Starting phenix.real_space_refine on Sat Aug 23 07:36:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gub_34272/08_2025/8gub_34272_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gub_34272/08_2025/8gub_34272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gub_34272/08_2025/8gub_34272_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gub_34272/08_2025/8gub_34272_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gub_34272/08_2025/8gub_34272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gub_34272/08_2025/8gub_34272.map" } resolution = 2.73 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= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 73 5.16 5 C 6594 2.51 5 N 1790 2.21 5 O 1898 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7998 Classifications: {'peptide': 977} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 931} Chain breaks: 4 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2330 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.12, per 1000 atoms: 0.20 Number of scatterers: 10358 At special positions: 0 Unit cell: (87.822, 119.952, 119.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 F 3 9.00 O 1898 8.00 N 1790 7.00 C 6594 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: 0.90 Conformation dependent library (CDL) restraints added in 381.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 51.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.606A pdb=" N PHE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.866A pdb=" N ARG A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.797A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.656A pdb=" N ASP A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.569A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.944A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.919A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.703A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.697A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.604A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.555A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.511A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 removed outlier: 3.671A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.186A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.592A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.643A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 911 removed outlier: 4.214A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 945 removed outlier: 4.026A pdb=" N PHE A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 974 through 994 removed outlier: 3.736A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.613A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 3.945A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1020 removed outlier: 3.738A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1026 Processing helix chain 'A' and resid 1031 through 1050 Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.557A pdb=" N GLU B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.079A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.549A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.789A pdb=" N GLN B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 506 Processing helix chain 'B' and resid 518 through 584 removed outlier: 3.574A pdb=" N ILE B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.509A pdb=" N GLN B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.853A pdb=" N ASN B 595 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36 removed outlier: 3.721A pdb=" N MET A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.496A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 212 removed outlier: 6.559A pdb=" N ASP A 203 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 198 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 197 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA A 289 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 13.928A pdb=" N SER A 199 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.653A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 340 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.608A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.778A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 431 removed outlier: 3.526A pdb=" N THR A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AB2, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AB3, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB4, first strand: chain 'B' and resid 377 through 381 removed outlier: 4.180A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 355 " --> pdb=" O TYR B 426 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1437 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: 1.98 