Starting phenix.real_space_refine on Mon Jul 28 18:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gub_34272/07_2025/8gub_34272_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gub_34272/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gub_34272/07_2025/8gub_34272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gub_34272/07_2025/8gub_34272.map" model { file = "/net/cci-nas-00/data/ceres_data/8gub_34272/07_2025/8gub_34272_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gub_34272/07_2025/8gub_34272_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.88, per 1000 atoms: 0.66 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.47 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: 3.82 Time building geometry restraints manager: 3.01 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- 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 : 34.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (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 TRP 0.017 0.001 TRP B 583 HIS 0.004 0.001 HIS A 47 PHE 0.015 0.002 PHE A 667 TYR 0.009 0.001 TYR A 904 ARG 0.007 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.23941 ( 495) hydrogen bonds : angle 7.94627 ( 1437) covalent geometry : bond 0.00824 (10575) covalent geometry : angle 0.61966 (14264) *********************** 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 : 1.376 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: 1.4970 time to fit residues: 322.2423 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 : 2.025 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 809 GLN A 879 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4220 r_free = 0.4220 target = 0.195800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145890 restraints weight = 10914.783| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.11 r_work: 0.3626 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2037 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= 0.140 Angle : 0.609 9.047 14264 Z= 0.319 Chirality : 0.044 0.271 1538 Planarity : 0.004 0.039 1832 Dihedral : 5.949 72.539 1395 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.91 % Allowed : 9.14 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1241 helix: 1.60 (0.22), residues: 592 sheet: -0.55 (0.43), residues: 156 loop : -0.46 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 552 HIS 0.004 0.001 HIS A 676 PHE 0.023 0.002 PHE A 667 TYR 0.015 0.002 TYR A 56 ARG 0.005 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.05146 ( 495) hydrogen bonds : angle 4.53672 ( 1437) covalent geometry : bond 0.00309 (10575) covalent geometry : angle 0.60879 (14264) *********************** 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 196 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7888 (mm110) cc_final: 0.7652 (mp-120) REVERT: A 76 GLU cc_start: 0.6342 (mt-10) cc_final: 0.6103 (mm-30) REVERT: A 130 MET cc_start: 0.7566 (mmm) cc_final: 0.6743 (mmt) REVERT: A 179 LYS cc_start: 0.7248 (tptp) cc_final: 0.6868 (mmmm) REVERT: A 265 TYR cc_start: 0.7165 (m-10) cc_final: 0.6871 (m-10) REVERT: A 282 MET cc_start: 0.7588 (tpp) cc_final: 0.7312 (tpp) REVERT: A 352 ASP cc_start: 0.7697 (m-30) cc_final: 0.7459 (m-30) REVERT: A 384 ASN cc_start: 0.7826 (t0) cc_final: 0.7184 (m-40) REVERT: A 441 MET cc_start: 0.8360 (ttm) cc_final: 0.8133 (ttm) REVERT: A 453 GLU cc_start: 0.6945 (tt0) cc_final: 0.6437 (tm-30) REVERT: A 474 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: A 697 MET cc_start: 0.8162 (tpt) cc_final: 0.7900 (mmp) REVERT: A 732 MET cc_start: 0.6828 (tpt) cc_final: 0.6299 (mmm) REVERT: A 734 PHE cc_start: 0.8118 (t80) cc_final: 0.7872 (t80) REVERT: A 738 GLN cc_start: 0.7078 (mm110) cc_final: 0.6821 (mp10) REVERT: A 745 MET cc_start: 0.8090 (tpt) cc_final: 0.7729 (mmm) REVERT: A 780 TRP cc_start: 0.7973 (t-100) cc_final: 0.7739 (t-100) REVERT: A 794 PHE cc_start: 0.8623 (p90) cc_final: 0.8319 (p90) REVERT: A 852 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6701 (mtm-85) REVERT: A 886 LYS