints weight = 26094.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131797 restraints weight = 20508.235| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19484 Z= 0.148 Angle : 0.767 12.381 26440 Z= 0.370 Chirality : 0.044 0.248 3012 Planarity : 0.004 0.043 3336 Dihedral : 5.477 46.878 2598 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.60 % Allowed : 19.04 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2356 helix: 0.38 (0.14), residues: 1376 sheet: -3.36 (0.44), residues: 56 loop : -2.48 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 629 HIS 0.005 0.001 HIS B 185 PHE 0.031 0.002 PHE B 531 TYR 0.021 0.002 TYR B 270 ARG 0.006 0.001 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 960) hydrogen bonds : angle 4.51194 ( 2760) covalent geometry : bond 0.00337 (19484) covalent geometry : angle 0.76667 (26440) *********************** 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 636 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 541 time to evaluate : 2.006 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: A 244 PHE cc_start: 0.8175 (t80) cc_final: 0.7744 (t80) REVERT: A 281 THR cc_start: 0.8142 (m) cc_final: 0.7906 (p) REVERT: A 294 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7382 (mm-30) REVERT: A 309 ASP cc_start: 0.7405 (t0) cc_final: 0.7175 (t0) REVERT: A 311 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8007 (p) REVERT: A 339 TYR cc_start: 0.8360 (t80) cc_final: 0.8010 (t80) REVERT: A 425 PHE cc_start: 0.7351 (m-10) cc_final: 0.7007 (m-10) REVERT: A 428 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8634 (tp) REVERT: A 492 ARG cc_start: 0.7467 (ptt90) cc_final: 0.7189 (ptt90) REVERT: A 583 TRP cc_start: 0.7607 (t60) cc_final: 0.7305 (t60) REVERT: B 44 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6489 (mp) REVERT: B 45 TRP cc_start: 0.6983 (t-100) cc_final: 0.6701 (m100) REVERT: B 107 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: B 214 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: B 281 THR cc_start: 0.8295 (m) cc_final: 0.7907 (p) REVERT: B 294 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7240 (mm-30) REVERT: B 464 ASN cc_start: 0.7927 (t160) cc_final: 0.7489 (t0) REVERT: B 526 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7601 (t80) REVERT: C 281 THR cc_start: 0.8661 (m) cc_final: 0.8346 (p) REVERT: C 282 GLU cc_start: 0.7958 (mp0) cc_final: 0.7707 (tt0) REVERT: C 311 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8038 (p) REVERT: C 339 TYR cc_start: 0.8709 (t80) cc_final: 0.8219 (t80) REVERT: C 467 TYR cc_start: 0.7897 (t80) cc_final: 0.7678 (t80) REVERT: C 583 TRP cc_start: 0.7688 (t60) cc_final: 0.7195 (t60) REVERT: C 616 SER cc_start: 0.8599 (t) cc_final: 0.8305 (p) REVERT: C 629 TRP cc_start: 0.7515 (m-10) cc_final: 0.7301 (m100) REVERT: D 40 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8774 (tm-30) REVERT: D 44 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7236 (mp) REVERT: D 118 GLN cc_start: 0.6354 (tm-30) cc_final: 0.6112 (tm-30) REVERT: D 260 MET cc_start: 0.8370 (tpp) cc_final: 0.8123 (tpp) REVERT: D 440 MET cc_start: 0.7738 (tmm) cc_final: 0.7438 (tpp) REVERT: D 528 MET cc_start: 0.8101 (tmm) cc_final: 0.7805 (tmm) REVERT: D 583 TRP cc_start: 0.7645 (t60) cc_final: 0.7247 (t60) outliers start: 95 outliers final: 45 residues processed: 593 average time/residue: 0.2772 time to fit residues: 257.5371 Evaluate side-chains 542 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 489 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 428 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 549 VAL 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 143 VAL Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 279 ASP 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 456 PHE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 526 TYR 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 159 LEU 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 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 254 VAL Chi-restraints excluded: chain D residue 279 ASP 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 456 PHE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 541 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 79 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 464 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 267 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 464 ASN C 546 ASN C 596 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 D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130244 restraints weight = 37946.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130881 restraints weight = 25519.