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1736 1.30 - 1.43: 2686 1.43 - 1.55: 6035 1.55 - 1.68: 6 1.68 - 1.81: 112 Bond restraints: 10575 Sorted by residual: bond pdb=" C9 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.738 1.521 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.734 1.521 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.566 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C5 1LT A1101 " pdb=" C6 1LT A1101 " ideal model delta sigma weight residual 1.525 1.351 0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " ideal model delta sigma weight residual 1.291 1.415 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 10570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 14225 3.68 - 7.37: 36 7.37 - 11.05: 1 11.05 - 14.74: 0 14.74 - 18.42: 2 Bond angle restraints: 14264 Sorted by residual: angle pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 88.90 107.32 -18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" N1 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 118.47 134.47 -16.00 3.00e+00 1.11e-01 2.85e+01 angle pdb=" C CYS A 971 " pdb=" N THR A 972 " pdb=" CA THR A 972 " ideal model delta sigma weight residual 120.28 127.27 -6.99 1.34e+00 5.57e-01 2.72e+01 angle pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 126.74 117.02 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 115.40 108.21 7.19 3.00e+00 1.11e-01 5.75e+00 ... (remaining 14259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5769 17.67 - 35.34: 584 35.34 - 53.01: 95 53.01 - 70.67: 12 70.67 - 88.34: 16 Dihedral angle restraints: 6476 sinusoidal: 2777 harmonic: 3699 Sorted by residual: dihedral pdb=" CA MET A 922 " pdb=" C MET A 922 " pdb=" N VAL A 923 " pdb=" CA VAL A 923 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN B 591 " pdb=" C GLN B 591 " pdb=" N LYS B 592 " pdb=" CA LYS B 592 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 258 " pdb=" C ASP A 258 " pdb=" N GLU A 259 " pdb=" CA GLU A 259 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 806 0.028 - 0.056: 482 0.056 - 0.084: 162 0.084 - 0.111: 65 0.111 - 0.139: 23 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CG LEU A 793 " pdb=" CB LEU A 793 " pdb=" CD1 LEU A 793 " pdb=" CD2 LEU A 793 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO A 562 " pdb=" N PRO A 562 " pdb=" C PRO A 562 " pdb=" CB PRO A 562 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ASN A 918 " pdb=" N ASN A 918 " pdb=" C ASN A 918 " pdb=" CB ASN A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1535 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 103 " -0.024 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 104 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 538 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 539 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 539 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 539 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 158 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 159 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.019 5.00e-02 4.00e+02 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 124 2.58 - 3.16: 9663 3.16 - 3.74: 15682 3.74 - 4.32: 23165 4.32 - 4.90: 37719 Nonbonded interactions: 86353 Sorted by model distance: nonbonded pdb=" NH2 ARG A 401 " pdb=" O PRO A 458 " model vdw 1.994 3.120 nonbonded pdb=" OH TYR A 584 " pdb=" OD1 ASP A 608 " model vdw 2.005 3.040 nonbonded pdb=" O SER A 292 " pdb=" NE2 GLN A 296 " model vdw 2.023 3.120 nonbonded pdb=" OG1 THR A 358 " pdb=" OH TYR A 389 " model vdw 2.055 3.040 nonbonded pdb=" N ARG A 19 " pdb=" O CYS A 36 " model vdw 2.061 3.120 ... (remaining 86348 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.290 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 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 : 0.008 0.217 10575 Z= 0.383 Angle : 0.620 18.425 14264 Z= 0.304 Chirality : 0.041 0.139 1538 Planarity : 0.003 0.037 1832 Dihedral : 14.425 88.342 4076 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 34.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: -0.28 (0.24), residues: 1241 helix: 0.70 (0.22), residues: 566 sheet: -1.12 (0.41), residues: 166 loop : -0.75 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.009 0.001 TYR A 904 PHE 0.015 0.002 PHE A 667 TRP 0.017 0.001 TRP B 583 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00824 (10575) covalent geometry : angle 0.61966 (14264) hydrogen bonds : bond 0.23941 ( 495) hydrogen bonds : angle 7.94627 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7141 (mm110) cc_final: 0.6867 (mp-120) REVERT: A 76 GLU cc_start: 0.5684 (mt-10) cc_final: 0.5423 (tm-30) REVERT: A 107 ASN cc_start: 0.6180 (t0) cc_final: 0.5893 (t0) REVERT: A 127 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6303 (mt-10) REVERT: A 130 MET cc_start: 