cc_start: 0.7645 (ptpt) cc_final: 0.6975 (pttm) REVERT: A 933 ASP cc_start: 0.8276 (t0) cc_final: 0.7782 (t70) REVERT: A 977 PHE cc_start: 0.8246 (t80) cc_final: 0.8033 (t80) REVERT: B 472 ARG cc_start: 0.6491 (tmm-80) cc_final: 0.6078 (ttm170) REVERT: B 479 MET cc_start: 0.6869 (mtp) cc_final: 0.6575 (mpp) REVERT: B 520 GLU cc_start: 0.7671 (tt0) cc_final: 0.7246 (pm20) REVERT: B 540 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6330 (t0) REVERT: B 547 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6529 (mt-10) REVERT: B 555 GLU cc_start: 0.6418 (tp30) cc_final: 0.6207 (tt0) REVERT: B 559 ILE cc_start: 0.6848 (mt) cc_final: 0.6602 (mp) outliers start: 22 outliers final: 10 residues processed: 185 average time/residue: 1.8238 time to fit residues: 360.0400 Evaluate side-chains 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 327 SER 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 121 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** A 936 HIS B 478 GLN B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.191665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140861 restraints weight = 11074.869| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.08 r_work: 0.3482 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10575 Z= 0.253 Angle : 0.660 8.742 14264 Z= 0.341 Chirality : 0.047 0.286 1538 Planarity : 0.005 0.042 1832 Dihedral : 6.350 83.267 1393 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 3.05 % Allowed : 11.66 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1241 helix: 1.19 (0.21), residues: 591 sheet: -0.69 (0.43), residues: 158 loop : -0.70 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 552 HIS 0.006 0.001 HIS A 362 PHE 0.027 0.002 PHE A 667 TYR 0.022 0.002 TYR A 182 ARG 0.007 0.001 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 495) hydrogen bonds : angle 4.55280 ( 1437) covalent geometry : bond 0.00620 (10575) covalent geometry : angle 0.66034 (14264) *********************** 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 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7977 (mm110) cc_final: 0.7743 (mp-120) REVERT: A 130 MET cc_start: 0.7640 (mmm) cc_final: 0.6962 (mmt) REVERT: A 172 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: A 179 LYS cc_start: 0.7357 (tptp) cc_final: 0.7056 (mmmm) REVERT: A 265 TYR cc_start: 0.7286 (m-10) cc_final: 0.6977 (m-10) REVERT: A 282 MET cc_start: 0.7509 (tpp) cc_final: 0.7220 (tpp) REVERT: A 384 ASN cc_start: 0.8105 (t0) cc_final: 0.7248 (m-40) REVERT: A 441 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8165 (ttm) REVERT: A 453 GLU cc_start: 0.6921 (tt0) cc_final: 0.6441 (tm-30) REVERT: A 474 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 697 MET cc_start: 0.8259 (tpt) cc_final: 0.8027 (mmp) REVERT: A 732 MET cc_start: 0.6794 (tpt) cc_final: 0.6242 (mmm) REVERT: A 739 MET cc_start: 0.8688 (mtt) cc_final: 0.8252 (mtt) REVERT: A 745 MET cc_start: 0.8323 (tpt) cc_final: 0.7964 (mmm) REVERT: A 767 GLU cc_start: 0.7025 (pm20) cc_final: 0.6635 (pm20) REVERT: A 794 PHE cc_start: 0.8561 (p90) cc_final: 0.8236 (p90) REVERT: A 852 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.6958 (mtm-85) REVERT: A 886 LYS cc_start: 0.7787 (ptpt) cc_final: 0.7046 (pttm) REVERT: A 933 ASP cc_start: 0.8348 (t0) cc_final: 0.7610 (t0) REVERT: B 345 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7145 (pt0) REVERT: B 472 ARG cc_start: 0.6548 (tmm-80) cc_final: 0.6181 (ttm170) REVERT: B 479 MET cc_start: 0.6621 (mtp) cc_final: 0.6293 (mpp) REVERT: B 520 GLU cc_start: 0.7662 (tt0) cc_final: 0.7251 (pm20) REVERT: B 540 ASP cc_start: 0.6919 (t70) cc_final: 0.6309 (t0) REVERT: B 555 GLU cc_start: 0.6685 (tp30) cc_final: 0.6359 (tt0) REVERT: B 559 ILE cc_start: 0.6982 (mt) cc_final: 0.6693 (mp) outliers start: 35 outliers final: 13 residues processed: 171 average time/residue: 1.2830 time to fit residues: 235.6715 Evaluate side-chains 155 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 172 GLU 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 