Starting phenix.real_space_refine on Tue Jul 29 17:11:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p23_17357/07_2025/8p23_17357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p23_17357/07_2025/8p23_17357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p23_17357/07_2025/8p23_17357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p23_17357/07_2025/8p23_17357.map" model { file = "/net/cci-nas-00/data/ceres_data/8p23_17357/07_2025/8p23_17357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p23_17357/07_2025/8p23_17357.cif" } resolution = 3.17 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 S 71 5.16 5 C 7126 2.51 5 N 2000 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 11399 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5510 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 665} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5735 Classifications: {'peptide': 715} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 693} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' ZN': 1, 'ATP': 2, 'CTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10830 SG CYS B 683 16.674 87.785 61.025 1.00102.46 S ATOM 10921 SG CYS B 695 14.070 86.300 63.500 1.00104.69 S ATOM 10943 SG CYS B 698 14.686 84.344 61.636 1.00105.10 S Time building chain proxies: 7.03, per 1000 atoms: 0.62 Number of scatterers: 11399 At special positions: 0 Unit cell: (82.422, 137.948, 118.861, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 71 16.00 P 15 15.00 O 2186 8.00 N 2000 7.00 C 7126 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: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 698 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 695 " 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 50.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 36 through 49 removed outlier: 4.390A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.979A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 4.157A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 Proline residue: A 136 - end of helix removed outlier: 3.727A pdb=" N ASP A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.625A pdb=" N CYS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.631A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 274 through 299 removed outlier: 3.691A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'A' and resid 367 through 378 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 455 through 487 removed outlier: 4.122A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 7.032A pdb=" N LYS A 491 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.310A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 570 removed outlier: 3.692A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.676A pdb=" N LYS A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.650A pdb=" N LEU A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.670A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.517A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 70 removed outlier: 4.095A pdb=" N ASP B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.801A pdb=" N ALA B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 3.890A pdb=" N ARG B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 removed outlier: 3.784A pdb=" N MET B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Proline residue: B 136 - end of helix removed outlier: 3.602A pdb=" N LEU B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.533A pdb=" N HIS B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.531A pdb=" N TYR B 163 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 196 through 210 removed outlier: 3.551A pdb=" N ALA B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 229 through 247 removed outlier: 4.367A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 299 removed outlier: 3.621A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.615A pdb=" N ARG B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.832A pdb=" N LEU B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 455 through 487 removed outlier: 3.579A pdb=" N ASP B 472 " --> pdb=" O ASP B 468 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 473 " --> pdb=" O ASN B 469 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.962A pdb=" N ILE B 517 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 4.001A pdb=" N LEU B 536 " --> pdb=" O CYS B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 570 removed outlier: 4.161A pdb=" N GLN B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 585 removed outlier: 4.161A pdb=" N GLY B 585 " --> pdb=" O GLY B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 585' Processing helix chain 'B' and resid 586 through 596 removed outlier: 3.979A pdb=" N LYS B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.625A pdb=" N ASP B 633 " --> pdb=" O PRO B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.514A pdb=" N THR B 650 " --> pdb=" O GLY B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.597A pdb=" N VAL B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 666 " --> pdb=" O MET B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 removed outlier: 3.612A pdb=" N LEU B 728 " --> pdb=" O LYS B 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158 removed outlier: 4.989A pdb=" N ASN A 435 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLY A 523 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 437 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLY A 525 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 439 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE A 527 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 441 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.818A pdb=" N VAL A 172 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER A 313 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE A 352 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 