0.6340 (mmm) cc_final: 0.5683 (mmp) REVERT: A 132 LYS cc_start: 0.7135 (mmtm) cc_final: 0.6858 (mptp) REVERT: A 152 ASP cc_start: 0.7107 (m-30) cc_final: 0.6630 (m-30) REVERT: A 164 MET cc_start: 0.6227 (mtt) cc_final: 0.6018 (mtm) REVERT: A 179 LYS cc_start: 0.6408 (tptp) cc_final: 0.6162 (mmmm) REVERT: A 265 TYR cc_start: 0.6397 (m-10) cc_final: 0.5975 (m-10) REVERT: A 282 MET cc_start: 0.6865 (tpp) cc_final: 0.6451 (tpp) REVERT: A 382 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: A 410 LYS cc_start: 0.7177 (tppp) cc_final: 0.6705 (tptp) REVERT: A 453 GLU cc_start: 0.6104 (tt0) cc_final: 0.5445 (tm-30) REVERT: A 579 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6793 (mt-10) REVERT: A 583 MET cc_start: 0.6887 (tpt) cc_final: 0.6499 (tpt) REVERT: A 677 ASN cc_start: 0.7441 (t0) cc_final: 0.6877 (t0) REVERT: A 697 MET cc_start: 0.7032 (tpt) cc_final: 0.6763 (mmp) REVERT: A 732 MET cc_start: 0.6052 (tpt) cc_final: 0.5845 (mmm) REVERT: A 739 MET cc_start: 0.6661 (mtm) cc_final: 0.6424 (mtt) REVERT: A 745 MET cc_start: 0.7042 (tpt) cc_final: 0.6556 (mmm) REVERT: A 772 MET cc_start: 0.6764 (mtp) cc_final: 0.6220 (mtp) REVERT: A 777 ARG cc_start: 0.6237 (mtm110) cc_final: 0.5497 (mmm160) REVERT: A 780 TRP cc_start: 0.7439 (t-100) cc_final: 0.6913 (t-100) REVERT: A 811 MET cc_start: 0.7512 (mtp) cc_final: 0.7239 (mtm) REVERT: A 852 ARG cc_start: 0.6085 (mtm-85) cc_final: 0.5604 (mtm-85) REVERT: A 886 LYS cc_start: 0.7576 (ptpt) cc_final: 0.6687 (pttm) REVERT: A 915 ASP cc_start: 0.7000 (t70) cc_final: 0.6730 (t70) REVERT: A 933 ASP cc_start: 0.7821 (t0) cc_final: 0.6973 (t0) REVERT: A 1010 MET cc_start: 0.7254 (mtm) cc_final: 0.6945 (mtt) REVERT: A 1029 ASP cc_start: 0.7031 (m-30) cc_final: 0.6692 (m-30) REVERT: B 421 ASP cc_start: 0.7794 (t0) cc_final: 0.7383 (m-30) REVERT: B 472 ARG cc_start: 0.6037 (tmm-80) cc_final: 0.5261 (ttm170) REVERT: B 479 MET cc_start: 0.5793 (mtp) cc_final: 0.5360 (mpp) REVERT: B 520 GLU cc_start: 0.7982 (tt0) cc_final: 0.7743 (tm-30) REVERT: B 555 GLU cc_start: 0.6061 (tp30) cc_final: 0.5720 (tt0) REVERT: B 559 ILE cc_start: 0.5862 (mt) cc_final: 0.5526 (mp) outliers start: 2 outliers final: 1 residues processed: 200 average time/residue: 0.5146 time to fit residues: 110.3337 Evaluate side-chains 156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS A1042 GLN B 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.194837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145561 restraints weight = 11052.730| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.08 r_work: 0.3539 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10575 Z= 0.147 Angle : 0.604 8.985 14264 Z= 0.317 Chirality : 0.044 0.271 1538 Planarity : 0.004 0.040 1832 Dihedral : 5.968 74.032 1395 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.91 % Allowed : 8.53 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.75 (0.25), residues: 1241 helix: 1.64 (0.22), residues: 589 sheet: -0.56 (0.43), residues: 156 loop : -0.47 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.014 0.001 TYR A 890 PHE 0.022 0.002 PHE A 667 TRP 0.018 0.001 TRP A 552 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00329 (10575) covalent geometry : angle 0.60435 (14264) hydrogen bonds : bond 0.05484 ( 495) hydrogen bonds : angle 4.63831 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7885 (mm110) cc_final: 0.7647 (mp-120) REVERT: A 76 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6083 (mm-30) REVERT: A 130 MET cc_start: 0.7563 (mmm) cc_final: 0.6728 (mmt) REVERT: A 132 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7690 (mptp) REVERT: A 164 MET cc_start: 0.7917 (mtt) cc_final: 0.7683 (mtp) REVERT: A 179 LYS cc_start: 0.7234 (tptp) cc_final: 0.6850 (mmmm) REVERT: A 265 TYR cc_start: 0.7248 (m-10) cc_final: 0.6932 (m-10) REVERT: A 282 MET cc_start: 0.7579 (tpp) cc_final: 0.7251 (tpp) REVERT: A 384 ASN cc_start: 0.7980 (t0) cc_final: 0.7266 (m-40) REVERT: A 441 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8122 (ttm) REVERT: A 453 GLU cc_start: 0.6959 (tt0) cc_final: 0.6420 (tm-30) REVERT: A 474 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: A 697 MET cc_start: 0.8194 (tpt) cc_final: 0.7940 (mmp) REVERT: A 732 MET cc_start: 0.6757 (tpt) cc_final: 0.6169 (mmm) REVERT: A 734 PHE cc_start: 0.8090 (t80) cc_final: 0.7853 (t80) REVERT: A 738 GLN cc_start: 0.7036 (mm110) cc_final: 0.6750 (mp10) REVERT: A 745 MET cc_start: 0.8090 (tpt) cc_final: 0.7715 (mmm) REVERT: A 772 MET cc_start: 0.7795 (mtp) cc_final: 0.7584 (mtp) REVERT: A 780 TRP cc_start: 0.7980 (t-100) cc_final: 0.7736 (t-100) REVERT: A 794 PHE cc_start: 0.8641 (p90) cc_final: 0.8320 (p90) REVERT: A 852 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6687 (mtm-85) REVERT: A 886 LYS cc_start: 0.7702 (ptpt) cc_final: 0.6972 (pttm) REVERT: A 933 ASP cc_start: 0.8270 (t0) cc_final: 0.7838 (t70) REVERT: A 977 PHE cc_start: 0.8243 (t80) cc_final: 0.8026 (t80) REVERT: B 472 ARG cc_start: 0.6482 (tmm-80) cc_final: 0.6068 (ttm170) REVERT: B 479 MET cc_start: 0.6897 (mtp) cc_final: 0.6579 (mpp) REVERT: B 540 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6441 (t0) REVERT: B 555 GLU cc_start: 0.6425 (tp30) cc_final: 0.6205 (tt0) REVERT: B 559 ILE cc_start: 0.6824 (mt) cc_final: 0.6530 (mp) outliers start: 22 outliers final: 10 residues processed: 182 average time/residue: 0.6322 time to fit residues: 123.2038 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 540 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.194436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144435 restraints weight = 11058.126| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.16 r_work: 0.3601 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10575 Z= 0.159 Angle : 0.565 8.696 14264 Z= 0.294 Chirality : 0.043 0.281 1538 Planarity : 0.004 0.042 1832 Dihedral : 5.898 75.296 1393 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.02 % Rotamer: Outliers : 2.61 % Allowed : 12.27 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1241 helix: 1.55 (0.22), residues: 593 sheet: -0.47 (0.43), residues: 155 loop : -0.60 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.020 0.002 TYR A 182 PHE 0.024 0.002 PHE A 667 TRP 0.015 0.001 TRP A 552 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00374 (10575) covalent geometry : angle 0.56535 (14264) hydrogen bonds : bond 0.04927 ( 495) hydrogen bonds : angle 4.30719 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7718 (mmm) cc_final: 0.7036 (mmt) REVERT: A 179 LYS cc_start: 0.7384 (tptp) cc_final: 0.7058 (mmmm) REVERT: A 249 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7505 (tmtt) REVERT: A 265 TYR cc_start: 0.7160 (m-10) cc_final: 0.6860 (m-10) REVERT: A 282 MET cc_start: 0.7540 (tpp) cc_final: 0.7222 (tpp) REVERT: A 384 ASN cc_start: 0.7971 (t0) cc_final: 0.7258 (m-40) REVERT: A 441 MET cc_start: 0.8349 (ttm) cc_final: 0.8105 (ttm) REVERT: A 453 GLU cc_start: 0.6908 (tt0) cc_final: 0.6364 (tm-30) REVERT: A 474 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: A 697 MET cc_start: 0.8168 (tpt) cc_final: 0.7955 (mmp) REVERT: A 732 MET cc_start: 0.6795 (tpt) cc_final: 0.6300 (mmm) REVERT: A 745 MET cc_start: 0.8330 (tpt) cc_final: 0.7980 (mmm) REVERT: A 767 GLU cc_start: 0.6951 (pm20) cc_final: 0.6368 (pm20) REVERT: A 768 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7457 (mp0) REVERT: A 789 MET cc_start: 0.7698 (mtt) cc_final: 0.7393 (mtm) REVERT: A 794 PHE cc_start: 0.8565 (p90) cc_final: 0.8239 (p90) REVERT: A 822 ASN cc_start: 0.7822 (t0) cc_final: 0.7334 (m-40) REVERT: A 825 GLN cc_start: 0.8531 (mm110) cc_final: 0.8269 (mm110) REVERT: A 852 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6938 (mtm-85) REVERT: A 886 LYS cc_start: 0.7647 (ptpt) cc_final: 0.6972 (pttm) REVERT: A 933 ASP cc_start: 0.8292 (t0) cc_final: 0.7608 (t0) REVERT: B 345 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: B 472 ARG cc_start: 0.6529 (tmm-80) cc_final: 0.6154 (ttm170) REVERT: B 479 MET cc_start: 0.6692 (mtp) cc_final: 0.6396 (mpp) REVERT: B 520 GLU cc_start: 0.7709 (tt0) cc_final: 0.7287 (pm20) REVERT: B 540 ASP cc_start: 0.6856 (t70) cc_final: 0.6279 (t0) REVERT: B 555 GLU cc_start: 0.6827 (tp30) cc_final: 0.6474 (tt0) REVERT: B 559 ILE cc_start: 0.7002 (mt) cc_final: 0.6754 (mp) outliers start: 30 outliers final: 12 residues processed: 174 average time/residue: 0.6058 time to fit residues: 113.6369 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.194210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144212 restraints weight = 11036.273| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.08 r_work: 0.3600 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10575 Z= 0.163 Angle : 0.564 8.800 14264 Z= 0.293 Chirality : 0.043 0.276 1538 Planarity : 0.004 0.043 1832 Dihedral : 5.988 78.757 1393 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 3.05 % Allowed : 13.66 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.56 (0.24), residues: 1241 helix: 1.46 (0.22), residues: 594 sheet: -0.42 (0.43), residues: 155 loop : -0.65 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.016 0.001 TYR B 470 PHE 0.023 0.002 PHE A 667 TRP 0.014 0.001 TRP A 552 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00389 (10575) covalent geometry : angle 0.56419 (14264) hydrogen bonds : bond 0.04701 ( 495) hydrogen bonds : angle 4.19597 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7941 (mp-120) REVERT: A 130 MET cc_start: 0.7696 (mmm) cc_final: 0.7012 (mmt) REVERT: A 172 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 179 LYS cc_start: 0.7206 (tptp) cc_final: 0.6835 (mttm) REVERT: A 265 