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131282 restraints weight = 20487.078| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19484 Z= 0.135 Angle : 0.750 13.728 26440 Z= 0.356 Chirality : 0.044 0.244 3012 Planarity : 0.004 0.043 3336 Dihedral : 5.275 46.971 2598 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.55 % Allowed : 19.77 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2356 helix: 0.66 (0.14), residues: 1392 sheet: -2.37 (0.58), residues: 56 loop : -2.36 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 629 HIS 0.005 0.001 HIS D 582 PHE 0.028 0.002 PHE B 531 TYR 0.034 0.002 TYR D 526 ARG 0.005 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 960) hydrogen bonds : angle 4.32856 ( 2760) covalent geometry : bond 0.00309 (19484) covalent geometry : angle 0.74966 (26440) *********************** 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 613 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 519 time to evaluate : 2.187 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: A 44 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6823 (mp) REVERT: A 107 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: A 174 ASN cc_start: 0.6475 (t0) cc_final: 0.6202 (t0) REVERT: A 244 PHE cc_start: 0.8172 (t80) cc_final: 0.7820 (t80) REVERT: A 281 THR cc_start: 0.8218 (m) cc_final: 0.7713 (p) REVERT: A 282 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6824 (mm-30) REVERT: A 294 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7330 (mm-30) REVERT: A 331 MET cc_start: 0.6430 (mtt) cc_final: 0.6105 (mtt) REVERT: A 339 TYR cc_start: 0.8442 (t80) cc_final: 0.7947 (t80) REVERT: A 492 ARG cc_start: 0.7387 (ptt90) cc_final: 0.7137 (ptt90) REVERT: A 583 TRP cc_start: 0.7612 (t60) cc_final: 0.7329 (t60) REVERT: B 44 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6698 (mp) REVERT: B 45 TRP cc_start: 0.7038 (t-100) cc_final: 0.6710 (m100) REVERT: B 107 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: B 281 THR cc_start: 0.8287 (m) cc_final: 0.8031 (p) REVERT: B 294 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7140 (mm-30) REVERT: B 307 ILE cc_start: 0.8901 (mm) cc_final: 0.8686 (mm) REVERT: B 464 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 526 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7609 (t80) REVERT: C 107 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6585 (m-80) REVERT: C 261 GLN cc_start: 0.8779 (mm-40) cc_final: 0.7914 (tp40) REVERT: C 281 THR cc_start: 0.8614 (m) cc_final: 0.8356 (p) REVERT: C 339 TYR cc_start: 0.8754 (t80) cc_final: 0.8074 (t80) REVERT: C 502 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8989 (mm) REVERT: C 515 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 520 LEU cc_start: 0.8696 (mt) cc_final: 0.8334 (mp) REVERT: C 583 TRP cc_start: 0.7679 (t60) cc_final: 0.7181 (t60) REVERT: C 616 SER cc_start: 0.8558 (t) cc_final: 0.8273 (p) REVERT: D 44 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7359 (mp) REVERT: D 260 MET cc_start: 0.8300 (tpp) cc_final: 0.7835 (tpp) REVERT: D 261 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7996 (tm-30) REVERT: D 440 MET cc_start: 0.7740 (tmm) cc_final: 0.7505 (tpp) REVERT: D 583 TRP cc_start: 0.7668 (t60) cc_final: 0.7269 (t60) outliers start: 94 outliers final: 40 residues processed: 578 average time/residue: 0.2793 time to fit residues: 252.9735 Evaluate side-chains 531 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 482 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 CYS 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 549 VAL 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 254 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 342 CYS 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 464 ASN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR 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 472 PHE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 564 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 297 ILE Chi-restraints excluded: chain D residue 308 LEU 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 456 PHE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 511 ILE 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 122 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 306 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 257 GLN B 596 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3953 r_free = 0.3953 target = 0.155892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127909 restraints weight = 37918.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130094 restraints weight = 24782.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131209 restraints weight = 18512.803| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19484 Z= 0.130 Angle : 0.745 13.914 26440 Z= 0.354 Chirality : 0.043 0.185 3012 Planarity : 0.004 0.036 3336 Dihedral : 5.122 48.389 2598 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.12 % Allowed : 21.46 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2356 helix: 0.76 (0.14), residues: 1412 sheet: -1.63 (0.62), residues: 56 loop : -2.33 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 613 HIS 0.004 0.001 HIS D 582 PHE 0.025 0.002 PHE C 256 TYR 0.032 0.001 TYR D 526 ARG 0.007 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 960) hydrogen bonds : angle 4.22996 ( 2760) covalent geometry : bond 0.00294 (19484) covalent geometry : angle 0.74461 (26440) *********************** 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 597 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 512 time to evaluate : 2.309 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: 