342 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 484 VAL 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 Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.194955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145331 restraints weight = 10987.536| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.20 r_work: 0.3600 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2680 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= 0.132 Angle : 0.536 8.838 14264 Z= 0.280 Chirality : 0.042 0.280 1538 Planarity : 0.004 0.043 1832 Dihedral : 6.089 84.089 1393 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 3.13 % Allowed : 14.10 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1241 helix: 1.48 (0.22), residues: 594 sheet: -0.34 (0.44), residues: 150 loop : -0.66 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 552 HIS 0.004 0.001 HIS A 665 PHE 0.022 0.001 PHE A 667 TYR 0.015 0.001 TYR B 470 ARG 0.003 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 495) hydrogen bonds : angle 4.15907 ( 1437) covalent geometry : bond 0.00305 (10575) covalent geometry : angle 0.53586 (14264) *********************** 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 191 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7685 (mmm) cc_final: 0.6962 (mmt) REVERT: A 179 LYS cc_start: 0.7241 (tptp) cc_final: 0.6851 (mmmm) REVERT: A 265 TYR cc_start: 0.7181 (m-10) cc_final: 0.6859 (m-10) REVERT: A 269 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7849 (tp40) REVERT: A 282 MET cc_start: 0.7550 (tpp) cc_final: 0.7303 (tpp) REVERT: A 384 ASN cc_start: 0.8004 (t0) cc_final: 0.7270 (m-40) REVERT: A 441 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8143 (ttm) REVERT: A 453 GLU cc_start: 0.6883 (tt0) cc_final: 0.6345 (tm-30) REVERT: A 732 MET cc_start: 0.6759 (tpt) cc_final: 0.6290 (mmm) REVERT: A 735 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5904 (tm) REVERT: A 739 MET cc_start: 0.8616 (mtt) cc_final: 0.8395 (mtt) REVERT: A 745 MET cc_start: 0.8312 (tpt) cc_final: 0.8031 (mmm) REVERT: A 789 MET cc_start: 0.7579 (mtt) cc_final: 0.7245 (mtm) REVERT: A 794 PHE cc_start: 0.8576 (p90) cc_final: 0.8313 (p90) REVERT: A 822 ASN cc_start: 0.7853 (t0) cc_final: 0.7409 (m-40) REVERT: A 852 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6845 (mtm-85) REVERT: A 886 LYS cc_start: 0.7660 (ptpt) cc_final: 0.6973 (pttm) REVERT: A 933 ASP cc_start: 0.8302 (t0) cc_final: 0.7590 (t0) REVERT: B 364 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5434 (mpp) REVERT: B 472 ARG cc_start: 0.6466 (tmm-80) cc_final: 0.6168 (ttm170) REVERT: B 479 MET cc_start: 0.6804 (mtp) cc_final: 0.6477 (mpp) REVERT: B 520 GLU cc_start: 0.7626 (tt0) cc_final: 0.7317 (pm20) REVERT: B 540 ASP cc_start: 0.6836 (t70) cc_final: 0.6254 (t0) REVERT: B 547 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6690 (mt-10) REVERT: B 555 GLU cc_start: 0.7026 (tp30) cc_final: 0.6661 (tt0) REVERT: B 559 ILE cc_start: 0.7068 (mt) cc_final: 0.6843 (mp) outliers start: 36 outliers final: 15 residues processed: 177 average time/residue: 1.2019 time to fit residues: 230.1062 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 718 ILE Chi-restraints excluded: chain A residue 735 LEU 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 972 THR Chi-restraints excluded: chain A residue 993 GLN 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 41 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.193008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142629 restraints weight = 10957.595| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.08 r_work: 0.3507 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10575 Z= 0.194 Angle : 0.595 8.852 14264 Z= 0.309 Chirality : 0.045 0.291 1538 Planarity : 0.005 0.043 1832 Dihedral : 6.406 89.038 1393 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 3.66 % Allowed : 14.88 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1241 helix: 1.36 (0.22), residues: 593 sheet: -0.53 (0.42), residues: 154 loop : -0.77 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 552 HIS 0.004 0.001 HIS A1048 PHE 0.025 0.002 PHE A 667 TYR 0.024 0.002 TYR A 182 ARG 0.004 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 495) hydrogen bonds : angle 4.25545 ( 1437) covalent geometry : bond 0.00473 (10575) covalent geometry : angle 0.59495 (14264) *********************** 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 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7583 (mmm) cc_final: 0.6887 (mmt) REVERT: A 179 LYS cc_start: 0.7184 (tptp) cc_final: 0.6783 (mmmm) REVERT: A 249 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7568 (tmtt) REVERT: A 265 TYR cc_start: 0.7112 (m-10) cc_final: 0.6792 (m-10) REVERT: A 269 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7894 (tp40) REVERT: A 282 MET cc_start: 0.7489 (tpp) cc_final: 0.7254 (tpp) REVERT: A 384 ASN cc_start: 0.8035 (t0) cc_final: 0.7267 (m-40) REVERT: A 441 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: A 453 GLU cc_start: 0.6788 (tt0) cc_final: 0.6342 (tm-30) REVERT: A 732 MET cc_start: 0.6738 (tpt) cc_final: 0.6206 (mmm) REVERT: A 739 MET cc_start: 0.8570 (mtt) cc_final: 0.8314 (mtt) REVERT: A 745 MET cc_start: 0.8350 (tpt) cc_final: 0.8064 (mmm) REVERT: A 794 PHE cc_start: 0.8607 (p90) cc_final: 0.8319 (p90) REVERT: A 822 ASN cc_start: 0.7906 (t0) cc_final: 0.7399 (m-40) REVERT: A 886 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7065 (pttm) REVERT: A 933 ASP cc_start: 0.8336 (t0) cc_final: 0.7566 (t0) REVERT: B 469 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: B 472 ARG cc_start: 0.6523 (tmm-80) cc_final: 0.6265 (ttm170) REVERT: B 479 MET cc_start: 0.6653 (mtp) cc_final: 0.6320 (mpp) REVERT: B 520 GLU cc_start: 0.7524 (tt0) cc_final: 0.7274 (pm20) REVERT: B 540 ASP cc_start: 0.6850 (t70) cc_final: 0.6284 (t0) REVERT: B 547 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6721 (mt-10) REVERT: B 555 GLU cc_start: 0.7039 (tp30) cc_final: 0.6621 (tt0) outliers start: 42 outliers final: 18 residues processed: 176 average time/residue: 1.2183 time to fit residues: 233.9165 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 172 GLU 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 342 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 650 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 469 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B 457 GLN 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 = 0.195867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145227 restraints weight = 11067.570| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.12 r_work: 0.3629 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10575 Z= 0.121 Angle : 0.521 8.786 14264 Z= 0.272 Chirality : 0.041 0.282 1538 Planarity : 0.004 0.043 1832 Dihedral : 6.111 87.933 1393 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 3.66 % Allowed : 15.84 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1241 helix: 1.58 (0.22), residues: 593 sheet: -0.61 (0.42), residues: 158 loop : -0.62 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 PHE 0.022 0.001 PHE A 667 TYR 0.013 0.001 TYR B 470 ARG 0.002 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 495) hydrogen bonds : angle 4.02538 ( 1437) covalent geometry : bond 0.00278 (10575) covalent geometry : angle 0.52050 (14264) *********************** 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 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7817 (m-80) cc_final: 0.7582 (m-80) REVERT: A 130 MET cc_start: 0.7604 (mmm) cc_final: 0.6863 (mmt) REVERT: A 179 LYS cc_start: 0.7188 (tptp) cc_final: 0.6774 (mmmm) REVERT: A 265 TYR cc_start: 0.7033 (m-10) cc_final: 0.6673 (m-10) REVERT: A 282 MET cc_start: 0.7481 (tpp) cc_final: 0.7249 (tpp) REVERT: A 384 ASN cc_start: 0.7972 (t0) cc_final: 0.7239 (m-40) REVERT: A 441 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8119 (ttm) REVERT: A 453 GLU cc_start: 0.6687 (tt0) cc_final: 0.6222 (tm-30) REVERT: A 561 