Starting phenix.real_space_refine on Thu Jul 2 19:32:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e1t_47420/07_2026/9e1t_47420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e1t_47420/07_2026/9e1t_47420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e1t_47420/07_2026/9e1t_47420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e1t_47420/07_2026/9e1t_47420.map" model { file = "/net/cci-nas-00/data/ceres_data/9e1t_47420/07_2026/9e1t_47420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e1t_47420/07_2026/9e1t_47420.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 56 5.16 5 C 6484 2.51 5 N 1686 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4990 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 3.21, per 1000 atoms: 0.32 Number of scatterers: 10032 At special positions: 0 Unit cell: (100.067, 95.105, 101.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 56 16.00 P 4 15.00 O 1800 8.00 N 1686 7.00 C 6484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 419 " distance=2.03 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: 0.68 Conformation dependent library (CDL) restraints added in 233.7 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 49.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 146 through 164 removed outlier: 3.755A pdb=" N HIS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.706A pdb=" N ILE A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.539A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.818A pdb=" N TYR A 220 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 223 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 225 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.966A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.996A pdb=" N GLY A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.674A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 396 through 406 removed outlier: 3.545A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.604A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 484 through 495 removed outlier: 4.099A pdb=" N LEU A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.515A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.622A pdb=" N HIS A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 removed outlier: 3.882A pdb=" N ILE A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.659A pdb=" N GLY A 633 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 635 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 636 - end of helix Processing helix chain 'A' and resid 638 through 645 removed outlier: 4.248A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 removed outlier: 3.625A pdb=" N ALA A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A 684 " --> pdb=" O ASN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'A' and resid 721 through 743 Processing helix chain 'A' and resid 744 through 750 removed outlier: 5.101A pdb=" N LYS A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 749 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 164 removed outlier: 3.756A pdb=" N HIS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.707A pdb=" N ILE B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.539A pdb=" N VAL B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.818A pdb=" N TYR B 220 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 223 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 225 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.966A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 311 through 328 removed outlier: 3.996A pdb=" N GLY B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.674A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.545A pdb=" N PHE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.604A pdb=" N PHE B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 484 through 495 removed outlier: 4.101A pdb=" N LEU B 488 " --> pdb=" O ARG B 484 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.514A pdb=" N ARG B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.621A pdb=" N HIS B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.883A pdb=" N ILE B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.660A pdb=" N GLY B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 635 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Proline