315 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LYS A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR A 317 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 643 through 645 removed outlier: 6.514A pdb=" N VAL A 643 " --> pdb=" O ASN A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 5.151A pdb=" N ASN B 435 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLY B 523 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER B 437 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLY B 525 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER B 439 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE B 527 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE B 441 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 526 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 173 removed outlier: 6.810A pdb=" N VAL B 172 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN B 219 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 316 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 221 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 317 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 414 removed outlier: 4.300A pdb=" N THR B 418 " --> pdb=" O MET B 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 678 through 679 444 hydrogen bonds defined for protein. 1278 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: 2.87 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1921 1.31 - 1.43: 3075 1.43 - 1.56: 6483 1.56 - 1.68: 25 1.68 - 1.81: 121 Bond restraints: 11625 Sorted by residual: bond pdb=" C TYR B 371 " pdb=" O TYR B 371 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.15e-02 7.56e+03 2.19e+01 bond pdb=" C VAL B 659 " pdb=" O VAL B 659 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.19e-02 7.06e+03 1.97e+01 bond pdb=" C ALA B 374 " pdb=" O ALA B 374 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.26e-02 6.30e+03 1.57e+01 bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.531 1.477 0.053 1.37e-02 5.33e+03 1.52e+01 bond pdb=" N ILE B 735 " pdb=" CA ILE B 735 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.30e-02 5.92e+03 1.34e+01 ... (remaining 11620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 15518 2.82 - 5.64: 165 5.64 - 8.46: 25 8.46 - 11.28: 5 11.28 - 14.10: 1 Bond angle restraints: 15714 Sorted by residual: angle pdb=" N GLN B 212 " pdb=" CA GLN B 212 " pdb=" C GLN B 212 " ideal model delta sigma weight residual 112.57 98.47 14.10 1.13e+00 7.83e-01 1.56e+02 angle pdb=" N HIS B 734 " pdb=" CA HIS B 734 " pdb=" C HIS B 734 " ideal model delta sigma weight residual 110.24 100.41 9.83 1.47e+00 4.63e-01 4.47e+01 angle pdb=" C ARG B 305 " pdb=" CA ARG B 305 " pdb=" CB ARG B 305 " ideal model delta sigma weight residual 109.80 99.24 10.56 1.61e+00 3.86e-01 4.30e+01 angle pdb=" N ASN B 213 " pdb=" CA ASN B 213 " pdb=" C ASN B 213 " ideal model delta sigma weight residual 112.54 103.50 9.04 1.51e+00 4.39e-01 3.59e+01 angle pdb=" N THR B 650 " pdb=" CA THR B 650 " pdb=" C THR B 650 " ideal model delta sigma weight residual 113.38 106.21 7.17 1.23e+00 6.61e-01 3.40e+01 ... (remaining 15709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6559 17.25 - 34.50: 354 34.50 - 51.75: 112 51.75 - 69.00: 40 69.00 - 86.25: 13 Dihedral angle restraints: 7078 sinusoidal: 2991 harmonic: 4087 Sorted by residual: dihedral pdb=" C CYS B 327 " pdb=" N CYS B 327 " pdb=" CA CYS B 327 " pdb=" CB CYS B 327 " ideal model delta harmonic sigma weight residual -122.60 -108.55 -14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C ARG B 305 " pdb=" N ARG B 305 " pdb=" CA ARG B 305 " pdb=" CB ARG B 305 " ideal model delta harmonic sigma weight residual -122.60 -109.48 -13.12 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CA VAL B 714 " pdb=" C VAL B 714 " pdb=" N GLY B 715 " pdb=" CA GLY B 715 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1582 0.091 - 0.182: 98 0.182 - 0.273: 11 0.273 - 0.363: 11 0.363 - 0.454: 1 Chirality restraints: 1703 Sorted by residual: chirality pdb=" CA LYS B 33 " pdb=" N LYS B 33 " pdb=" C LYS B 33 " pdb=" CB LYS B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA CYS B 327 " pdb=" N CYS B 327 " pdb=" C CYS B 327 " pdb=" CB CYS B 327 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA HIS B 734 " pdb=" N HIS B 734 " pdb=" C HIS B 734 " pdb=" CB HIS B 734 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1700 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 302 " -0.031 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C ILE B 302 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 302 " -0.040 2.00e-02 2.50e+03 pdb=" N HIS B 303 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 326 " -0.394 9.50e-02 1.11e+02 1.77e-01 1.91e+01 pdb=" NE ARG B 326 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 326 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 326 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 403 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO B 404 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " -0.041 5.00e-02 4.00e+02 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 254 2.65 - 3.21: 11071 3.21 - 3.78: 16233 3.78 - 4.34: 22097 4.34 - 4.90: 36886 Nonbonded interactions: 86541 Sorted by model distance: nonbonded pdb=" N CYS B 698 " pdb="ZN ZN B 804 " model vdw 2.090 2.310 nonbonded pdb=" O ALA A 391 " pdb=" OG1 THR A 392 " model vdw 2.139 3.040 nonbonded pdb=" O PHE B 526 " pdb=" OG SER B 610 " model vdw 2.155 3.040 nonbonded pdb=" O ASP B 403 " pdb=" N GLU B 405 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP B 633 " pdb=" NH2 ARG B 636 " model vdw 2.207 3.120 ... (remaining 86536 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 33 or resid 36 through 49 or resid 55 through 71 \ or resid 75 through 735 or resid 801)) selection = (chain 'B' and (resid 2 through 184 or resid 193 through 303 or resid 310 throug \ h 676 or (resid 