TYR cc_start: 0.7154 (m-10) cc_final: 0.6851 (m-10) REVERT: A 269 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7898 (tp40) REVERT: A 282 MET cc_start: 0.7486 (tpp) cc_final: 0.7279 (tpp) REVERT: A 384 ASN cc_start: 0.7967 (t0) cc_final: 0.7239 (m-40) REVERT: A 441 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8173 (ttm) REVERT: A 453 GLU cc_start: 0.6885 (tt0) cc_final: 0.6369 (tm-30) REVERT: A 732 MET cc_start: 0.6774 (tpt) cc_final: 0.6209 (mmm) REVERT: A 745 MET cc_start: 0.8326 (tpt) cc_final: 0.8027 (mmm) REVERT: A 794 PHE cc_start: 0.8566 (p90) cc_final: 0.8294 (p90) REVERT: A 822 ASN cc_start: 0.7861 (t0) cc_final: 0.7374 (m-40) REVERT: A 825 GLN cc_start: 0.8571 (mm110) cc_final: 0.8264 (mm110) REVERT: A 886 LYS cc_start: 0.7607 (ptpt) cc_final: 0.6945 (pttm) REVERT: A 956 LEU cc_start: 0.7553 (mt) cc_final: 0.7326 (tp) REVERT: B 345 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 472 ARG cc_start: 0.6482 (tmm-80) cc_final: 0.6183 (ttm170) REVERT: B 479 MET cc_start: 0.6790 (mtp) cc_final: 0.6462 (mpp) REVERT: B 520 GLU cc_start: 0.7526 (tt0) cc_final: 0.7266 (pm20) REVERT: B 540 ASP cc_start: 0.6862 (t70) cc_final: 0.6284 (t0) REVERT: B 547 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6684 (mt-10) REVERT: B 555 GLU cc_start: 0.6878 (tp30) cc_final: 0.6558 (tt0) REVERT: B 559 ILE cc_start: 0.7049 (mt) cc_final: 0.6811 (mp) outliers start: 35 outliers final: 14 residues processed: 171 average time/residue: 0.5262 time to fit residues: 96.9715 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.195127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145354 restraints weight = 10981.154| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.01 r_work: 0.3625 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10575 Z= 0.135 Angle : 0.537 8.738 14264 Z= 0.279 Chirality : 0.042 0.288 1538 Planarity : 0.004 0.043 1832 Dihedral : 5.891 77.539 1393 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 3.22 % Allowed : 14.88 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.62 (0.24), residues: 1241 helix: 1.55 (0.22), residues: 594 sheet: -0.42 (0.42), residues: 155 loop : -0.68 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.021 0.001 TYR A 182 PHE 0.022 0.002 PHE A 667 TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (10575) covalent geometry : angle 0.53733 (14264) hydrogen bonds : bond 0.04357 ( 495) hydrogen bonds : angle 4.09428 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7875 (m-80) cc_final: 0.7555 (m-80) REVERT: A 130 MET cc_start: 0.7597 (mmm) cc_final: 0.6924 (mmt) REVERT: A 172 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 179 LYS cc_start: 0.7160 (tptp) cc_final: 0.6785 (mttm) REVERT: A 265 TYR cc_start: 0.7118 (m-10) cc_final: 0.6789 (m-10) REVERT: A 269 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7855 (tp40) REVERT: A 282 MET cc_start: 0.7485 (tpp) cc_final: 0.7273 (tpp) REVERT: A 384 ASN cc_start: 0.8018 (t0) cc_final: 0.7256 (m-40) REVERT: A 441 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8129 (ttm) REVERT: A 453 GLU cc_start: 0.6791 (tt0) cc_final: 0.6343 (tm-30) REVERT: A 732 MET cc_start: 0.6699 (tpt) cc_final: 0.6111 (mmm) REVERT: A 745 MET cc_start: 0.8299 (tpt) cc_final: 0.7970 (mmm) REVERT: A 780 TRP cc_start: 0.8204 (t-100) cc_final: 0.7862 (t-100) REVERT: A 789 MET cc_start: 0.7656 (mtt) cc_final: 0.7318 (mtm) REVERT: A 822 ASN cc_start: 0.7857 (t0) cc_final: 0.7338 (m-40) REVERT: A 825 GLN cc_start: 0.8537 (mm110) cc_final: 0.8257 (mm110) REVERT: A 886 LYS cc_start: 0.7594 (ptpt) cc_final: 0.6927 (pttm) REVERT: A 933 ASP cc_start: 0.8205 (t0) cc_final: 0.7567 (t0) REVERT: A 1029 ASP cc_start: 0.7609 (m-30) cc_final: 0.7199 (m-30) REVERT: B 472 ARG cc_start: 0.6471 (tmm-80) cc_final: 0.6192 (ttm170) REVERT: B 479 MET cc_start: 0.6664 (mtp) cc_final: 0.6353 (mpp) REVERT: B 520 GLU cc_start: 0.7512 (tt0) cc_final: 0.7271 (pm20) REVERT: B 540 ASP cc_start: 0.6761 (t70) cc_final: 0.6200 (t0) REVERT: B 547 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6718 (mt-10) REVERT: B 555 GLU cc_start: 0.6927 (tp30) cc_final: 0.6568 (tt0) REVERT: B 559 ILE cc_start: 0.6954 (mt) cc_final: 0.6717 (mp) outliers start: 37 outliers final: 14 residues processed: 173 average time/residue: 0.5754 time to fit residues: 107.1171 Evaluate side-chains 164 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.195477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144925 restraints weight = 11149.625| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.20 r_work: 0.3542 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10575 Z= 0.129 Angle : 0.526 8.696 14264 Z= 0.273 Chirality : 0.042 0.291 1538 Planarity : 0.004 0.044 1832 Dihedral : 5.774 74.569 1393 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.48 % Allowed : 15.67 