residue: B 636 - end of helix Processing helix chain 'B' and resid 638 through 645 removed outlier: 4.248A pdb=" N THR B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 691 removed outlier: 3.624A pdb=" N ALA B 683 " --> pdb=" O TRP B 679 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'B' and resid 721 through 743 Processing helix chain 'B' and resid 744 through 750 removed outlier: 5.101A pdb=" N LYS B 748 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR B 749 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.389A pdb=" N ILE A 138 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS A 171 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 140 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 173 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 142 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS A 139 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 241 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 270 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY A 298 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N GLY A 268 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 247 removed outlier: 5.976A pdb=" N VAL A 358 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 removed outlier: 6.781A pdb=" N ILE A 499 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N HIS A 532 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 501 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 534 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU A 503 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER A 500 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 476 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA A 502 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA A 478 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 661 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR A 660 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG A 664 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N LYS A 590 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 695 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.925A pdb=" N PHE A 597 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.390A pdb=" N ILE B 138 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS B 171 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 140 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 173 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 142 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS B 139 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU B 241 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 141 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 270 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY B 298 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N GLY B 268 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 267 " --> pdb=" O TYR B 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 247 removed outlier: 5.976A pdb=" N VAL B 358 " --> pdb=" O HIS B 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 456 through 457 removed outlier: 6.781A pdb=" N ILE B 499 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N HIS B 532 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 501 " --> pdb=" O HIS B 532 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL B 534 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 503 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER B 500 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 476 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA B 502 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA B 478 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 661 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 660 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG B 664 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N LYS B 590 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 695 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.925A pdb=" N PHE B 597 " --> pdb=" O HIS B 705 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1068 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: 1.48 Time building geometry restraints manager: 0.92 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: 3174 1.34 - 1.46: 