0.7315 (OUTLIER) cc_final: 0.6996 (mp) REVERT: A 107 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: A 244 PHE cc_start: 0.8240 (t80) cc_final: 0.7891 (t80) REVERT: A 281 THR cc_start: 0.8199 (m) cc_final: 0.7628 (p) REVERT: A 282 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 294 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7269 (mm-30) REVERT: A 339 TYR cc_start: 0.8571 (t80) cc_final: 0.7979 (t80) REVERT: A 492 ARG cc_start: 0.7401 (ptt90) cc_final: 0.7139 (ptt90) REVERT: A 583 TRP cc_start: 0.7645 (t60) cc_final: 0.7356 (t60) REVERT: B 44 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6770 (mp) REVERT: B 45 TRP cc_start: 0.7118 (t-100) cc_final: 0.6777 (m100) REVERT: B 107 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: B 218 LEU cc_start: 0.8818 (tp) cc_final: 0.8494 (tp) REVERT: B 241 LEU cc_start: 0.7774 (mm) cc_final: 0.7506 (mm) REVERT: B 281 THR cc_start: 0.8438 (m) cc_final: 0.7800 (p) REVERT: B 282 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 294 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7093 (mm-30) REVERT: B 307 ILE cc_start: 0.8884 (mm) cc_final: 0.8655 (mm) REVERT: B 315 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 464 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7656 (t0) REVERT: B 467 TYR cc_start: 0.8034 (t80) cc_final: 0.7493 (t80) REVERT: B 526 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7604 (t80) REVERT: B 603 MET cc_start: 0.7434 (tmm) cc_final: 0.7209 (tmm) REVERT: C 107 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: C 261 GLN cc_start: 0.8755 (mm-40) cc_final: 0.7753 (tm-30) REVERT: C 281 THR cc_start: 0.8673 (m) cc_final: 0.8460 (p) REVERT: C 315 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: C 339 TYR cc_start: 0.8759 (t80) cc_final: 0.8068 (t80) REVERT: C 583 TRP cc_start: 0.7633 (t60) cc_final: 0.7394 (t60) REVERT: C 616 SER cc_start: 0.8571 (t) cc_final: 0.8301 (p) REVERT: D 34 ASP cc_start: 0.7164 (m-30) cc_final: 0.6955 (t0) REVERT: D 44 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7517 (mp) REVERT: D 218 LEU cc_start: 0.8974 (tp) cc_final: 0.8456 (tp) REVERT: D 260 MET cc_start: 0.8219 (tpp) cc_final: 0.7850 (tpp) REVERT: D 261 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7976 (tm-30) REVERT: D 301 LYS cc_start: 0.7176 (mtmt) cc_final: 0.6630 (mmtt) REVERT: D 440 MET cc_start: 0.7842 (tmm) cc_final: 0.7572 (tpp) REVERT: D 583 TRP cc_start: 0.7737 (t60) cc_final: 0.7358 (t60) outliers start: 85 outliers final: 40 residues processed: 557 average time/residue: 0.2780 time to fit residues: 243.5438 Evaluate side-chains 522 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 472 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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 342 CYS 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 441 VAL Chi-restraints excluded: chain A residue 456 PHE 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 315 GLU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 342 CYS 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 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 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 254 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 342 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 456 PHE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 511 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 134 optimal weight: 0.1980 chunk 81 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 168 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 258 HIS A 464 ASN B 40 GLN B 257 GLN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.156295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130473 restraints weight = 38162.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131232 restraints weight = 24697.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131431 restraints weight = 19347.695| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19484 Z= 0.126 Angle : 0.733 13.788 26440 Z= 0.346 Chirality : 0.042 0.185 3012 Planarity : 0.004 0.034 3336 Dihedral : 5.044 49.812 2598 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.02 % Allowed : 22.63 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2356 helix: 0.94 (0.14), residues: 1380 sheet: -1.41 (0.63), residues: 56 loop : -2.19 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 613 HIS 0.003 0.001 HIS B 582 PHE 0.033 0.002 PHE B 434 TYR 0.030 0.001 TYR A 526 ARG 0.007 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 960) hydrogen bonds : angle 4.16817 ( 2760) covalent geometry : bond 0.00278 (19484) covalent geometry : angle 0.73291 (26440) *********************** 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 571 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 488 time to evaluate : 2.200 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 107 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: A 244 PHE cc_start: 0.8296 (t80) cc_final: 0.7965 (t80) REVERT: A 281 THR cc_start: 0.8391 (m) cc_final: 0.7858 (p) REVERT: A 294 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7222 (mm-30) REVERT: A 315 