705 and (name N or name CA or name C or name O or name CB )) or \ resid 706 through 707 or (resid 708 and (name N or name CA or name C or name O o \ r name CB )) or resid 713 through 735 or resid 803)) } 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: 1.670 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: 0.110 Process input model: 29.000 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.004 0.054 11628 Z= 0.236 Angle : 0.692 14.103 15714 Z= 0.426 Chirality : 0.051 0.454 1703 Planarity : 0.006 0.177 2015 Dihedral : 13.197 86.251 4442 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.81 % Favored : 93.68 % Rotamer: Outliers : 4.71 % Allowed : 7.77 % Favored : 87.52 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 7.50 % 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: -0.94 (0.24), residues: 1377 helix: 1.35 (0.22), residues: 627 sheet: 0.03 (0.52), residues: 113 loop : -2.99 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 720 HIS 0.003 0.001 HIS B 303 PHE 0.010 0.001 PHE A 224 TYR 0.026 0.001 TYR B 371 ARG 0.006 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.16120 ( 444) hydrogen bonds : angle 5.93029 ( 1278) metal coordination : bond 0.00079 ( 3) covalent geometry : bond 0.00358 (11625) covalent geometry : angle 0.69248 (15714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.7766 (m-70) cc_final: 0.7203 (m-70) REVERT: A 100 MET cc_start: 0.6549 (tmm) cc_final: 0.6284 (tmm) REVERT: A 117 MET cc_start: 0.6051 (mtp) cc_final: 0.5674 (mtp) REVERT: A 138 VAL cc_start: 0.8220 (p) cc_final: 0.8014 (m) REVERT: A 140 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 238 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6853 (mm-30) REVERT: A 239 GLU cc_start: 0.6886 (tp30) cc_final: 0.6609 (mm-30) REVERT: A 241 LYS cc_start: 0.7557 (tppp) cc_final: 0.7295 (ttmt) REVERT: A 244 GLU cc_start: 0.7225 (tm-30) cc_final: 0.7011 (tm-30) REVERT: A 271 GLN cc_start: 0.7487 (pp30) cc_final: 0.7151 (pp30) REVERT: A 313 SER cc_start: 0.7493 (p) cc_final: 0.7158 (m) REVERT: A 316 ASN cc_start: 0.7722 (m-40) cc_final: 0.7441 (m-40) REVERT: A 342 ASN cc_start: 0.7132 (t0) cc_final: 0.6793 (t0) REVERT: A 352 ILE cc_start: 0.8582 (pp) cc_final: 0.8347 (pt) REVERT: A 360 ASN cc_start: 0.7690 (t0) cc_final: 0.7106 (t0) REVERT: A 476 LYS cc_start: 0.7965 (tppp) cc_final: 0.7636 (tppt) REVERT: A 564 GLU cc_start: 0.6230 (pt0) cc_final: 0.5972 (pt0) REVERT: A 594 GLN cc_start: 0.7287 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 603 ASP cc_start: 0.6924 (t70) cc_final: 0.6668 (t0) REVERT: A 622 LEU cc_start: 0.8041 (mt) cc_final: 0.7791 (mm) REVERT: A 642 TYR cc_start: 0.7449 (m-80) cc_final: 0.6816 (t80) REVERT: A 674 ASN cc_start: 0.7271 (m110) cc_final: 0.6870 (m-40) REVERT: A 719 ARG cc_start: 0.6654 (mtp180) cc_final: 0.6123 (mtp180) REVERT: B 21 MET cc_start: 0.7287 (ptm) cc_final: 0.6987 (ptm) REVERT: B 86 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 145 GLU cc_start: 0.7423 (pm20) cc_final: 0.7218 (pm20) REVERT: B 148 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7631 (mtm110) REVERT: B 214 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 238 GLU cc_start: 0.7018 (tp30) cc_final: 0.6817 (tp30) REVERT: B 239 GLU cc_start: 0.7989 (tp30) cc_final: 0.7402 (tp30) REVERT: B 299 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6136 (mpm) REVERT: B 301 THR cc_start: 0.8207 (m) cc_final: 0.7853 (m) REVERT: B 303 HIS cc_start: 0.6394 (m90) cc_final: 0.6163 (m90) REVERT: B 376 LYS cc_start: 0.7872 (tppt) cc_final: 0.7635 (ttpp) REVERT: B 397 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 429 THR cc_start: 0.8086 (t) cc_final: 0.7726 (p) REVERT: B 483 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7789 (mm-40) REVERT: B 511 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6447 (tm-30) REVERT: B 560 ASP cc_start: 0.7436 (m-30) cc_final: 0.7231 (m-30) REVERT: B 603 ASP cc_start: 0.7154 (t0) cc_final: 0.6776 (t0) REVERT: B 611 ASN cc_start: 0.6347 (p0) cc_final: 0.6054 (p0) REVERT: B 654 SER cc_start: 0.6162 (OUTLIER) cc_final: 0.5518 (p) REVERT: B 729 HIS cc_start: 0.7526 (t70) cc_final: 0.7274 (t-170) outliers start: 57 outliers final: 26 residues processed: 384 average time/residue: 0.2770 time to fit residues: 143.3845 Evaluate side-chains 337 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.0040 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.0010 chunk 108 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 0.0970 overall best weight: 0.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 114 ASN A 182 HIS A 278 GLN A 300 ASN A 395 GLN A 506 ASN A 675 HIS A 676 ASN B 78 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 541 HIS B 572 ASN B 652 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118099 restraints weight = 16239.731| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.27 r_work: 0.3499 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11628 Z= 0.121 Angle : 0.585 7.432 15714 Z= 0.307 Chirality : 0.043 0.266 1703 Planarity : 0.004 0.076 2015 Dihedral : 12.303 86.484 1741 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.74 % Favored : 93.90 % Rotamer: Outliers : 4.21 % Allowed : 13.64 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.65 (0.24), residues: 1377 helix: 1.55 (0.22), residues: 628 sheet: -0.02 (0.53), residues: 106 loop : -2.72 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS A 182 PHE 0.015 0.001 PHE A 383 TYR 0.010 0.001 TYR A 80 ARG 0.004 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 444) hydrogen bonds : angle 4.09858 ( 1278) metal coordination : bond 0.00093 ( 3) covalent geometry : bond 0.00254 (11625) covalent geometry : angle 0.58548 (15714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8226 (mtpp) REVERT: A 21 MET cc_start: 0.6831 (mpt) cc_final: 0.6586 (mtp) REVERT: A 30 HIS cc_start: 0.7953 (m-70) cc_final: 0.7685 (m-70) REVERT: A 100 MET cc_start: 