1883 1.46 - 1.57: 5147 1.57 - 1.69: 6 1.69 - 1.81: 94 Bond restraints: 10304 Sorted by residual: bond pdb=" N GLY B 678 " pdb=" CA GLY B 678 " ideal model delta sigma weight residual 1.449 1.464 -0.014 1.45e-02 4.76e+03 9.73e-01 bond pdb=" N GLY A 678 " pdb=" CA GLY A 678 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.75e-01 bond pdb=" CA ASN B 357 " pdb=" C ASN B 357 " ideal model delta sigma weight residual 1.533 1.526 0.007 9.60e-03 1.09e+04 5.69e-01 bond pdb=" CA ASN A 357 " pdb=" C ASN A 357 " ideal model delta sigma weight residual 1.533 1.526 0.007 9.60e-03 1.09e+04 5.44e-01 bond pdb=" CB VAL A 153 " pdb=" CG1 VAL A 153 " ideal model delta sigma weight residual 1.521 1.505 0.016 3.30e-02 9.18e+02 2.50e-01 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 13382 0.78 - 1.57: 505 1.57 - 2.35: 38 2.35 - 3.14: 47 3.14 - 3.92: 12 Bond angle restraints: 13984 Sorted by residual: angle pdb=" N ILE A 714 " pdb=" CA ILE A 714 " pdb=" C ILE A 714 " ideal model delta sigma weight residual 110.30 107.03 3.27 9.70e-01 1.06e+00 1.14e+01 angle pdb=" N ILE B 714 " pdb=" CA ILE B 714 " pdb=" C ILE B 714 " ideal model delta sigma weight residual 110.30 107.06 3.24 9.70e-01 1.06e+00 1.12e+01 angle pdb=" C ILE B 714 " pdb=" CA ILE B 714 " pdb=" CB ILE B 714 " ideal model delta sigma weight residual 111.81 115.48 -3.67 1.25e+00 6.40e-01 8.60e+00 angle pdb=" C ILE A 714 " pdb=" CA ILE A 714 " pdb=" CB ILE A 714 " ideal model delta sigma weight residual 111.81 115.43 -3.62 1.25e+00 6.40e-01 8.38e+00 angle pdb=" N THR A 715 " pdb=" CA THR A 715 " pdb=" C THR A 715 " ideal model delta sigma weight residual 111.11 114.39 -3.28 1.20e+00 6.94e-01 7.49e+00 ... (remaining 13979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 5816 15.28 - 30.56: 232 30.56 - 45.84: 52 45.84 - 61.12: 14 61.12 - 76.40: 22 Dihedral angle restraints: 6136 sinusoidal: 2552 harmonic: 3584 Sorted by residual: dihedral pdb=" CA TYR A 660 " pdb=" C TYR A 660 " pdb=" N VAL A 661 " pdb=" CA VAL A 661 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA TYR B 660 " pdb=" C TYR B 660 " pdb=" N VAL B 661 " pdb=" CA VAL B 661 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 661 " pdb=" C VAL A 661 " pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 896 0.027 - 0.053: 402 0.053 - 0.080: 125 0.080 - 0.106: 51 0.106 - 0.133: 36 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA VAL A 662 " pdb=" N VAL A 662 " pdb=" C VAL A 662 " pdb=" CB VAL A 662 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B 662 " pdb=" N VAL B 662 " pdb=" C VAL B 662 " pdb=" CB VAL B 662 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE B 211 " pdb=" N ILE B 211 " pdb=" C ILE B 211 " pdb=" CB ILE B 211 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1507 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 352 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO A 353 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 352 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 353 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 353 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 353 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 338 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.03e+00 pdb=" C PHE A 338 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE A 338 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 339 " -0.006 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 144 2.67 - 3.23: 9315 3.23 - 3.78: 15393 3.78 - 4.34: 22488 4.34 - 4.90: 36518 Nonbonded interactions: 83858 Sorted by model distance: nonbonded pdb=" OH TYR A 602 " pdb=" OH TYR B 602 " model vdw 2.108 3.040 nonbonded pdb="MN MN B 801 " pdb=" O1B UDP B 802 " model vdw 2.172 3.060 nonbonded pdb="MN MN A 900 " pdb=" O1B UDP A 901 " model vdw 2.173 3.060 nonbonded pdb=" O PHE B 677 " pdb=" OH TYR B 723 " model vdw 2.183 3.040 nonbonded pdb=" O PHE A 677 " pdb=" OH TYR A 723 " model vdw 2.183 3.040 ... (remaining 83853 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.002 0.016 10306 Z= 0.092 Angle : 0.379 3.925 13988 Z= 0.215 Chirality : 0.039 0.133 1510 Planarity : 0.003 0.028 1758 Dihedral : 10.616 76.403 3810 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1192 helix: 0.64 (0.26), residues: 464 sheet: -0.12 (0.40), residues: 166 loop : 0.49 