GLU cc_start: 0.8002 (mp0) cc_final: 0.7745 (mp0) REVERT: A 339 TYR cc_start: 0.8571 (t80) cc_final: 0.8010 (t80) REVERT: A 456 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8199 (t80) REVERT: A 583 TRP cc_start: 0.7623 (t60) cc_final: 0.7369 (t60) REVERT: B 44 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6821 (mp) REVERT: B 45 TRP cc_start: 0.7107 (t-100) cc_final: 0.6800 (m100) REVERT: B 107 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: B 118 GLN cc_start: 0.4949 (tt0) cc_final: 0.4749 (tt0) REVERT: B 261 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7899 (tm-30) REVERT: B 281 THR cc_start: 0.8405 (m) cc_final: 0.7704 (p) REVERT: B 282 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 294 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7062 (mm-30) REVERT: B 307 ILE cc_start: 0.8810 (mm) cc_final: 0.8604 (mm) REVERT: B 315 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: B 456 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8100 (t80) REVERT: B 464 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7582 (t0) REVERT: B 526 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7639 (t80) REVERT: C 107 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: C 261 GLN cc_start: 0.8764 (mm-40) cc_final: 0.7894 (tm-30) REVERT: C 307 ILE cc_start: 0.8943 (mm) cc_final: 0.8713 (mm) REVERT: C 315 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 339 TYR cc_start: 0.8787 (t80) cc_final: 0.8075 (t80) REVERT: C 440 MET cc_start: 0.6893 (tpp) cc_final: 0.6559 (tpp) REVERT: C 583 TRP cc_start: 0.7730 (t60) cc_final: 0.7440 (t60) REVERT: C 616 SER cc_start: 0.8562 (t) cc_final: 0.8320 (p) REVERT: D 34 ASP cc_start: 0.7238 (m-30) cc_final: 0.7025 (t0) REVERT: D 220 LEU cc_start: 0.8336 (mm) cc_final: 0.8108 (mm) REVERT: D 261 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7973 (tm-30) REVERT: D 294 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7528 (mm-30) REVERT: D 301 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6649 (mmtt) REVERT: D 373 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.5681 (tt) REVERT: D 440 MET cc_start: 0.7751 (tmm) cc_final: 0.7532 (tpp) REVERT: D 474 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5697 (ptt) REVERT: D 583 TRP cc_start: 0.7763 (t60) cc_final: 0.7375 (t60) outliers start: 83 outliers final: 43 residues processed: 538 average time/residue: 0.2728 time to fit residues: 232.3690 Evaluate side-chains 515 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 460 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 CYS 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 441 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 464 ASN 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 342 CYS 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 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 B residue 526 TYR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 368 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 501 ILE 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 297 ILE Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 373 LEU 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 456 PHE 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 511 ILE 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 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 0.0270 chunk 113 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 572 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN D 127 ASN D 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127131 restraints weight = 37933.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129322 restraints weight = 25018.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130803 restraints weight = 18600.955| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19484 Z= 0.130 Angle : 0.753 15.479 26440 Z= 0.354 Chirality : 0.043 0.197 3012 Planarity : 0.004 0.034 3336 Dihedral : 5.024 50.687 2598 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.88 % Allowed : 23.30 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2356 helix: 1.02 (0.14), residues: 1400 sheet: -1.10 (0.64), residues: 56 loop : -2.15 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 613 HIS 0.004 0.001 HIS D 522 PHE 0.027 0.001 PHE B 434 TYR 0.018 0.001 TYR B 216 ARG 0.010 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 960) hydrogen bonds : angle 4.18763 ( 2760) covalent geometry : bond 0.00292 (19484) covalent geometry : angle 0.75278 (26440) *********************** 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 563 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 483 time to evaluate : 2.772 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 107 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: A 281 THR cc_start: 0.8668 (m) cc_final: 0.8171 (p) REVERT: A 315 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 339 TYR cc_start: 0.8680 (t80) cc_final: 0.8102 (t80) REVERT: A 456 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8185 (t80) REVERT: A 583 TRP cc_start: 0.7674 (t60) cc_final: 0.7398 (t60) REVERT: B 45 TRP cc_start: 0.7187 (t-100) cc_final: 0.6858 (m100) REVERT: B 107 