0.7298 (tmm) cc_final: 0.6912 (tmm) REVERT: A 117 MET cc_start: 0.6675 (mtp) cc_final: 0.6270 (mtp) REVERT: A 238 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 239 GLU cc_start: 0.7603 (tp30) cc_final: 0.7113 (mm-30) REVERT: A 241 LYS cc_start: 0.8070 (tppp) cc_final: 0.7760 (ttmt) REVERT: A 244 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 264 GLU cc_start: 0.7595 (pm20) cc_final: 0.7376 (pm20) REVERT: A 313 SER cc_start: 0.7894 (p) cc_final: 0.7584 (m) REVERT: A 316 ASN cc_start: 0.8047 (m-40) cc_final: 0.7774 (m-40) REVERT: A 319 THR cc_start: 0.7750 (m) cc_final: 0.7282 (t) REVERT: A 342 ASN cc_start: 0.7721 (t0) cc_final: 0.7333 (t0) REVERT: A 352 ILE cc_start: 0.8573 (pp) cc_final: 0.8323 (pt) REVERT: A 357 ARG cc_start: 0.8244 (ttt90) cc_final: 0.7975 (ttt180) REVERT: A 360 ASN cc_start: 0.7799 (t0) cc_final: 0.7229 (t0) REVERT: A 462 MET cc_start: 0.7335 (ttm) cc_final: 0.6984 (ttp) REVERT: A 590 LYS cc_start: 0.7712 (mppt) cc_final: 0.7440 (mppt) REVERT: A 594 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 603 ASP cc_start: 0.7209 (t70) cc_final: 0.6933 (t0) REVERT: A 642 TYR cc_start: 0.8127 (m-80) cc_final: 0.7562 (t80) REVERT: A 674 ASN cc_start: 0.7827 (m110) cc_final: 0.7382 (m-40) REVERT: A 719 ARG cc_start: 0.6722 (mtp180) cc_final: 0.6486 (mtp180) REVERT: A 725 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7681 (mt) REVERT: B 21 MET cc_start: 0.7618 (ptm) cc_final: 0.7210 (ptm) REVERT: B 24 ILE cc_start: 0.8440 (mm) cc_final: 0.8057 (mm) REVERT: B 28 MET cc_start: 0.6522 (mmm) cc_final: 0.6113 (mmm) REVERT: B 86 GLN cc_start: 0.8319 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 145 GLU cc_start: 0.7874 (pm20) cc_final: 0.7576 (pm20) REVERT: B 148 ARG cc_start: 0.7965 (ttt-90) cc_final: 0.7754 (mtp85) REVERT: B 214 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 239 GLU cc_start: 0.8228 (tp30) cc_final: 0.7655 (tp30) REVERT: B 293 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 299 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.5793 (mpm) REVERT: B 342 ASN cc_start: 0.7884 (t0) cc_final: 0.7651 (t0) REVERT: B 372 LYS cc_start: 0.8992 (tppt) cc_final: 0.8494 (tppt) REVERT: B 376 LYS cc_start: 0.7975 (tppt) cc_final: 0.7673 (ttpp) REVERT: B 397 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 398 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8782 (mtmt) REVERT: B 429 THR cc_start: 0.8365 (t) cc_final: 0.8037 (p) REVERT: B 507 LEU cc_start: 0.7343 (pt) cc_final: 0.7003 (pp) REVERT: B 511 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6821 (tm-30) REVERT: B 560 ASP cc_start: 0.8067 (m-30) cc_final: 0.7767 (m-30) REVERT: B 603 ASP cc_start: 0.7576 (t0) cc_final: 0.7088 (t0) REVERT: B 623 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7724 (ttmm) REVERT: B 645 ILE cc_start: 0.8210 (pt) cc_final: 0.7991 (mt) REVERT: B 654 SER cc_start: 0.6089 (OUTLIER) cc_final: 0.5315 (p) REVERT: B 657 GLU cc_start: 0.7779 (tp30) cc_final: 0.7483 (tp30) REVERT: B 719 ARG cc_start: 0.8270 (mtp180) cc_final: 0.8038 (mtm110) outliers start: 51 outliers final: 29 residues processed: 343 average time/residue: 0.2861 time to fit residues: 132.9805 Evaluate side-chains 334 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 675 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 282 ASN B 541 HIS B 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111555 restraints weight = 16457.849| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.30 r_work: 0.3385 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11628 Z= 0.207 Angle : 0.635 7.267 15714 Z= 0.340 Chirality : 0.047 0.267 1703 Planarity : 0.005 0.085 2015 Dihedral : 11.395 86.286 1714 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.48 % Favored : 92.16 % Rotamer: Outliers : 4.55 % Allowed : 15.45 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.87 (0.23), residues: 1377 helix: 1.23 (0.21), residues: 636 sheet: 0.45 (0.53), residues: 107 loop : -2.84 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.017 0.001 HIS B 541 PHE 0.024 0.002 PHE A 526 TYR 0.016 0.002 TYR B 236 ARG 0.005 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.06168 ( 444) hydrogen bonds : angle 4.26226 ( 1278) metal coordination : bond 0.00282 ( 3) covalent geometry : bond 0.00478 (11625) covalent geometry : angle 0.63514 (15714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8305 (mtpp) REVERT: A 30 HIS cc_start: 0.8012 (m-70) cc_final: 0.7781 (m-70) REVERT: A 45 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: A 55 MET cc_start: 0.6982 (mpp) cc_final: 0.6673 (tpp) REVERT: A 100 MET cc_start: 0.7526 (tmm) cc_final: 0.7150 (tmm) REVERT: A 117 MET cc_start: 0.6718 (mtp) cc_final: 0.6224 (mtp) REVERT: A 238 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 241 LYS cc_start: 0.8222 (tppp) cc_final: 0.7923 (ttmt) REVERT: A 244 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 264 GLU cc_start: 0.7698 (pm20) cc_final: 0.7475 (pm20) REVERT: A 271 GLN cc_start: 0.8178 (pp30) cc_final: 0.7797 (pp30) REVERT: A 319 THR cc_start: 0.7969 (m) cc_final: 0.7364 (t) REVERT: A 334 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7997 (mp10) REVERT: A 342 ASN cc_start: 0.7805 (t0) cc_final: 0.7388 (t0) REVERT: A 352 ILE cc_start: 0.8626 (pp) cc_final: 0.8417 (pt) REVERT: A 360 ASN cc_start: 0.7912 (t0) cc_final: 0.7286 (t0) REVERT: A 380 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7758 (ttp80) REVERT: A 414 MET cc_start: 0.7122 (tmm) cc_final: 0.6692 (tmm) REVERT: A 462 MET cc_start: 0.7789 (ttm) cc_final: 0.7476 (ttp) REVERT: A 476 LYS cc_start: 0.8580 (tppp) cc_final: 0.8297 (tppt) REVERT: A 507 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6924 (pp) REVERT: A 590 LYS cc_start: 0.7923 (mppt) cc_final: 0.7652 (mppt) REVERT: A 594 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 603 ASP cc_start: 0.7275 (t70) cc_final: 0.6998 (t0) REVERT: A 719 ARG cc_start: 0.6795 (mtp180) cc_final: 0.6532 (mtp180) REVERT: A 725 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7695 (mt) REVERT: B 21 MET cc_start: 0.7858 (ptm) cc_final: 0.7472 (ptm) REVERT: B 24 ILE cc_start: 0.8529 (mm) cc_final: 0.8057 (mm) REVERT: B 28 MET cc_start: 0.6986 (mmm) cc_final: 0.6446 (mmm) REVERT: B 86 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 127 MET cc_start: 0.8679 (mmm) cc_final: 0.8459 (mmt) REVERT: B 148 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7838 (mtm110) REVERT: B 214 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7764 (mt-10) REVERT: B 239 GLU cc_start: 0.8380 (tp30) cc_final: 0.7744 (tp30) REVERT: B 293 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 372 LYS cc_start: 0.9009 (tppt) cc_final: 0.8553 (tppt) REVERT: B 376 LYS cc_start: 0.8039 (tppt) cc_final: 0.7756 (ttpp) REVERT: B 380 ARG cc_start: 0.8599 (tpt-90) cc_final: 0.8382 (ttt-90) REVERT: B 397 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 398 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8836 (mtmt) REVERT: B 429 THR cc_start: 0.8429 (t) cc_final: 0.8100 (p) REVERT: B 437 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.8024 (m) REVERT: B 451 MET cc_start: 0.8209 (ttm) cc_final: 0.7801 (mtp) REVERT: B 511 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6905 (tm-30) REVERT: B 557 TYR cc_start: 0.8252 (t80) cc_final: 0.7841 (t80) REVERT: B 560 ASP cc_start: 0.8057 (m-30) cc_final: 0.7724 (m-30) REVERT: B 590 LYS cc_start: 0.7579 (mtmt) cc_final: 0.7359 (mttt) REVERT: B 603 ASP cc_start: 0.7814 (t0) cc_final: 0.7318 (t0) REVERT: B 611 ASN cc_start: 0.7724 (p0) cc_final: 0.7493 (p0) REVERT: B 654 SER cc_start: 0.6262 (OUTLIER) cc_final: 0.5551 (p) REVERT: B 657 GLU cc_start: 0.7839 (tp30) cc_final: 0.7426 (tp30) outliers start: 55 outliers final: 37 residues processed: 355 average time/residue: 0.2635 time to fit residues: 126.4952 Evaluate side-chains 357 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 10 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110143 restraints weight = 16576.852| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.27 r_work: 0.3373 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11628 Z= 0.203 Angle : 0.630 7.720 15714 Z= 0.338 Chirality : 0.046 0.284 1703 Planarity : 0.005 0.089 2015 Dihedral : 11.118 88.479 1712 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.06 % Favored : 91.58 % Rotamer: Outliers : 4.71 % Allowed : 17.44 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.89 (0.23), residues: 1377 helix: 1.25 (0.21), residues: 630 sheet: 0.33 (0.53), residues: 107 loop : -2.83 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.005 0.001 HIS B 541 PHE 0.021 0.002 PHE A 526 TYR 0.015 0.002 TYR B 164 ARG 0.004 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.06186 ( 444) hydrogen bonds : angle 4.23101 ( 1278) metal coordination : bond 0.00296 ( 3) covalent geometry : bond 0.00467 (11625) covalent geometry : angle 0.63033 (15714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8381 (mtpt) REVERT: A 11 ARG cc_start: 0.7299 (mtt-85) cc_final: 0.6886 (mtt-85) REVERT: A 25 ARG cc_start: 0.7929 (mpt-90) cc_final: 0.7469 (mpt-90) REVERT: A 30 HIS cc_start: 0.8009 (m-70) cc_final: 0.7785 (m-70) REVERT: A 45 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: A 55 MET cc_start: 0.7028 (mpp) cc_final: 0.6708 (tpp) REVERT: A 100 MET cc_start: 0.7597 (tmm) cc_final: 0.7197 (tmm) REVERT: A 114 ASN cc_start: 0.7372 (m-40) cc_final: 0.7168 (m-40) REVERT: A 117 MET cc_start: 0.6662 (mtp) cc_final: 0.6175 (mtp) REVERT: A 241 LYS cc_start: 0.8177 (tppp) cc_final: 0.7907 (ttmt) REVERT: A 244 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 264 GLU cc_start: 0.7716 (pm20) cc_final: 0.7489 (pm20) REVERT: A 271 GLN cc_start: 0.8212 (pp30) cc_final: 0.7811 (pp30) REVERT: A 293 GLU cc_start: 0.8174 (tp30) cc_final: 0.7950 (tm-30) REVERT: A 316 ASN cc_start: 0.8179 (m-40) cc_final: 0.7975 (m-40) REVERT: A 319 THR cc_start: 0.7829 (m) cc_final: 0.7245 (p) REVERT: A 342 ASN cc_start: 0.7804 (t0) cc_final: 0.7396 (t0) REVERT: A 352 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8342 (pt) REVERT: A 360 ASN cc_start: 0.7848 (t0) cc_final: 0.7249 (t0) REVERT: A 364 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 382 PHE cc_start: 0.8532 (p90) cc_final: 0.8329 (p90) REVERT: A 414 MET cc_start: 0.7152 (tmm) cc_final: 0.6834 (tmm) REVERT: A 462 MET cc_start: 0.7893 (ttm) cc_final: 0.7573 (ttp) REVERT: A 476 LYS cc_start: 0.8513 (tppp) cc_final: 0.8248 (tppt) REVERT: A 507 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7100 (pp) REVERT: A 529 LEU cc_start: 0.8846 (tm) cc_final: 0.8508 (tt) REVERT: A 594 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 603 ASP cc_start: 0.7254 (t70) cc_final: 0.6996 (t0) REVERT: A 606 TYR cc_start: 0.8561 (p90) cc_final: 0.8192 (p90) REVERT: A 642 TYR cc_start: 0.8120 (m-80) cc_final: 0.7596 (t80) REVERT: A 662 MET cc_start: 0.7478 (ttp) cc_final: 0.6958 (ptp) REVERT: A 719 ARG cc_start: 0.6850 (mtp180) cc_final: 0.6545 (mtp180) REVERT: A 725 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7689 (mt) REVERT: B 21 MET cc_start: 0.7844 (ptm) cc_final: 0.7480 (ptm) REVERT: B 24 ILE cc_start: 0.8558 (mm) cc_final: 0.8035 (mm) REVERT: B 28 MET cc_start: 0.7208 (mmm) cc_final: 0.6610 (mmm) REVERT: B 86 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 148 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7866 (mtm110) REVERT: B 219 GLN cc_start: 0.8514 (mp10) cc_final: 0.7973 (mp10) REVERT: B 345 THR cc_start: 0.8346 (t) cc_final: 0.8127 (p) REVERT: B 376 LYS cc_start: 0.7999 (tppt) cc_final: 0.7783 (ttpp) REVERT: B 380 ARG cc_start: 0.8600 (tpt-90) cc_final: 0.8367 (ttt-90) REVERT: B 397 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 429 THR cc_start: 0.8425 (t) cc_final: 0.8105 (t) REVERT: B 557 TYR cc_start: 0.8286 (t80) cc_final: 0.7878 (t80) REVERT: B 560 ASP cc_start: 