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.009 0.001 TYR A 573 PHE 0.006 0.001 PHE B 355 TRP 0.008 0.001 TRP B 316 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (10304) covalent geometry : angle 0.37942 / 0.22 (13984) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 0.35680 / 0.18 ( 4) hydrogen bonds : bond 0.15558 / 10.98 ( 386) hydrogen bonds : angle 6.26236 / 4.67 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8347 (tt0) cc_final: 0.8139 (tm-30) REVERT: A 220 TYR cc_start: 0.7220 (m-80) cc_final: 0.7015 (m-80) REVERT: A 275 ASP cc_start: 0.7277 (m-30) cc_final: 0.6999 (p0) REVERT: A 291 LEU cc_start: 0.7120 (tt) cc_final: 0.6193 (mm) REVERT: A 425 VAL cc_start: 0.8281 (t) cc_final: 0.7886 (p) REVERT: B 179 GLU cc_start: 0.8444 (tt0) cc_final: 0.8235 (tm-30) REVERT: B 230 THR cc_start: 0.8366 (m) cc_final: 0.8140 (p) REVERT: B 275 ASP cc_start: 0.7227 (m-30) cc_final: 0.6989 (p0) REVERT: B 291 LEU cc_start: 0.7245 (tt) cc_final: 0.6342 (mm) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.4449 time to fit residues: 121.7059 Evaluate side-chains 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS A 264 GLN A 335 GLN A 359 GLN A 494 HIS A 553 HIS A 634 HIS A 705 HIS B 163 HIS B 169 HIS ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 359 GLN B 494 HIS B 553 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120986 restraints weight = 13724.439| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.67 r_work: 0.3434 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10306 Z= 0.178 Angle : 0.554 9.542 13988 Z= 0.295 Chirality : 0.043 0.141 1510 Planarity : 0.004 0.028 1758 Dihedral : 10.905 87.387 1400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.87 % Allowed : 11.30 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1192 helix: 0.52 (0.24), residues: 468 sheet: -0.47 (0.43), residues: 160 loop : 0.39 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.011 0.002 TYR B 558 PHE 0.019 0.002 PHE A 355 TRP 0.017 0.001 TRP B 316 HIS 0.005 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (10304) covalent geometry : angle 0.55454 / 0.30 (13984) SS BOND : bond 0.00111 / 0.06 ( 2) SS BOND : angle 0.04275 / 0.02 ( 4) hydrogen bonds : bond 0.04161 / 2.84 ( 386) hydrogen bonds : angle 4.93201 / 3.71 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.371 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: A 275 ASP cc_start: 0.7297 (m-30) cc_final: 0.7029 (p0) REVERT: A 291 LEU cc_start: 0.7100 (tt) cc_final: 0.6354 (mm) REVERT: A 402 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6958 (mp) REVERT: B 291 LEU cc_start: 0.7221 (tt) cc_final: 0.6530 (mm) REVERT: B 339 ASN cc_start: 0.7185 (m-40) cc_final: 0.6863 (m-40) REVERT: B 425 VAL cc_start: 0.8379 (p) cc_final: 0.7568 (p) REVERT: B 602 TYR cc_start: 0.6890 (m-80) cc_final: 0.6497 (m-10) REVERT: B 749 TYR cc_start: 0.7432 (m-80) cc_final: 0.7190 (m-80) outliers start: 31 outliers final: 7 residues processed: 184 average time/residue: 0.3935 time to fit residues: 78.5006 Evaluate side-chains 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS A 457 HIS B 457 HIS B 634 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.152413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119382 restraints weight = 13878.386| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.46 r_work: 0.3391 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10306 Z= 0.294 Angle : 0.633 7.706 13988 Z= 0.340 Chirality : 0.047 0.155 1510 Planarity : 0.005 0.054 1758 Dihedral : 11.078 89.329 1400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.26 % Allowed : 12.87 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1192 helix: 0.02 (0.23), residues: 460 sheet: -0.67 (0.43), residues: 140 loop : -0.10 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 665 TYR 0.026 0.003 TYR A 723 PHE 0.020 0.002 PHE B 460 TRP 0.017 0.002 TRP B 316 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.29 (10304) covalent geometry : angle 0.63279 / 0.34 (13984) SS BOND : bond 0.00117 / 0.06 ( 2) SS BOND : angle 0.64768 / 0.33 ( 4) hydrogen bonds : bond 0.04822 / 3.32 ( 386) hydrogen bonds : angle 5.02909 / 3.67 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6419 (pm20) REVERT: A 275 ASP cc_start: 0.7334 (m-30) cc_final: 0.7066 (p0) REVERT: A 291 LEU cc_start: 