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8135 (mp) REVERT: A 732 MET cc_start: 0.6737 (tpt) cc_final: 0.5984 (mmm) REVERT: A 735 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5861 (tm) REVERT: A 739 MET cc_start: 0.8556 (mtt) cc_final: 0.8167 (mtt) REVERT: A 745 MET cc_start: 0.8333 (tpt) cc_final: 0.8080 (mmm) REVERT: A 780 TRP cc_start: 0.8204 (t-100) cc_final: 0.7877 (t-100) REVERT: A 789 MET cc_start: 0.7494 (mtt) cc_final: 0.7177 (mtm) REVERT: A 794 PHE cc_start: 0.8495 (p90) cc_final: 0.8228 (p90) REVERT: A 822 ASN cc_start: 0.7865 (t0) cc_final: 0.7369 (m-40) REVERT: A 886 LYS cc_start: 0.7689 (ptpt) cc_final: 0.6946 (pttm) REVERT: A 933 ASP cc_start: 0.8315 (t0) cc_final: 0.7544 (t0) REVERT: B 364 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5581 (tmt) REVERT: B 472 ARG cc_start: 0.6349 (tmm-80) cc_final: 0.6141 (ttm170) REVERT: B 479 MET cc_start: 0.6720 (mtp) cc_final: 0.6364 (mpp) REVERT: B 520 GLU cc_start: 0.7513 (tt0) cc_final: 0.7215 (pm20) REVERT: B 540 ASP cc_start: 0.6773 (t70) cc_final: 0.6205 (t0) REVERT: B 547 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6693 (mt-10) outliers start: 42 outliers final: 16 residues processed: 173 average time/residue: 1.1282 time to fit residues: 211.5375 Evaluate side-chains 161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 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 561 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 735 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0020 chunk 87 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS A 931 HIS B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.194417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144195 restraints weight = 11114.194| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.07 r_work: 0.3534 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3021 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= 0.158 Angle : 0.564 8.843 14264 Z= 0.293 Chirality : 0.043 0.301 1538 Planarity : 0.004 0.044 1832 Dihedral : 6.014 82.531 1393 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1241 helix: 1.53 (0.22), residues: 593 sheet: -0.58 (0.42), residues: 159 loop : -0.65 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.002 PHE A 667 TYR 0.017 0.001 TYR A 904 ARG 0.003 0.000 ARG A 916 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 495) hydrogen bonds : angle 4.08734 ( 1437) covalent geometry : bond 0.00377 (10575) covalent geometry : angle 0.56439 (14264) *********************** 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 172 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7578 (mmm) cc_final: 0.6831 (mmt) REVERT: A 179 LYS cc_start: 0.7158 (tptp) cc_final: 0.6742 (mmmm) REVERT: A 265 TYR cc_start: 0.7041 (m-10) cc_final: 0.6700 (m-10) REVERT: A 282 MET cc_start: 0.7465 (tpp) cc_final: 0.7213 (tpp) REVERT: A 384 ASN cc_start: 0.8058 (t0) cc_final: 0.7257 (m-40) REVERT: A 441 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8169 (ttm) REVERT: A 453 GLU cc_start: 0.6739 (tt0) cc_final: 0.6263 (tm-30) REVERT: A 732 MET cc_start: 0.6719 (tpt) cc_final: 0.6047 (mmm) REVERT: A 739 MET cc_start: 0.8565 (mtt) cc_final: 0.8332 (mtt) REVERT: A 780 TRP cc_start: 0.8228 (t-100) cc_final: 0.7898 (t-100) REVERT: A 789 MET cc_start: 0.7699 (mtt) cc_final: 0.7322 (mtm) REVERT: A 822 ASN cc_start: 0.7892 (t0) cc_final: 0.7394 (m-40) REVERT: A 886 LYS cc_start: 0.7785 (ptpt) cc_final: 0.7036 (pttm) REVERT: A 933 ASP cc_start: 0.8269 (t0) cc_final: 0.7509 (t0) REVERT: B 345 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: B 364 MET cc_start: 0.6038 (OUTLIER) cc_final: 0.5619 (tmt) REVERT: B 469 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: B 479 MET cc_start: 0.6715 (mtp) cc_final: 0.6372 (mpp) REVERT: B 520 GLU cc_start: 0.7414 (tt0) cc_final: 0.7025 (pm20) REVERT: B 540 ASP cc_start: 0.6786 (t70) cc_final: 0.6253 (t0) REVERT: B 547 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6671 (mt-10) REVERT: B 559 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6442 (mp) outliers start: 29 outliers final: 17 residues processed: 160 average time/residue: 1.1363 time to fit residues: 196.8686 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 204 LYS 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 483 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 679 THR 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 469 GLU Chi-restraints excluded: chain B residue 559 ILE 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 91 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 875 HIS A 879 GLN B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.194841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144750 restraints weight = 10996.785| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.22 r_work: 0.3610 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3110 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= 0.148 Angle : 0.555 8.809 14264 Z= 0.288 Chirality : 0.043 0.306 1538 Planarity : 0.004 0.045 1832 Dihedral : 5.877 78.595 1393 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 18.28 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1241 helix: 1.49 (0.22), residues: 595 sheet: -0.62 (0.42), residues: 159 loop : -0.60 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.002 PHE A 794 TYR 0.018 0.001 TYR A 904 ARG 0.002 0.000 ARG A 916 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 495) hydrogen bonds : angle 4.04851 ( 1437) covalent geometry : bond 0.00353 (10575) covalent geometry : angle 0.55508 (14264) *********************** 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 177 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7621 (mmm) cc_final: 0.6895 (mmt) REVERT: A 179 LYS cc_start: 0.7167 (tptp) cc_final: 0.6745 (mmmm) REVERT: A 265 TYR cc_start: 0.7037 (m-10) cc_final: 0.6699 (m-10) REVERT: A 282 MET cc_start: 0.7431 (tpp) cc_final: 0.7192 (tpp) REVERT: A 384 ASN cc_start: 0.8032 (t0) cc_final: 0.7244 (m-40) REVERT: A 441 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8166 (ttm) REVERT: A 453 GLU cc_start: 0.6697 (tt0) cc_final: 0.6188 (tm-30) REVERT: A 561 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 628 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8753 (tt) REVERT: A 732 MET cc_start: 0.6733 (tpt) cc_final: 0.6207 (mmm) REVERT: A 735 LEU cc_start: 0.6141 (tt) cc_final: 0.5864 (tm) REVERT: A 739 MET cc_start: 0.8527 (mtt) cc_final: 0.8050 (mtt) REVERT: A 780 TRP cc_start: 0.8202 (t-100) cc_final: 0.7878 (t-100) REVERT: A 789 MET cc_start: 0.7667 (mtt) cc_final: 0.7322 (mtm) REVERT: A 822 ASN cc_start: 0.7886 (t0) cc_final: 0.7381 (m-40) REVERT: A 886 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7078 (pttm) REVERT: A 933 ASP cc_start: 0.8289 (t0) cc_final: 0.7496 (t0) REVERT: A 1029 ASP cc_start: 0.7623 (m-30) cc_final: 0.7211 (m-30) REVERT: B 364 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5612 (tmt) REVERT: B 469 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: B 479 MET cc_start: 0.6797 (mtp) cc_final: 0.6434 (mpp) REVERT: B 520 GLU cc_start: 0.7354 (tt0) cc_final: 0.7016 (pm20) REVERT: B 540 ASP cc_start: 0.6777 (t70) cc_final: 0.6249 (t0) REVERT: B 547 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6685 (mt-10) REVERT: B 559 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6461 (mp) outliers start: 34 outliers final: 21 residues processed: 165 average time/residue: 1.1097 time to fit residues: 198.9404 Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 204 LYS 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 433 THR 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 561 ILE 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 679 THR 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 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 469 GLU Chi-restraints excluded: chain B residue 559 ILE 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 82 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 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 = 0.4209 r_free = 0.4209 target = 0.194988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144394 restraints weight = 11103.454| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.16 r_work: 0.3543 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10575 Z= 0.147 Angle : 0.558 8.865 14264 Z= 0.289 Chirality : 0.043 0.317 1538 Planarity : 0.004 0.045 1832 Dihedral : 5.823 76.981 1393 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.13 % Allowed : 18.28 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1241 helix: 1.49 (0.22), residues: 595 sheet: -0.62 (0.42), residues: 159 loop : -0.59 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.005 0.001 HIS A 450 PHE 0.023 0.002 PHE A 667 TYR 0.018 0.001 TYR A 904 ARG 0.003 0.000 ARG A 916 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 495) hydrogen bonds : angle 4.05105 ( 1437) covalent geometry : bond 0.00348 (10575) covalent geometry : angle 0.55838 (14264) *********************** 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 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7623 (mmm) cc_final: 0.6898 (mmt) REVERT: A 172 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: A 179 LYS cc_start: 0.7155 (tptp) cc_final: 0.6730 (mmmm) REVERT: A 265 TYR cc_start: 0.7038 (m-10) cc_final: 0.6697 (m-10) REVERT: A 282 MET cc_start: 0.7416 (tpp) cc_final: 0.7171 (tpp) REVERT: A 332 SER cc_start: 0.8155 (m) cc_final: 0.7954 (t) REVERT: A 384 ASN cc_start: 0.8048 (t0) cc_final: 0.7244 (m-40) REVERT: A 441 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8164 (ttm) REVERT: A 453 GLU cc_start: 0.6689 (tt0) cc_final: 0.6179 (tm-30) REVERT: A 561 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 628 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8689 (tt) REVERT: A 732 MET cc_start: 0.6645 (tpt) cc_final: 0.6129 (mmm) REVERT: A 735 LEU cc_start: 0.6143 (tt) cc_final: 0.5872 (tm) REVERT: A 739 MET cc_start: 0.8529 (mtt) cc_final: 0.8076 (mtt) REVERT: A 780 TRP cc_start: 0.8203 (t-100) cc_final: 0.7874 (t-100) REVERT: A 789 MET cc_start: 0.7693 (mtt) cc_final: 0.7335 (mtm) REVERT: A 822 ASN cc_start: 0.7901 (t0) cc_final: 0.7393 (m-40) REVERT: A 825 GLN cc_start: 0.8573 (mm110) cc_final: 0.8213 (mm110) REVERT: A 886 LYS cc_start: 0.7782 (ptpt) cc_final: 0.7056 (pttm) REVERT: A 933 ASP cc_start: 0.8263 (t0) cc_final: 0.7465 (t0) REVERT: A 1029 ASP cc_start: 0.7627 (m-30) cc_final: 0.7226 (m-30) REVERT: B 364 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5594 (tmt) REVERT: B 469 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6358 (tt0) REVERT: B 479 MET cc_start: 0.6804 (mtp) cc_final: 0.6432 (mpp) REVERT: B 520 GLU cc_start: 0.7351 (tt0) cc_final: 0.7022 (pm20) REVERT: B 547 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6653 (mt-10) REVERT: B 559 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6420 (mp) outliers start: 36 outliers final: 23 residues processed: 160 average time/residue: 1.1101 time to fit residues: 193.1712 Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 204 LYS 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 433 THR 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 561 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 679 THR 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 345 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 559 ILE 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 98 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 = 0.4227 r_free = 0.4227 target = 0.196917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145707 restraints weight = 11055.550| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.38 r_work: 0.3541 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10575 Z= 0.119 Angle : 0.528 9.148 14264 Z= 0.274 Chirality : 0.042 0.324 1538 Planarity : 0.004 0.045 1832 Dihedral : 5.566 72.585 1393 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.87 % Allowed : 18.36 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1241 helix: 1.64 (0.22), residues: 