0.8053 (m-30) cc_final: 0.7823 (m-30) REVERT: B 578 THR cc_start: 0.8189 (m) cc_final: 0.7855 (p) REVERT: B 590 LYS cc_start: 0.7545 (mtmt) cc_final: 0.7318 (mttt) REVERT: B 603 ASP cc_start: 0.7788 (t0) cc_final: 0.7350 (t0) REVERT: B 611 ASN cc_start: 0.7981 (p0) cc_final: 0.7417 (p0) REVERT: B 654 SER cc_start: 0.6214 (OUTLIER) cc_final: 0.5426 (p) REVERT: B 719 ARG cc_start: 0.8255 (mtp180) cc_final: 0.8031 (mtm180) outliers start: 57 outliers final: 41 residues processed: 354 average time/residue: 0.2770 time to fit residues: 132.7823 Evaluate side-chains 363 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112338 restraints weight = 16473.813| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.27 r_work: 0.3366 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11628 Z= 0.194 Angle : 0.633 7.818 15714 Z= 0.338 Chirality : 0.046 0.329 1703 Planarity : 0.005 0.089 2015 Dihedral : 10.913 87.779 1709 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.35 % Favored : 91.29 % Rotamer: Outliers : 5.45 % Allowed : 17.27 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.84 (0.23), residues: 1377 helix: 1.34 (0.21), residues: 628 sheet: 0.34 (0.52), residues: 107 loop : -2.86 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 399 HIS 0.005 0.001 HIS B 216 PHE 0.014 0.002 PHE A 438 TYR 0.015 0.002 TYR B 236 ARG 0.008 0.001 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.06093 ( 444) hydrogen bonds : angle 4.15784 ( 1278) metal coordination : bond 0.00272 ( 3) covalent geometry : bond 0.00446 (11625) covalent geometry : angle 0.63337 (15714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 327 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8372 (mtpt) REVERT: A 11 ARG cc_start: 0.7473 (mtt-85) cc_final: 0.7066 (mtt-85) REVERT: A 17 GLU cc_start: 0.7686 (pp20) cc_final: 0.7305 (pp20) REVERT: A 25 ARG cc_start: 0.7951 (mpt-90) cc_final: 0.7488 (mpt-90) REVERT: A 30 HIS cc_start: 0.8028 (m-70) cc_final: 0.7819 (m-70) REVERT: A 45 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: A 100 MET cc_start: 0.7602 (tmm) cc_final: 0.7213 (tmm) REVERT: A 114 ASN cc_start: 0.7319 (m-40) cc_final: 0.7115 (m-40) REVERT: A 117 MET cc_start: 0.6679 (mtp) cc_final: 0.6152 (mtp) REVERT: A 241 LYS cc_start: 0.8164 (tppp) cc_final: 0.7839 (mtmt) REVERT: A 243 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 244 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 264 GLU cc_start: 0.7652 (pm20) cc_final: 0.7392 (pm20) REVERT: A 319 THR cc_start: 0.7823 (m) cc_final: 0.7234 (p) REVERT: A 342 ASN cc_start: 0.7833 (t0) cc_final: 0.7423 (t0) REVERT: A 352 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8331 (pt) REVERT: A 360 ASN cc_start: 0.7916 (t0) cc_final: 0.7340 (t0) REVERT: A 364 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 380 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7797 (ttp-170) REVERT: A 382 PHE cc_start: 0.8422 (p90) cc_final: 0.8217 (p90) REVERT: A 414 MET cc_start: 0.7203 (tmm) cc_final: 0.6810 (tmm) REVERT: A 462 MET cc_start: 0.7893 (ttm) cc_final: 0.7577 (ttp) REVERT: A 507 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7092 (pp) REVERT: A 510 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7796 (pp20) REVERT: A 529 LEU cc_start: 0.8836 (tm) cc_final: 0.8501 (tt) REVERT: A 594 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 603 ASP cc_start: 0.7300 (t70) cc_final: 0.7037 (t0) REVERT: A 606 TYR cc_start: 0.8541 (p90) cc_final: 0.8215 (p90) REVERT: A 645 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8055 (pp) REVERT: A 719 ARG cc_start: 0.6845 (mtp180) cc_final: 0.6524 (mtp180) REVERT: B 21 MET cc_start: 0.7853 (ptm) cc_final: 0.7482 (ptm) REVERT: B 24 ILE cc_start: 0.8576 (mm) cc_final: 0.8026 (mm) REVERT: B 28 MET cc_start: 0.7343 (mmm) cc_final: 0.6742 (mmm) REVERT: B 86 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 148 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7869 (mtm110) REVERT: B 214 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7682 (mt-10) REVERT: B 219 GLN cc_start: 0.8512 (mp10) cc_final: 0.7916 (mp10) REVERT: B 239 GLU cc_start: 0.8393 (tp30) cc_final: 0.7645 (tp30) REVERT: B 293 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 380 ARG cc_start: 0.8605 (tpt-90) cc_final: 0.8383 (ttt-90) REVERT: B 397 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 429 THR cc_start: 0.8395 (t) cc_final: 0.8048 (p) REVERT: B 456 GLU cc_start: 0.7529 (mp0) cc_final: 0.7166 (mm-30) REVERT: B 537 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6447 (mt) REVERT: B 557 TYR cc_start: 0.8250 (t80) cc_final: 0.7881 (t80) REVERT: B 560 ASP cc_start: 0.8089 (m-30) cc_final: 0.7836 (m-30) REVERT: B 578 THR cc_start: 0.8253 (m) cc_final: 0.7885 (p) REVERT: B 603 ASP cc_start: 0.7845 (t0) cc_final: 0.7384 (t0) REVERT: B 654 SER cc_start: 0.6158 (OUTLIER) cc_final: 0.5355 (p) REVERT: B 657 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7635 (mm-30) outliers start: 66 outliers final: 48 residues processed: 354 average time/residue: 0.2873 time to fit residues: 138.5428 Evaluate side-chains 377 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 321 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 67 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113977 restraints weight = 16732.062| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.33 r_work: 0.3382 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11628 Z= 0.151 Angle : 0.612 8.977 15714 Z= 0.326 Chirality : 0.045 0.350 1703 Planarity : 0.005 0.089 2015 Dihedral : 10.640 84.932 1709 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.26 % Favored : 92.37 % Rotamer: Outliers : 5.21 % Allowed : 18.68 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.76 (0.23), residues: 1377 helix: 1.42 (0.21), residues: 633 sheet: 0.19 (0.52), residues: 110 loop : -2.84 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.003 0.001 HIS B 216 PHE 