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.67 (0.24), residues: 1241 helix: 1.63 (0.22), residues: 593 sheet: -0.51 (0.42), residues: 159 loop : -0.66 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.015 0.001 TYR B 470 PHE 0.022 0.002 PHE A 794 TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (10575) covalent geometry : angle 0.52608 (14264) hydrogen bonds : bond 0.04168 ( 495) hydrogen bonds : angle 4.00005 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.6832 (mp-120) REVERT: A 95 PHE cc_start: 0.6548 (t80) cc_final: 0.6319 (t80) REVERT: A 130 MET cc_start: 0.7627 (mmm) cc_final: 0.6929 (mmt) REVERT: A 172 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 179 LYS cc_start: 0.7153 (tptp) cc_final: 0.6775 (mttm) REVERT: A 249 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7534 (tmtt) REVERT: A 265 TYR cc_start: 0.7115 (m-10) cc_final: 0.6767 (m-10) REVERT: A 269 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: A 282 MET cc_start: 0.7485 (tpp) cc_final: 0.7266 (tpp) REVERT: A 384 ASN cc_start: 0.8001 (t0) cc_final: 0.7249 (m-40) REVERT: A 441 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8146 (ttm) REVERT: A 453 GLU cc_start: 0.6776 (tt0) cc_final: 0.6335 (tm-30) REVERT: A 732 MET cc_start: 0.6628 (tpt) cc_final: 0.5777 (mmm) REVERT: A 745 MET cc_start: 0.8308 (tpt) cc_final: 0.8012 (mmm) REVERT: A 767 GLU cc_start: 0.6935 (pm20) cc_final: 0.6652 (pm20) REVERT: A 780 TRP cc_start: 0.8179 (t-100) cc_final: 0.7857 (t-100) REVERT: A 822 ASN cc_start: 0.7934 (t0) cc_final: 0.7420 (m-40) REVERT: A 825 GLN cc_start: 0.8600 (mm110) cc_final: 0.8340 (mm-40) REVERT: A 886 LYS cc_start: 0.7582 (ptpt) cc_final: 0.6912 (pttm) REVERT: A 933 ASP cc_start: 0.8189 (t0) cc_final: 0.7537 (t0) REVERT: A 1029 ASP cc_start: 0.7635 (m-30) cc_final: 0.7238 (m-30) REVERT: B 364 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5524 (tmt) REVERT: B 472 ARG cc_start: 0.6368 (tmm-80) cc_final: 0.6158 (ttm170) REVERT: B 479 MET cc_start: 0.6736 (mtp) cc_final: 0.6410 (mpp) REVERT: B 520 GLU cc_start: 0.7544 (tt0) cc_final: 0.7217 (pm20) REVERT: B 540 ASP cc_start: 0.6807 (t70) cc_final: 0.6225 (t0) REVERT: B 547 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6671 (mt-10) REVERT: B 555 GLU cc_start: 0.7095 (tp30) cc_final: 0.6875 (tt0) outliers start: 40 outliers final: 20 residues processed: 173 average time/residue: 0.5693 time to fit residues: 105.8775 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.196581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146047 restraints weight = 10995.438| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.16 r_work: 0.3623 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10575 Z= 0.114 Angle : 0.514 8.623 14264 Z= 0.268 Chirality : 0.041 0.301 1538 Planarity : 0.004 0.044 1832 Dihedral : 5.615 70.070 1393 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 17.06 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.79 (0.24), residues: 1241 helix: 1.73 (0.22), residues: 594 sheet: -0.54 (0.42), residues: 158 loop : -0.56 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.014 0.001 TYR B 470 PHE 0.026 0.001 PHE A 794 TRP 0.012 0.001 TRP A 552 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00258 (10575) covalent geometry : angle 0.51406 (14264) hydrogen bonds : bond 0.03970 ( 495) hydrogen bonds : angle 3.92936 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7735 (mmm) cc_final: 0.6962 (mmt) REVERT: A 172 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 179 LYS cc_start: 0.7041 (tptp) cc_final: 0.6635 (mttm) REVERT: A 265 TYR cc_start: 0.7045 (m-10) cc_final: 0.6712 (m-10) REVERT: A 282 MET cc_start: 0.7465 (tpp) cc_final: 0.7237 (tpp) REVERT: A 384 ASN cc_start: 0.7916 (t0) cc_final: 0.7197 (m-40) REVERT: A 441 MET cc_start: 0.8382 (ttm) cc_final: 0.8147 (ttm) REVERT: A 453 GLU cc_start: 0.6749 (tt0) cc_final: 0.6289 (tm-30) REVERT: A 732 MET cc_start: 0.6549 (tpt) cc_final: 0.6017 (mmm) REVERT: A 745 MET cc_start: 0.8288 (tpt) cc_final: 0.7970 (mmm) REVERT: A 780 TRP cc_start: 0.8153 (t-100) cc_final: 0.7843 (t-100) REVERT: A 789 MET cc_start: 0.7592 (mtt) cc_final: 0.7217 (mtm) REVERT: A 822 ASN cc_start: 0.7907 (t0) cc_final: 0.7375 (m-40) REVERT: A 886 LYS cc_start: 0.7553 (ptpt) cc_final: 0.6889 (pttm) REVERT: A 933 ASP cc_start: 0.8195 (t0) cc_final: 0.7537 (t0) REVERT: A 1029 ASP cc_start: 0.7624 (m-30) cc_final: 0.7217 (m-30) REVERT: B 364 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5770 (mtt) REVERT: B 472 ARG cc_start: 0.6387 (tmm-80) cc_final: 0.6163 (ttm170) REVERT: B 479 MET cc_start: 0.6655 (mtp) cc_final: 0.6326 (mpp) REVERT: B 520 GLU cc_start: 0.7418 (tt0) cc_final: 0.7019 (pm20) REVERT: B 540 ASP cc_start: 0.6808 (t70) cc_final: 0.6262 (t0) REVERT: B 547 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6699 (mt-10) REVERT: B 555 GLU cc_start: 0.7071 (tp30) cc_final: 0.6829 (tt0) outliers start: 33 outliers final: 20 residues processed: 162 average time/residue: 0.4870 time to fit residues: 85.7484 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.193777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143452 restraints weight = 11046.873| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.11 r_work: 0.3522 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10575 Z= 0.187 Angle : 0.591 8.097 14264 Z= 0.305 Chirality : 0.044 0.309 1538 Planarity : 0.004 0.045 1832 Dihedral : 5.881 71.778 1393 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 18.10 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.52 (0.24), residues: 1241 helix: 1.47 (0.22), residues: 592 sheet: -0.59 (0.42), residues: 159 loop : -0.67 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.019 0.002 TYR B 470 PHE 0.023 0.002 PHE A 667 TRP 0.012 0.001 TRP A 552 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00456 (10575) covalent geometry : angle 0.59079 (14264) hydrogen bonds : bond 0.04565 ( 495) hydrogen bonds : angle 4.11497 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7862 (m-80) cc_final: 0.7603 (m-80) REVERT: A 130 MET cc_start: 0.7605 (mmm) cc_final: 0.6887 (mmt) REVERT: A 179 LYS cc_start: 0.7124 (tptp) cc_final: 0.6711 (mmmm) REVERT: A 265 TYR cc_start: 0.7039 (m-10) cc_final: 0.6731 (m-10) REVERT: A 282 MET cc_start: 0.7517 (tpp) cc_final: 0.7277 (tpp) REVERT: A 384 ASN cc_start: 0.8077 (t0) cc_final: 0.7263 (m-40) REVERT: A 441 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8181 (ttm) REVERT: A 453 GLU cc_start: 0.6814 (tt0) cc_final: 0.6352 (tm-30) REVERT: A 628 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8761 (tt) REVERT: A 732 MET cc_start: 0.6524 (tpt) cc_final: 0.5914 (mmm) REVERT: A 745 MET cc_start: 0.8346 (tpt) cc_final: 0.8100 (mmm) REVERT: A 780 TRP cc_start: 0.8188 (t-100) cc_final: 0.7891 (t-100) REVERT: A 789 MET cc_start: 0.7787 (mtt) cc_final: 0.7363 (mtm) REVERT: A 822 ASN cc_start: 0.7917 (t0) cc_final: 0.7392 (m-40) REVERT: A 886 LYS cc_start: 0.7658 (ptpt) cc_final: 0.6959 (pttm) REVERT: A 933 ASP cc_start: 0.8237 (t0) cc_final: 0.7522 (t0) REVERT: A 1029 ASP cc_start: 0.7638 (m-30) cc_final: 0.7231 (m-30) REVERT: B 345 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6999 (pt0) REVERT: B 472 ARG cc_start: 0.6409 (tmm-80) cc_final: 0.6180 (ttm170) REVERT: B 479 MET cc_start: 0.6760 (mtp) cc_final: 0.6422 (mpp) REVERT: B 520 GLU cc_start: 0.7410 (tt0) cc_final: 0.7031 (pm20) REVERT: B 540 ASP cc_start: 0.6803 (t70) cc_final: 0.6273 (t0) REVERT: B 555 GLU cc_start: 0.7101 (tp30) cc_final: 0.6683 (tt0) REVERT: B 559 ILE cc_start: 0.7070 (mt) cc_final: 0.6847 (mp) outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 0.5658 time to fit residues: 97.9594 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 95 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 26 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS B 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.198078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147564 restraints weight = 11012.822| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.25 r_work: 0.3646 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10575 Z= 0.104 Angle : 0.511 8.809 14264 Z= 0.266 Chirality : 0.040 0.305 1538 Planarity : 0.004 0.045 1832 Dihedral : 5.359 59.405 1393 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 18.62 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1241 helix: 1.71 (0.22), residues: 594 sheet: -0.50 (0.43), residues: 158 loop : -0.52 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.012 0.001 TYR B 470 PHE 0.021 0.001 PHE A 667 TRP 0.013 0.001 TRP A 552 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00221 (10575) covalent geometry : angle 0.51106 (14264) hydrogen bonds : bond 0.03734 ( 495) hydrogen bonds : angle 3.85523 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7739 (mmm) cc_final: 0.6816 (mmt) REVERT: A 132 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7606 (mptp) REVERT: A 179 LYS cc_start: 0.7075 (tptp) cc_final: 0.6667 (mttm) REVERT: A 265 TYR cc_start: 0.6949 (m-10) cc_final: 0.6599 (m-80) REVERT: A 282 MET cc_start: 0.7497 (tpp) cc_final: 0.7271 (tpp) REVERT: A 384 ASN cc_start: 0.7913 (t0) cc_final: 0.7248 (m-40) REVERT: A 441 MET cc_start: 0.8358 (ttm) cc_final: 0.8130 (ttm) REVERT: A 453 GLU cc_start: 0.6588 (tt0) cc_final: 0.6141 (tm-30) REVERT: A 489 MET cc_start: 0.6069 (tpp) cc_final: 0.5808 (mmm) REVERT: A 621 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7414 (tttp) REVERT: A 732 MET cc_start: 0.6552 (tpt) cc_final: 0.5995 (mmm) REVERT: A 745 MET cc_start: 0.8322 (tpt) cc_final: 0.8053 (mmm) REVERT: A 765 ARG cc_start: 0.7364 (mtt180) cc_final: 