593 sheet: -0.59 (0.42), residues: 161 loop : -0.58 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A 450 PHE 0.026 0.002 PHE A 794 TYR 0.015 0.001 TYR A 904 ARG 0.003 0.000 ARG B 503 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 495) hydrogen bonds : angle 3.92623 ( 1437) covalent geometry : bond 0.00273 (10575) covalent geometry : angle 0.52839 (14264) ********************** 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 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7769 (mmm) cc_final: 0.7013 (mmt) REVERT: A 172 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: A 179 LYS cc_start: 0.7055 (tptp) cc_final: 0.6620 (mmmm) REVERT: A 265 TYR cc_start: 0.7000 (m-10) cc_final: 0.6653 (m-10) REVERT: A 282 MET cc_start: 0.7479 (tpp) cc_final: 0.7233 (tpp) REVERT: A 332 SER cc_start: 0.8115 (m) cc_final: 0.7883 (t) REVERT: A 384 ASN cc_start: 0.8020 (t0) cc_final: 0.7247 (m-40) REVERT: A 441 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8149 (ttm) REVERT: A 453 GLU cc_start: 0.6609 (tt0) cc_final: 0.6127 (tm-30) REVERT: A 561 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 628 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 732 MET cc_start: 0.6633 (tpt) cc_final: 0.6099 (mmm) REVERT: A 735 LEU cc_start: 0.6119 (tt) cc_final: 0.5886 (tm) REVERT: A 739 MET cc_start: 0.8493 (mtt) cc_final: 0.8113 (mtt) REVERT: A 746 ASP cc_start: 0.8404 (t0) cc_final: 0.7995 (m-30) REVERT: A 780 TRP cc_start: 0.8208 (t-100) cc_final: 0.7876 (t-100) REVERT: A 789 MET cc_start: 0.7567 (mtt) cc_final: 0.7219 (mtm) REVERT: A 822 ASN cc_start: 0.7940 (t0) cc_final: 0.7418 (m-40) REVERT: A 825 GLN cc_start: 0.8567 (mm110) cc_final: 0.8192 (mm110) REVERT: A 886 LYS cc_start: 0.7746 (ptpt) cc_final: 0.6998 (pttm) REVERT: A 933 ASP cc_start: 0.8254 (t0) cc_final: 0.7469 (t0) REVERT: A 1029 ASP cc_start: 0.7638 (m-30) cc_final: 0.7257 (m-30) REVERT: B 364 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5825 (mtt) REVERT: B 469 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6243 (tt0) REVERT: B 479 MET cc_start: 0.6771 (mtp) cc_final: 0.6380 (mpp) REVERT: B 520 GLU cc_start: 0.7352 (tt0) cc_final: 0.7021 (pm20) REVERT: B 547 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6711 (mt-10) REVERT: B 559 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6544 (tt) outliers start: 33 outliers final: 19 residues processed: 161 average time/residue: 1.1787 time to fit residues: 208.3354 Evaluate side-chains 161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 172 GLU 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 561 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 679 THR 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 345 GLU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 559 ILE 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 100 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 450 HIS ** 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 = 0.4216 r_free = 0.4216 target = 0.195469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144916 restraints weight = 10955.523| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.10 r_work: 0.3618 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10575 Z= 0.140 Angle : 0.552 9.233 14264 Z= 0.285 Chirality : 0.042 0.321 1538 Planarity : 0.004 0.046 1832 Dihedral : 5.527 68.811 1393 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.70 % Allowed : 18.45 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1241 helix: 1.58 (0.22), residues: 595 sheet: -0.55 (0.42), residues: 161 loop : -0.57 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.004 0.001 HIS A 450 PHE 0.023 0.002 PHE A 667 TYR 0.018 0.001 TYR A 904 ARG 0.002 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 495) hydrogen bonds : angle 3.95895 ( 1437) covalent geometry : bond 0.00331 (10575) covalent geometry : angle 0.55224 (14264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10118.40 seconds wall clock time: 180 minutes 15.39 seconds (10815.39 seconds total)