0.7195 (tt) cc_final: 0.6290 (mm) REVERT: A 338 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 402 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6971 (mp) REVERT: B 220 TYR cc_start: 0.7693 (m-80) cc_final: 0.7467 (m-80) REVERT: B 264 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6175 (pm20) REVERT: B 291 LEU cc_start: 0.7397 (tt) cc_final: 0.6606 (mm) REVERT: B 339 ASN cc_start: 0.7157 (m-40) cc_final: 0.6686 (m-40) outliers start: 46 outliers final: 9 residues processed: 169 average time/residue: 0.3851 time to fit residues: 70.8877 Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 719 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 14 optimal weight: 0.0980 chunk 91 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 454 HIS B 264 GLN B 345 ASN B 454 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124319 restraints weight = 13920.459| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.58 r_work: 0.3507 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10306 Z= 0.101 Angle : 0.499 10.534 13988 Z= 0.266 Chirality : 0.041 0.202 1510 Planarity : 0.003 0.028 1758 Dihedral : 10.575 89.249 1400 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.15 % Allowed : 14.26 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1192 helix: 0.24 (0.23), residues: 480 sheet: -1.00 (0.41), residues: 160 loop : 0.38 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 665 TYR 0.022 0.001 TYR A 723 PHE 0.019 0.001 PHE A 744 TRP 0.025 0.001 TRP B 316 HIS 0.003 0.000 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (10304) covalent geometry : angle 0.49915 / 0.27 (13984) SS BOND : bond 0.00038 / 0.02 ( 2) SS BOND : angle 0.24601 / 0.12 ( 4) hydrogen bonds : bond 0.03245 / 2.17 ( 386) hydrogen bonds : angle 4.76135 / 3.47 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.361 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 220 TYR cc_start: 0.7436 (m-80) cc_final: 0.7195 (m-80) REVERT: A 223 MET cc_start: 0.7015 (mtt) cc_final: 0.6763 (mtm) REVERT: A 275 ASP cc_start: 0.7292 (m-30) cc_final: 0.7013 (p0) REVERT: A 291 LEU cc_start: 0.7231 (tt) cc_final: 0.6453 (mm) REVERT: A 343 LYS cc_start: 0.7602 (ttpp) cc_final: 0.7253 (tttt) REVERT: A 738 MET cc_start: 0.7983 (ptt) cc_final: 0.7482 (ptt) REVERT: B 220 TYR cc_start: 0.7614 (m-80) cc_final: 0.7306 (m-80) REVERT: B 291 LEU cc_start: 0.7411 (tt) cc_final: 0.6667 (mm) REVERT: B 339 ASN cc_start: 0.7079 (m-40) cc_final: 0.6724 (m-40) REVERT: B 402 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6821 (mp) REVERT: B 602 TYR cc_start: 0.6967 (m-80) cc_final: 0.6573 (m-10) REVERT: B 619 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6711 (mpt) outliers start: 34 outliers final: 9 residues processed: 171 average time/residue: 0.4243 time to fit residues: 79.0302 Evaluate side-chains 137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 ASN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.155805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122302 restraints weight = 13963.468| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.63 r_work: 0.3463 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10306 Z= 0.125 Angle : 0.521 8.909 13988 Z= 0.272 Chirality : 0.041 0.136 1510 Planarity : 0.004 0.037 1758 Dihedral : 10.545 89.889 1400 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.06 % Allowed : 16.30 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1192 helix: 0.45 (0.23), residues: 476 sheet: -0.99 (0.40), residues: 160 loop : 0.33 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 665 TYR 0.023 0.001 TYR B 723 PHE 0.015 0.001 PHE A 355 TRP 0.024 0.001 TRP B 316 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (10304) covalent geometry : angle 0.52085 / 0.27 (13984) SS BOND : bond 0.00008 / 0.00 ( 2) SS BOND : angle 0.32733 / 0.17 ( 4) hydrogen bonds : bond 0.03362 / 2.29 ( 386) hydrogen bonds : angle 4.65139 / 3.45 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.7013 (mtt) cc_final: 0.6765 (mtm) REVERT: A 275 ASP cc_start: 0.7363 (m-30) cc_final: 0.7049 (p0) REVERT: A 291 LEU cc_start: 0.7210 (tt) cc_final: 0.6503 (mm) REVERT: A 338 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6361 (t80) REVERT: A 343 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7282 (tttt) REVERT: A 402 