0.017 0.002 PHE B 421 TYR 0.011 0.001 TYR B 236 ARG 0.006 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 444) hydrogen bonds : angle 3.95461 ( 1278) metal coordination : bond 0.00182 ( 3) covalent geometry : bond 0.00346 (11625) covalent geometry : angle 0.61199 (15714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 317 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8264 (mmmm) REVERT: A 11 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.7017 (mtt-85) REVERT: A 17 GLU cc_start: 0.7695 (pp20) cc_final: 0.7253 (pp20) REVERT: A 25 ARG cc_start: 0.8004 (mpt-90) cc_final: 0.7526 (mpt-90) REVERT: A 45 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: A 55 MET cc_start: 0.6923 (tpp) cc_final: 0.6612 (tpp) REVERT: A 100 MET cc_start: 0.7611 (tmm) cc_final: 0.7224 (tmm) REVERT: A 117 MET cc_start: 0.6722 (mtp) cc_final: 0.6476 (mtp) REVERT: A 219 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7303 (mm110) REVERT: A 241 LYS cc_start: 0.8101 (tppp) cc_final: 0.7759 (mtmt) REVERT: A 244 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 264 GLU cc_start: 0.7672 (pm20) cc_final: 0.7399 (pm20) REVERT: A 287 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8157 (mmm160) REVERT: A 292 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7911 (mmm) REVERT: A 293 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 319 THR cc_start: 0.7781 (m) cc_final: 0.7201 (t) REVERT: A 342 ASN cc_start: 0.7802 (t0) cc_final: 0.7388 (t0) REVERT: A 352 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8337 (pt) REVERT: A 360 ASN cc_start: 0.7852 (t0) cc_final: 0.7226 (t0) REVERT: A 364 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 380 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7892 (ttp-170) REVERT: A 407 TYR cc_start: 0.8276 (p90) cc_final: 0.8059 (p90) REVERT: A 414 MET cc_start: 0.7138 (tmm) cc_final: 0.6720 (tmm) REVERT: A 462 MET cc_start: 0.7758 (ttm) cc_final: 0.7460 (ttp) REVERT: A 492 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8249 (mm-40) REVERT: A 496 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7243 (mp) REVERT: A 507 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7067 (pp) REVERT: A 510 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7758 (pp20) REVERT: A 529 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 590 LYS cc_start: 0.7965 (mppt) cc_final: 0.7764 (mppt) REVERT: A 594 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 603 ASP cc_start: 0.7297 (t70) cc_final: 0.7026 (t0) REVERT: A 606 TYR cc_start: 0.8497 (p90) cc_final: 0.8164 (p90) REVERT: A 642 TYR cc_start: 0.8119 (m-80) cc_final: 0.7600 (t80) REVERT: A 645 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (pp) REVERT: A 725 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7684 (mt) REVERT: B 21 MET cc_start: 0.7817 (ptm) cc_final: 0.7448 (ptm) REVERT: B 24 ILE cc_start: 0.8557 (mm) cc_final: 0.7978 (mm) REVERT: B 28 MET cc_start: 0.7319 (mmm) cc_final: 0.6667 (mmm) REVERT: B 86 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 132 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7529 (mm-30) REVERT: B 148 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7854 (mtm110) REVERT: B 162 ASP cc_start: 0.7570 (p0) cc_final: 0.7246 (p0) REVERT: B 214 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 219 GLN cc_start: 0.8493 (mp10) cc_final: 0.8097 (mm-40) REVERT: B 238 GLU cc_start: 0.7850 (tp30) cc_final: 0.7567 (tp30) REVERT: B 239 GLU cc_start: 0.8372 (tp30) cc_final: 0.7653 (tp30) REVERT: B 293 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 397 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 429 THR cc_start: 0.8381 (t) cc_final: 0.8039 (p) REVERT: B 456 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: B 496 LEU cc_start: 0.8410 (tt) cc_final: 0.8209 (tt) REVERT: B 507 LEU cc_start: 0.7427 (pt) cc_final: 0.7057 (pp) REVERT: B 537 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6408 (mt) REVERT: B 557 TYR cc_start: 0.8161 (t80) cc_final: 0.7742 (t80) REVERT: B 560 ASP cc_start: 0.8098 (m-30) cc_final: 0.7830 (m-30) REVERT: B 578 THR cc_start: 0.8157 (m) cc_final: 0.7822 (p) REVERT: B 603 ASP cc_start: 0.7772 (t0) cc_final: 0.7361 (t0) REVERT: B 654 SER cc_start: 0.6129 (OUTLIER) cc_final: 0.5323 (p) REVERT: B 657 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7611 (mm-30) outliers start: 63 outliers final: 45 residues processed: 346 average time/residue: 0.2825 time to fit residues: 131.9861 Evaluate side-chains 368 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 309 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 654 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113799 restraints weight = 16751.855| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.32 r_work: 0.3386 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11628 Z= 0.148 Angle : 0.606 8.473 15714 Z= 0.324 Chirality : 0.045 0.328 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.389 82.463 1707 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.59 % Rotamer: Outliers : 5.70 % Allowed : 19.09 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 (0.23), residues: 1377 helix: 1.48 (0.21), residues: 633 sheet: 0.16 (0.50), residues: 115 loop : -2.83 (0.22), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.013 0.002 PHE A 393 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 444) hydrogen bonds : angle 3.88819 ( 1278) metal coordination : bond 0.00176 ( 3) covalent geometry : bond 0.00338 (11625) covalent geometry : angle 0.60576 (15714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 312 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8322 (mmmt) REVERT: A 11 ARG cc_start: 0.7413 (mtt-85) cc_final: 0.7005 (mtt-85) REVERT: A 17 GLU cc_start: 0.7665 (pp20) cc_final: 0.7260 (pp20) REVERT: A 25 ARG cc_start: 0.7946 (mpt-90) cc_final: 0.7631 (mpt-90) REVERT: A 45 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: A 55 