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: B 110 MET cc_start: 0.7852 (mmm) cc_final: 0.7509 (mmm) REVERT: B 130 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4753 (mmm) REVERT: B 241 LEU cc_start: 0.7634 (mm) cc_final: 0.7269 (mm) REVERT: B 261 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7982 (tm-30) REVERT: B 281 THR cc_start: 0.8355 (m) cc_final: 0.7619 (p) REVERT: B 282 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 315 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: B 464 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7672 (t0) REVERT: B 467 TYR cc_start: 0.8141 (t80) cc_final: 0.7713 (t80) REVERT: B 526 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7801 (t80) REVERT: B 542 ASP cc_start: 0.7140 (m-30) cc_final: 0.6588 (m-30) REVERT: B 580 ASP cc_start: 0.8414 (m-30) cc_final: 0.8175 (t0) REVERT: B 603 MET cc_start: 0.7548 (tmm) cc_final: 0.7267 (tmm) REVERT: C 34 ASP cc_start: 0.6919 (m-30) cc_final: 0.6547 (m-30) REVERT: C 107 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6768 (m-80) REVERT: C 174 ASN cc_start: 0.7561 (m110) cc_final: 0.7218 (t0) REVERT: C 228 HIS cc_start: 0.5230 (m-70) cc_final: 0.4671 (p-80) REVERT: C 261 GLN cc_start: 0.8770 (mm-40) cc_final: 0.7999 (tm-30) REVERT: C 280 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7374 (tt) REVERT: C 294 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7475 (mm-30) REVERT: C 315 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: C 339 TYR cc_start: 0.8816 (t80) cc_final: 0.8255 (t80) REVERT: C 390 LEU cc_start: 0.8318 (mp) cc_final: 0.7978 (tp) REVERT: C 440 MET cc_start: 0.7038 (tpp) cc_final: 0.6754 (tpp) REVERT: C 515 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 583 TRP cc_start: 0.7663 (t60) cc_final: 0.7401 (t60) REVERT: D 34 ASP cc_start: 0.7137 (m-30) cc_final: 0.6857 (t0) REVERT: D 260 MET cc_start: 0.7999 (tpp) cc_final: 0.7612 (tpp) REVERT: D 261 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8001 (tm-30) REVERT: D 294 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7505 (mm-30) REVERT: D 440 MET cc_start: 0.7779 (tmm) cc_final: 0.7458 (mmm) REVERT: D 474 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5716 (ptt) REVERT: D 542 ASP cc_start: 0.7312 (m-30) cc_final: 0.6943 (m-30) REVERT: D 583 TRP cc_start: 0.7885 (t60) cc_final: 0.7504 (t60) REVERT: D 632 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7801 (ptt90) REVERT: D 634 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8184 (mt-10) outliers start: 80 outliers final: 39 residues processed: 525 average time/residue: 0.3237 time to fit residues: 268.3010 Evaluate side-chains 508 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 456 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 GLU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 368 LEU 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 456 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 342 CYS 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 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 B residue 526 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 315 GLU 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 456 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 81 THR 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 372 LEU 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 460 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 155 optimal weight: 0.0050 chunk 231 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 185 HIS C 257 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.155000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128364 restraints weight = 37215.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129027 restraints weight = 25180.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129295 restraints weight = 20418.838| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19484 Z= 0.135 Angle : 0.784 15.508 26440 Z= 0.368 Chirality : 0.043 0.199 3012 Planarity : 0.004 0.063 3336 Dihedral : 5.029 49.964 2598 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.25 % Allowed : 24.27 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2356 helix: 0.99 (0.14), residues: 1384 sheet: -0.90 (0.63), residues: 56 loop : -2.15 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 629 HIS 0.004 0.001 HIS D 522 PHE 0.035 0.002 PHE C 434 TYR 0.016 0.001 TYR B 216 ARG 0.011 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 960) hydrogen bonds : angle 4.21899 ( 2760) covalent geometry : bond 0.00309 (19484) covalent geometry : angle 0.78410 (26440) *********************** 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 544 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 477 time to evaluate : 2.199 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: A 34 ASP cc_start: 0.7074 (m-30) cc_final: 0.6532 (m-30) REVERT: A 107 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: A 281 THR cc_start: 0.8479 (m) cc_final: 0.8050 (p) REVERT: A 301 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6734 (mmtt) REVERT: A 315 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: A 339 TYR cc_start: 