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6800 (mp) REVERT: A 738 MET cc_start: 0.8078 (ptt) cc_final: 0.7563 (ptt) REVERT: B 220 TYR cc_start: 0.7620 (m-80) cc_final: 0.7244 (m-80) REVERT: B 291 LEU cc_start: 0.7354 (tt) cc_final: 0.6636 (mm) REVERT: B 402 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6860 (mp) REVERT: B 602 TYR cc_start: 0.7123 (m-80) cc_final: 0.6581 (m-80) REVERT: B 619 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6703 (mpt) outliers start: 33 outliers final: 9 residues processed: 152 average time/residue: 0.4406 time to fit residues: 72.8737 Evaluate side-chains 129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.0570 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.157760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125179 restraints weight = 13941.223| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.55 r_work: 0.3474 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10306 Z= 0.124 Angle : 0.517 10.097 13988 Z= 0.272 Chirality : 0.041 0.136 1510 Planarity : 0.004 0.037 1758 Dihedral : 10.440 88.833 1400 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.43 % Allowed : 16.57 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1192 helix: 0.52 (0.23), residues: 476 sheet: -1.37 (0.38), residues: 180 loop : 0.44 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 665 TYR 0.029 0.001 TYR B 723 PHE 0.017 0.001 PHE A 460 TRP 0.025 0.001 TRP B 316 HIS 0.002 0.001 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (10304) covalent geometry : angle 0.51725 / 0.27 (13984) SS BOND : bond 0.00007 / 0.00 ( 2) SS BOND : angle 0.29344 / 0.15 ( 4) hydrogen bonds : bond 0.03318 / 2.26 ( 386) hydrogen bonds : angle 4.66346 / 3.45 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7451 (m-80) cc_final: 0.7146 (m-80) REVERT: A 223 MET cc_start: 0.7024 (mtt) cc_final: 0.6798 (mtm) REVERT: A 275 ASP cc_start: 0.7355 (m-30) cc_final: 0.7044 (p0) REVERT: A 291 LEU cc_start: 0.7412 (tt) cc_final: 0.6644 (mm) REVERT: A 343 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7217 (tttt) REVERT: A 402 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6808 (mp) REVERT: A 619 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6736 (mpt) REVERT: A 679 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7213 (t60) REVERT: A 738 MET cc_start: 0.8065 (ptt) cc_final: 0.7436 (ptt) REVERT: B 162 PHE cc_start: 0.7441 (t80) cc_final: 0.6780 (t80) REVERT: B 220 TYR cc_start: 0.7667 (m-80) cc_final: 0.7305 (m-80) REVERT: B 291 LEU cc_start: 0.7359 (tt) cc_final: 0.6652 (mm) REVERT: B 327 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.3295 (ttt) REVERT: B 402 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6898 (mp) REVERT: B 407 TYR cc_start: 0.5832 (t80) cc_final: 0.5577 (t80) REVERT: B 619 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6718 (mpt) outliers start: 37 outliers final: 14 residues processed: 154 average time/residue: 0.4012 time to fit residues: 67.4925 Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122718 restraints weight = 14050.055| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.69 r_work: 0.3482 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10306 Z= 0.115 Angle : 0.528 10.771 13988 Z= 0.274 Chirality : 0.041 0.145 1510 Planarity : 0.004 0.040 1758 Dihedral : 10.347 88.265 1400 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.87 % Allowed : 17.69 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1192 helix: 0.57 (0.24), residues: 480 sheet: -1.36 (0.38), residues: 180 loop : 0.45 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 665 TYR 0.024 0.001 TYR B 723 PHE 0.021 0.001 PHE A 744 TRP 0.028 0.001 TRP B 316 HIS 0.002 0.000 HIS A 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (10304) covalent geometry : angle 0.52768 / 0.27 (13984) SS BOND : bond 0.00009 / 0.00 ( 2) SS BOND : angle 0.25183 / 0.13 ( 4) hydrogen bonds : bond 0.03232 / 2.19 ( 386) hydrogen bonds : angle 4.64043 / 3.43 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7477 (m-80) cc_final: 0.7146 (m-80) REVERT: A 223 MET cc_start: 0.7018 (mtt) cc_final: 0.6757 (mtm) REVERT: A 275 ASP cc_start: 0.7396 (m-30) cc_final: 0.7066 (p0) REVERT: A 291 LEU cc_start: 0.7393 (tt) cc_final: 0.6598 (mm) REVERT: A 338 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6479 (t80) REVERT: A 343 LYS cc_start: 0.7599 (ttpp) cc_final: 0.7265 (tttt) REVERT: A 402 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6822 (mp) REVERT: A 738 MET cc_start: 0.8129 (ptt) cc_final: 0.7732 (ptt) REVERT: B 162 PHE cc_start: 0.7543 (t80) cc_final: 0.6827 (t80) REVERT: B 220 TYR cc_start: 0.7676 (m-80) cc_final: 0.7304 (m-80) REVERT: B 291 LEU cc_start: 0.7352 (tt) cc_final: 0.6641 (mm) REVERT: B 327 MET cc_start: 0.4655 (OUTLIER) cc_final: 0.3197 (ttt) REVERT: B 402 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6851 (mp) REVERT: B 407 TYR cc_start: 0.5848 (t80) cc_final: 0.5572 (t80) REVERT: B 619 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6647 (mpt) REVERT: B 679 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7085 (t60) outliers start: 31 outliers final: 12 residues processed: 156 average time/residue: 0.4270 time to fit residues: 72.1468 Evaluate side-chains 134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 679 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 0.0060 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120613 restraints weight = 14106.219| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.55 r_work: 0.3432 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10306 Z= 0.163 Angle : 0.589 11.822 13988 Z= 0.304 Chirality : 0.042 0.145 1510 Planarity : 0.004 0.042 1758 Dihedral : 10.511 88.257 1400 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.87 % Allowed : 18.24 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1192 helix: 0.45 (0.24), residues: 476 sheet: -0.71 (0.43), residues: 140 loop : 0.22 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 448 TYR 0.022 0.002 TYR B 723 PHE 0.015 0.002 PHE B 460 TRP 0.025 0.001 TRP A 316 HIS 0.003 0.001 HIS A 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (10304) covalent geometry : angle 0.58879 / 0.30 (13984) SS BOND : bond 0.00029 / 0.02 ( 2) SS BOND : angle 0.38694 / 0.20 ( 4) hydrogen bonds : bond 0.03689 / 2.52 ( 386) hydrogen bonds : angle 4.74783 / 3.50 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7562 (m-80) cc_final: 0.7339 (m-80) REVERT: A 223 MET cc_start: 0.7037 (mtt) cc_final: 0.6770 (mtm) REVERT: A 275 ASP cc_start: 0.7372 (m-30) cc_final: 0.7058 (p0) REVERT: A 291 LEU cc_start: 0.7439 (tt) cc_final: 0.6669 (mm) REVERT: A 343 LYS cc_start: 0.7605 (ttpp) cc_final: 0.7290 (tttt) REVERT: A 482 MET cc_start: 0.7175 (tpt) cc_final: 0.6323 (tpp) REVERT: A 602 TYR cc_start: 0.7017 (m-80) cc_final: 0.6358 (m-80) REVERT: A 679 TRP cc_start: 0.8286 (OUTLIER) cc_final: 0.7246 (t60) REVERT: A 738 MET cc_start: 0.8180 (ptt) cc_final: 0.7933 (ptt) REVERT: B 220 TYR cc_start: 0.7734 (m-80) cc_final: 0.7385 (m-80) REVERT: B 291 LEU cc_start: 0.7576 (tt) cc_final: 0.6815 (mm) REVERT: B 402 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6914 (mp) REVERT: B 602 TYR cc_start: 0.7046 (m-10) cc_final: 0.6392 (m-10) REVERT: B 619 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6696 (mpt) outliers start: 31 outliers final: 11 residues processed: 143 average time/residue: 0.3964 time to fit residues: 61.8664 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN B 339 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.156344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123402 restraints weight = 14153.390| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.69 r_work: 0.3493 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10306 Z= 0.113 Angle : 0.566 12.384 13988 Z= 0.291 Chirality : 0.041 0.145 1510 Planarity : 0.003 0.041 1758 Dihedral : 10.338 87.505 1400 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.04 % Allowed : 19.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1192 helix: 0.48 (0.24), residues: 482 sheet: -1.11 (0.41), residues: 160 loop : 0.36 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 448 TYR 0.019 0.001 TYR B 723 PHE 0.025 0.001 PHE A 744 TRP 0.031 0.001 TRP B 316 HIS 0.002 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10304) covalent geometry : angle 0.56644 / 0.29 (13984) SS BOND : bond 0.00005 / 0.00 ( 2) SS BOND : angle 0.24402 / 0.12 ( 4) hydrogen bonds : bond 0.03275 / 2.23 ( 386) hydrogen bonds : angle 4.73123 / 3.50 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7523 (m-80) cc_final: 0.7305 (m-80) REVERT: A 223 MET