0.7110 (mtt180) REVERT: A 780 TRP cc_start: 0.8183 (t-100) cc_final: 0.7822 (t-100) REVERT: A 789 MET cc_start: 0.7383 (mtt) cc_final: 0.7076 (mtm) REVERT: A 822 ASN cc_start: 0.7891 (t0) cc_final: 0.7383 (m-40) REVERT: A 886 LYS cc_start: 0.7580 (ptpt) cc_final: 0.6905 (pttm) REVERT: A 933 ASP cc_start: 0.8186 (t0) cc_final: 0.7498 (t0) REVERT: A 1029 ASP cc_start: 0.7615 (m-30) cc_final: 0.7224 (m-30) REVERT: B 364 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5655 (mtt) REVERT: B 406 ASN cc_start: 0.8635 (m-40) cc_final: 0.8408 (m-40) REVERT: B 472 ARG cc_start: 0.6360 (tmm-80) cc_final: 0.6146 (ttm170) REVERT: B 479 MET cc_start: 0.6747 (mtp) cc_final: 0.6393 (mpp) REVERT: B 520 GLU cc_start: 0.7342 (tt0) cc_final: 0.7016 (pm20) REVERT: B 555 GLU cc_start: 0.7089 (tp30) cc_final: 0.6877 (tt0) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.5580 time to fit residues: 95.1983 Evaluate side-chains 152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.195646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144112 restraints weight = 10925.829| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.19 r_work: 0.3539 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10575 Z= 0.147 Angle : 0.551 9.194 14264 Z= 0.286 Chirality : 0.043 0.326 1538 Planarity : 0.004 0.046 1832 Dihedral : 5.307 59.948 1393 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.65 % Allowed : 19.15 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.73 (0.24), residues: 1241 helix: 1.63 (0.22), residues: 593 sheet: -0.43 (0.43), residues: 159 loop : -0.56 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.016 0.001 TYR B 470 PHE 0.022 0.002 PHE A 667 TRP 0.011 0.001 TRP A 552 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00351 (10575) covalent geometry : angle 0.55074 (14264) hydrogen bonds : bond 0.04104 ( 495) hydrogen bonds : angle 3.94776 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7610 (mmm) cc_final: 0.6775 (mmt) REVERT: A 132 LYS cc_start: 0.7808 (mmtm) cc_final: 0.7587 (mptp) REVERT: A 179 LYS cc_start: 0.7004 (tptp) cc_final: 0.6590 (mttm) REVERT: A 265 TYR cc_start: 0.6974 (m-10) cc_final: 0.6636 (m-80) REVERT: A 282 MET cc_start: 0.7475 (tpp) cc_final: 0.7231 (tpp) REVERT: A 384 ASN cc_start: 0.8025 (t0) cc_final: 0.7246 (m-40) REVERT: A 441 MET cc_start: 0.8384 (ttm) cc_final: 0.8160 (ttm) REVERT: A 453 GLU cc_start: 0.6694 (tt0) cc_final: 0.6199 (tm-30) REVERT: A 561 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8125 (mp) REVERT: A 732 MET cc_start: 0.6615 (tpt) cc_final: 0.6042 (mmm) REVERT: A 780 TRP cc_start: 0.8148 (t-100) cc_final: 0.7812 (t-100) REVERT: A 789 MET cc_start: 0.7721 (mtt) cc_final: 0.7361 (mtm) REVERT: A 822 ASN cc_start: 0.7907 (t0) cc_final: 0.7367 (m-40) REVERT: A 886 LYS cc_start: 0.7633 (ptpt) cc_final: 0.6920 (pttm) REVERT: A 933 ASP cc_start: 0.8194 (t0) cc_final: 0.7467 (t0) REVERT: A 1029 ASP cc_start: 0.7636 (m-30) cc_final: 0.7233 (m-30) REVERT: B 364 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5730 (mtt) REVERT: B 472 ARG cc_start: 0.6349 (tmm-80) cc_final: 0.6125 (ttm170) REVERT: B 479 MET cc_start: 0.6786 (mtp) cc_final: 0.6409 (mpp) REVERT: B 520 GLU cc_start: 0.7341 (tt0) cc_final: 0.7022 (pm20) REVERT: B 540 ASP cc_start: 0.6777 (t70) cc_final: 0.6276 (t0) REVERT: B 555 GLU cc_start: 0.7137 (tp30) cc_final: 0.6742 (tt0) REVERT: B 559 ILE cc_start: 0.7133 (mt) cc_final: 0.6908 (mp) outliers start: 19 outliers final: 17 residues processed: 153 average time/residue: 0.5229 time to fit residues: 86.5805 Evaluate side-chains 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS B 527 ASN ** B 595 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 = 0.4236 r_free = 0.4236 target = 0.197713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147284 restraints weight = 11024.776| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.16 r_work: 0.3646 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10575 Z= 0.109 Angle : 0.522 9.299 14264 Z= 0.271 Chirality : 0.041 0.318 1538 Planarity : 0.004 0.046 1832 Dihedral : 4.908 58.588 1393 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.09 % Allowed : 18.80 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 aren not related in a simple way. whole: 0.86 (0.24), residues: 1241 helix: 1.74 (0.22), residues: 594 sheet: -0.45 (0.43), residues: 158 loop : -0.48 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 916 TYR 0.013 0.001 TYR B 470 PHE 0.020 0.001 PHE A 667 TRP 0.012 0.001 TRP A 552 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00242 (10575) covalent geometry : angle 0.52217 (14264) hydrogen bonds : bond 0.03733 ( 495) hydrogen bonds : angle 3.83703 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.08 seconds wall clock time: 74 minutes 46.11 seconds (4486.11 seconds total)