0.8632 (t80) cc_final: 0.8121 (t80) REVERT: A 456 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8300 (t80) REVERT: A 542 ASP cc_start: 0.7024 (m-30) cc_final: 0.6268 (m-30) REVERT: A 583 TRP cc_start: 0.7756 (t60) cc_final: 0.7436 (t60) REVERT: B 45 TRP cc_start: 0.7277 (t-100) cc_final: 0.6703 (m100) REVERT: B 107 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: B 130 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4686 (mmm) REVERT: B 261 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8110 (tm-30) REVERT: B 281 THR cc_start: 0.8332 (m) cc_final: 0.7604 (p) REVERT: B 282 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7025 (mm-30) REVERT: B 315 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: B 463 CYS cc_start: 0.7823 (m) cc_final: 0.7564 (m) REVERT: B 464 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7659 (t0) REVERT: B 467 TYR cc_start: 0.8088 (t80) cc_final: 0.7681 (t80) REVERT: B 526 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7898 (t80) REVERT: B 580 ASP cc_start: 0.8478 (m-30) cc_final: 0.8213 (t0) REVERT: B 603 MET cc_start: 0.7551 (tmm) cc_final: 0.7282 (tmm) REVERT: C 34 ASP cc_start: 0.6979 (m-30) cc_final: 0.6756 (m-30) REVERT: C 107 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: C 139 ARG cc_start: 0.7061 (mmt-90) cc_final: 0.6814 (mmm-85) REVERT: C 228 HIS cc_start: 0.5385 (m-70) cc_final: 0.4687 (p-80) REVERT: C 261 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8107 (tm-30) REVERT: C 294 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7513 (mm-30) REVERT: C 315 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 339 TYR cc_start: 0.8839 (t80) cc_final: 0.8272 (t80) REVERT: C 390 LEU cc_start: 0.8452 (mp) cc_final: 0.8100 (tp) REVERT: C 440 MET cc_start: 0.7003 (tpp) cc_final: 0.6709 (tpp) REVERT: C 472 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: C 515 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7037 (mm-30) REVERT: C 583 TRP cc_start: 0.7684 (t60) cc_final: 0.7432 (t60) REVERT: D 34 ASP cc_start: 0.7243 (m-30) cc_final: 0.6960 (t0) REVERT: D 173 VAL cc_start: 0.8498 (m) cc_final: 0.8271 (m) REVERT: D 218 LEU cc_start: 0.8912 (tt) cc_final: 0.8358 (mm) REVERT: D 260 MET cc_start: 0.8033 (tpp) cc_final: 0.7658 (tpp) REVERT: D 261 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8042 (tm-30) REVERT: D 294 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7519 (mm-30) REVERT: D 301 LYS cc_start: 0.7454 (mtmt) cc_final: 0.6988 (mmtt) REVERT: D 321 TRP cc_start: 0.8177 (t-100) cc_final: 0.7695 (t-100) REVERT: D 436 VAL cc_start: 0.9336 (m) cc_final: 0.8997 (p) REVERT: D 440 MET cc_start: 0.7769 (tmm) cc_final: 0.7489 (mmm) REVERT: D 583 TRP cc_start: 0.7915 (t60) cc_final: 0.7499 (t60) outliers start: 67 outliers final: 39 residues processed: 509 average time/residue: 0.2805 time to fit residues: 223.2070 Evaluate side-chains 512 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 462 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 GLU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 342 CYS 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 428 LEU 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 B residue 526 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE 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 D residue 81 THR 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 372 LEU 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 460 LEU 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 201 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 257 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.147752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118536 restraints weight = 38190.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120616 restraints weight = 25055.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122062 restraints weight = 18563.673| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19484 Z= 0.210 Angle : 0.871 17.062 26440 Z= 0.417 Chirality : 0.047 0.214 3012 Planarity : 0.004 0.047 3336 Dihedral : 5.273 51.267 2598 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.96 % Allowed : 25.34 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2356 helix: 0.72 (0.14), residues: 1372 sheet: -1.03 (0.64), residues: 56 loop : -2.02 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 29 HIS 0.005 0.001 HIS A 582 PHE 0.033 0.002 PHE A 553 TYR 0.017 0.002 TYR D 555 ARG 0.008 0.001 ARG B 615 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 960) hydrogen bonds : angle 4.53101 ( 2760) covalent geometry : bond 0.00491 (19484) covalent geometry : angle 0.87089 (26440) *********************** 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: 61 poor density : 499 time to evaluate : 2.274 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 34 ASP cc_start: 0.7132 (m-30) cc_final: 0.6607 (m-30) REVERT: A 107 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: A 139 ARG cc_start: 0.7263 (mmt-90) cc_final: 0.6828 (mmm-85) REVERT: A 228 HIS cc_start: 0.5150 (m-70) cc_final: 0.4630 (p-80) REVERT: A 281 THR cc_start: 0.8716 (m) cc_final: 0.8225 (p) REVERT: A 301 LYS cc_start: 0.7211 (mtmt) cc_final: 0.6840 (mmtt) REVERT: A 315 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: A 515 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6698 (mm-30) REVERT: A 583 TRP cc_start: 0.7976 (t60) cc_final: 0.7758 (t60) REVERT: B 107 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: B 222 TYR cc_start: 0.7132 (m-80) cc_final: 0.6925 (m-80) REVERT: B 261 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8078 (tm-30) REVERT: B 281 THR cc_start: 0.8462 (m) cc_final: 0.7698 (p) REVERT: B 282 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6959 (mm-30) REVERT: B 315 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 390 LEU cc_start: 0.8463 (mt) cc_final: 0.8219 (tp) REVERT: B 464 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7836 (t0) REVERT: B 474 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.6071 (ptt) REVERT: B 542 ASP cc_start: 0.7290 (m-30) cc_final: 0.6817 (m-30) REVERT: C 34 ASP cc_start: 0.7155 (m-30) cc_final: 0.6835 (m-30) REVERT: C 107 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: C 174 ASN cc_start: 0.8140 (m110) cc_final: 0.7416 (t0) REVERT: C 222 TYR cc_start: 0.7285 (m-80) cc_final: 0.6946 (m-80) REVERT: C 228 HIS cc_start: 0.5234 (m-70) cc_final: 0.4484 (p-80) REVERT: C 261 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8103 (tm-30) REVERT: C 294 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 301 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7683 (mtmt) REVERT: C 315 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 390 LEU cc_start: 0.8454 (mp) cc_final: 0.8123 (tp) REVERT: C 454 MET cc_start: 0.8643 (ttm) cc_final: 0.8227 (ttp) REVERT: C 465 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9080 (t) REVERT: C 583 TRP cc_start: 0.7786 (t60) cc_final: 0.7495 (t60) REVERT: D 218 LEU cc_start: 0.8758 (tt) cc_final: 0.8255 (mm) REVERT: D 228 HIS cc_start: 0.5208 (m-70) cc_final: 0.4494 (p-80) REVERT: D 260 MET cc_start: 0.8187 (tpp) cc_final: 0.7744 (tpp) REVERT: D 261 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8108 (tm-30) REVERT: D 297 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7827 (tp) REVERT: D 301 LYS cc_start: 0.7561 (mtmt) cc_final: 0.7212 (mmtt) REVERT: D 339 TYR cc_start: 0.8883 (t80) cc_final: 0.8433 (t80) REVERT: D 436 VAL cc_start: 0.9415 (m) cc_final: 0.9191 (p) REVERT: D 440 MET cc_start: 0.7950 (tmm) cc_final: 0.7614 (mmm) REVERT: D 583 TRP cc_start: 0.8010 (t60) cc_final: 0.7679 (t60) outliers start: 61 outliers final: 36 residues processed: 530 average time/residue: 0.3686 time to fit residues: 306.5744 Evaluate side-chains 508 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 462 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 218 LEU 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 426 HIS 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 81 THR 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 342 CYS Chi-restraints excluded: chain B residue 352 LEU 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 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 C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 297 ILE 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 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 475 LEU 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 165 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 201 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 257 GLN D 91 ASN D 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125611 restraints weight = 37493.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126513 restraints weight = 23157.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126699 restraints weight = 18891.070| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.7794 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= 0.145 Angle : 0.865 16.499 26440 Z= 0.404 Chirality : 0.046 0.239 3012 Planarity : 0.004 0.036 3336 Dihedral : 5.198 50.791 2598 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.62 % Allowed : 27.66 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2356 helix: 0.90 (0.14), residues: 1348 sheet: -0.93 (0.61), residues: 56 loop : -2.02 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 629 HIS 0.005 0.001 HIS D 522 PHE 0.039 0.002 PHE A 553 TYR 0.023 0.002 TYR B 467 ARG 0.008 0.000 ARG C 492 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 960) hydrogen bonds : angle 4.42646 ( 2760) covalent geometry : bond 0.00325 (19484) covalent geometry : angle 0.86541 (26440) ********************** 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 526 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 472 time to evaluate : 2.082 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: 0.7148 (m-30) cc_final: 0.6701 (m-30) REVERT: A 107 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: A 139 ARG cc_start: 0.6973 (mmt-90) cc_final: 0.6592 (mmm-85) REVERT: A 228 HIS cc_start: 0.5227 (m-70) cc_final: 0.4613 (p-80) REVERT: A 261 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7880 (tm-30) REVERT: A 281 THR cc_start: 0.8630 (m) cc_final: 0.8222 (p) REVERT: A 301 LYS cc_start: 0.7141 (mtmt) cc_final: 0.6874 (mmtt) REVERT: A 315 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: A 439 THR cc_start: 0.8777 (t) cc_final: 0.8381 (m) REVERT: A 442 MET cc_start: 0.8144 (ptp) cc_final: 0.7846 (ptm) REVERT: A 583 TRP cc_start: 0.8002 (t60) cc_final: 0.7732 (t60) REVERT: B 34 ASP cc_start: 0.7019 (m-30) cc_final: 0.6631 (m-30) REVERT: B 45 TRP cc_start: 0.6919 (t-100) cc_final: 0.6266 (m100) REVERT: B 107 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: B 110 MET cc_start: 0.7398 (mmm) cc_final: 0.7177 (mmp) REVERT: B 116 GLU cc_start: 0.7377 (mp0) cc_final: 0.6974 (mp0) REVERT: B 261 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8145 (tm-30) REVERT: B 281 THR cc_start: 0.8318 (m) cc_final: 0.7668 (p) REVERT: B 282 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7146 (mm-30) REVERT: B 294 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7002 (mm-30) REVERT: B 301 LYS cc_start: 0.7323 (mtmt) cc_final: 0.6858 (mmtt) REVERT: B 315 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: B 390 LEU cc_start: 0.8483 (mt) cc_final: 0.8202 (tp) REVERT: B 464 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7899 (t0) REVERT: B 474 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.6041 (ptt) REVERT: B 603 MET cc_start: 0.7503 (tmm) cc_final: 0.7268 (tmm) REVERT: C 34 ASP cc_start: 0.7149 (m-30) cc_final: 0.6797 (m-30) REVERT: C 107 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: C 222 TYR cc_start: 0.7190 (m-80) cc_final: 0.6905 (m-80) REVERT: C 228 HIS cc_start: 0.5280 (m-70) cc_final: 0.4575 (p-80) REVERT: C 261 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8049 (tm-30) REVERT: C 294 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 301 LYS cc_start: 0.8509 (mmtt) cc_final: 0.7676 (mtmt) REVERT: C 390 LEU cc_start: 0.8440 (mp) cc_final: 0.8095 (tp) REVERT: C 454 MET cc_start: 0.8550 (ttm) cc_final: 0.8233 (ttp) REVERT: C 483 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: C 515 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7109 (mm-30) REVERT: C 583 TRP cc_start: 0.7697 (t60) cc_final: 0.7467 (t60) REVERT: D 129 ASN cc_start: 0.5690 (t0) cc_final: 0.5367 (t0) REVERT: D 218 LEU cc_start: 0.8807 (tt) cc_final: 0.8219 (mm) REVERT: D 228 HIS cc_start: 0.5207 (m-70) cc_final: 0.4680 (p-80) REVERT: D 260 MET cc_start: 0.8083 (tpp) cc_final: 0.7703 (tpp) REVERT: D 261 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8120 (tm-30) REVERT: D 294 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7499 (mm-30) REVERT: D 301 LYS cc_start: 0.7499 (mtmt) cc_final: 0.7197 (mmtm) REVERT: D 339 TYR cc_start: 0.8839 (t80) cc_final: 0.8307 (t80) REVERT: D 390 LEU cc_start: 0.8423 (mp) cc_final: 0.8145 (tp) REVERT: D 436 VAL cc_start: 0.9373 (m) cc_final: 0.9136 (p) REVERT: D 439 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8407 (m) REVERT: D 440 MET cc_start: 0.7697 (tmm) cc_final: 0.7367 (mmm) REVERT: D 483 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6333 (tp40) outliers start: 54 outliers final: 31 residues processed: 502 average time/residue: 0.2776 time to fit residues: 218.8399 Evaluate side-chains 485 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 444 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 218 LEU 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 426 HIS Chi-restraints excluded: chain A residue 456 PHE 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 205 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU 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 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 C residue 107 PHE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE 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 91 ASN 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 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 188 optimal weight: 1.9990 chunk 197 optimal weight: 0.0470 chunk 77 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 257 GLN D 185 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121988 restraints weight = 37909.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124057 restraints weight = 24961.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125239 restraints weight = 18525.576| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.7949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19484 Z= 0.161 Angle : 0.870 16.114 26440 Z= 0.411 Chirality : 0.046 0.221 3012 Planarity : 0.004 0.035 3336 Dihedral : 5.158 51.125 2598 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.96 % Favored : 91.00 % Rotamer: Outliers : 2.33 % Allowed : 28.73 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2356 helix: 0.79 (0.14), residues: 1376 sheet: -0.84 (0.62), residues: 56 loop : -2.11 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 613 HIS 0.006 0.001 HIS D 522 PHE 0.039 0.002 PHE A 553 TYR 0.026 0.002 TYR B 467 ARG 0.007 0.001 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 960) hydrogen bonds : angle 4.45626 ( 2760) covalent geometry : bond 0.00376 (19484) covalent geometry : angle 0.87008 (26440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7057.88 seconds wall clock time: 123 minutes 48.85 seconds (7428.85 seconds total)