cc_start: 0.6994 (mtt) cc_final: 0.6723 (mtm) REVERT: A 275 ASP cc_start: 0.7398 (m-30) cc_final: 0.7054 (p0) REVERT: A 291 LEU cc_start: 0.7393 (tt) cc_final: 0.6660 (mm) REVERT: A 343 LYS cc_start: 0.7607 (ttpp) cc_final: 0.7311 (tttt) REVERT: A 482 MET cc_start: 0.7180 (tpt) cc_final: 0.6011 (tpp) REVERT: A 602 TYR cc_start: 0.6890 (m-80) cc_final: 0.6275 (m-80) REVERT: A 738 MET cc_start: 0.8184 (ptt) cc_final: 0.7916 (ptt) REVERT: B 220 TYR cc_start: 0.7715 (m-80) cc_final: 0.7332 (m-80) REVERT: B 291 LEU cc_start: 0.7555 (tt) cc_final: 0.6821 (mm) REVERT: B 402 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6814 (mp) REVERT: B 482 MET cc_start: 0.6905 (tpt) cc_final: 0.6104 (tpp) REVERT: B 602 TYR cc_start: 0.6919 (m-10) cc_final: 0.6284 (m-10) REVERT: B 619 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6648 (mpt) outliers start: 22 outliers final: 9 residues processed: 146 average time/residue: 0.3941 time to fit residues: 62.8163 Evaluate side-chains 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.152696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119882 restraints weight = 14092.222| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.60 r_work: 0.3435 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 10306 Z= 0.198 Angle : 0.634 13.205 13988 Z= 0.330 Chirality : 0.044 0.157 1510 Planarity : 0.004 0.045 1758 Dihedral : 10.566 84.669 1400 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.04 % Allowed : 19.63 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1192 helix: 0.37 (0.24), residues: 476 sheet: -0.81 (0.44), residues: 140 loop : 0.05 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 448 TYR 0.019 0.002 TYR B 723 PHE 0.031 0.002 PHE B 460 TRP 0.031 0.002 TRP B 316 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (10304) covalent geometry : angle 0.63378 / 0.33 (13984) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 0.45628 / 0.23 ( 4) hydrogen bonds : bond 0.03971 / 2.73 ( 386) hydrogen bonds : angle 4.91218 / 3.68 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.7088 (mtt) cc_final: 0.6826 (mtm) REVERT: A 275 ASP cc_start: 0.7417 (m-30) cc_final: 0.7086 (p0) REVERT: A 291 LEU cc_start: 0.7411 (tt) cc_final: 0.6691 (mm) REVERT: A 343 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7335 (tttt) REVERT: A 449 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: A 482 MET cc_start: 0.7358 (tpt) cc_final: 0.6097 (tpp) REVERT: A 679 TRP cc_start: 0.8272 (OUTLIER) cc_final: 0.7109 (t60) REVERT: A 738 MET cc_start: 0.8249 (ptt) cc_final: 0.8001 (ptt) REVERT: B 220 TYR cc_start: 0.7770 (m-80) cc_final: 0.7452 (m-80) REVERT: B 291 LEU cc_start: 0.7470 (tt) cc_final: 0.6744 (mm) REVERT: B 402 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6954 (mp) REVERT: B 619 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6715 (mpt) REVERT: B 679 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.6899 (t60) outliers start: 22 outliers final: 10 residues processed: 139 average time/residue: 0.3723 time to fit residues: 56.6279 Evaluate side-chains 128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 679 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.155144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120188 restraints weight = 14173.155| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.69 r_work: 0.3477 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10306 Z= 0.140 Angle : 0.597 12.620 13988 Z= 0.310 Chirality : 0.042 0.141 1510 Planarity : 0.003 0.041 1758 Dihedral : 10.406 83.376 1400 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.48 % Allowed : 20.74 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1192 helix: 0.44 (0.24), residues: 478 sheet: -1.24 (0.41), residues: 160 loop : 0.22 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 448 TYR 0.018 0.001 TYR A 407 PHE 0.027 0.002 PHE A 744 TRP 0.035 0.001 TRP B 316 HIS 0.002 0.001 HIS B 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (10304) covalent geometry : angle 0.59740 / 0.31 (13984) SS BOND : bond 0.00016 / 0.01 ( 2) SS BOND : angle 0.31311 / 0.16 ( 4) hydrogen bonds : bond 0.03568 / 2.45 ( 386) hydrogen bonds : angle 4.84434 / 3.60 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.45 seconds wall clock time: 52 minutes 59.29 seconds (3179.29 seconds total)