MET cc_start: 0.6971 (tpp) cc_final: 0.6661 (tpp) REVERT: A 100 MET cc_start: 0.7607 (tmm) cc_final: 0.7232 (tmm) REVERT: A 117 MET cc_start: 0.6698 (mtp) cc_final: 0.6482 (mtp) REVERT: A 241 LYS cc_start: 0.8117 (tppp) cc_final: 0.7765 (mtmt) REVERT: A 243 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7675 (mp) REVERT: A 244 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 264 GLU cc_start: 0.7657 (pm20) cc_final: 0.7394 (pm20) REVERT: A 292 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: A 293 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 319 THR cc_start: 0.7742 (m) cc_final: 0.7156 (t) REVERT: A 342 ASN cc_start: 0.7819 (t0) cc_final: 0.7403 (t0) REVERT: A 352 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8301 (pt) REVERT: A 360 ASN cc_start: 0.7869 (t0) cc_final: 0.7250 (t0) REVERT: A 364 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 380 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7866 (ttp-170) REVERT: A 414 MET cc_start: 0.7102 (tmm) cc_final: 0.6675 (tmm) REVERT: A 462 MET cc_start: 0.7722 (ttm) cc_final: 0.7429 (ttp) REVERT: A 492 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8216 (mm-40) REVERT: A 496 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7225 (mp) REVERT: A 507 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7106 (pp) REVERT: A 510 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7736 (pp20) REVERT: A 529 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8434 (tt) REVERT: A 594 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 603 ASP cc_start: 0.7313 (t70) cc_final: 0.7039 (t0) REVERT: A 606 TYR cc_start: 0.8491 (p90) cc_final: 0.8169 (p90) REVERT: A 645 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 725 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7666 (mt) REVERT: B 21 MET cc_start: 0.7813 (ptm) cc_final: 0.7438 (ptm) REVERT: B 24 ILE cc_start: 0.8538 (mm) cc_final: 0.7930 (mm) REVERT: B 28 MET cc_start: 0.7396 (mmm) cc_final: 0.6750 (mmm) REVERT: B 86 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 132 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7536 (mm-30) REVERT: B 148 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.7866 (mtm110) REVERT: B 162 ASP cc_start: 0.7591 (p0) cc_final: 0.7253 (p0) REVERT: B 214 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7514 (mt-10) REVERT: B 219 GLN cc_start: 0.8475 (mp10) cc_final: 0.8150 (mm-40) REVERT: B 238 GLU cc_start: 0.7846 (tp30) cc_final: 0.7563 (tp30) REVERT: B 239 GLU cc_start: 0.8384 (tp30) cc_final: 0.7682 (tp30) REVERT: B 293 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 316 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: B 397 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 429 THR cc_start: 0.8361 (t) cc_final: 0.8026 (p) REVERT: B 507 LEU cc_start: 0.7489 (pt) cc_final: 0.7089 (pp) REVERT: B 534 VAL cc_start: 0.6521 (OUTLIER) cc_final: 0.6278 (m) REVERT: B 537 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6519 (mt) REVERT: B 557 TYR cc_start: 0.8149 (t80) cc_final: 0.7750 (t80) REVERT: B 560 ASP cc_start: 0.8087 (m-30) cc_final: 0.7825 (m-30) REVERT: B 570 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7351 (t70) REVERT: B 603 ASP cc_start: 0.7792 (t0) cc_final: 0.7397 (t0) REVERT: B 654 SER cc_start: 0.6237 (OUTLIER) cc_final: 0.5805 (p) REVERT: B 657 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7556 (mm-30) outliers start: 69 outliers final: 45 residues processed: 343 average time/residue: 0.3519 time to fit residues: 164.5630 Evaluate side-chains 372 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 657 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114651 restraints weight = 16572.495| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.33 r_work: 0.3394 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11628 Z= 0.141 Angle : 0.608 8.744 15714 Z= 0.325 Chirality : 0.044 0.264 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.188 80.345 1707 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.75 % Favored : 92.88 % Rotamer: Outliers : 5.37 % Allowed : 19.83 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1377 helix: 1.54 (0.21), residues: 632 sheet: 0.23 (0.50), residues: 115 loop : -2.79 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.004 0.001 HIS A 30 PHE 0.013 0.001 PHE A 393 TYR 0.011 0.001 TYR A 80 ARG 0.005 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 444) hydrogen bonds : angle 3.82410 ( 1278) metal coordination : bond 0.00153 ( 3) covalent geometry : bond 0.00320 (11625) covalent geometry : angle 0.60844 (15714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 301 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8337 (mmmt) REVERT: A 11 ARG cc_start: 0.7497 (mtt-85) cc_final: 0.7065 (mtt-85) REVERT: A 25 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.7613 (mpt-90) REVERT: A 45 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: A 55 MET cc_start: 0.6866 (tpp) cc_final: 0.6522 (tpp) REVERT: A 100 MET cc_start: 0.7585 (tmm) cc_final: 0.7217 (tmm) REVERT: A 117 MET cc_start: 0.6682 (mtp) cc_final: 0.6172 (mtp) REVERT: A 241 LYS cc_start: 0.8147 (tppp) cc_final: 0.7874 (mtmt) REVERT: A 244 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 264 GLU cc_start: 0.7683 (pm20) cc_final: 0.7408 (pm20) REVERT: A 274 GLU cc_start: 0.7667 (pt0) cc_final: 0.7458 (pt0) REVERT: A 292 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: A 293 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 319 THR cc_start: 0.7740 (m) cc_final: 0.7146 (t) REVERT: A 342 ASN cc_start: 0.7790 (t0) cc_final: 0.7372 (t0) REVERT: A 352 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8276 (pt) REVERT: A 360 ASN cc_start: 0.7858 (t0) cc_final: 0.7261 (t0) REVERT: A 364 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 414 MET cc_start: 0.7113 (tmm) cc_final: 0.6581 (tmm) REVERT: A 462 MET cc_start: 0.7657 (ttm) cc_final: 0.7376 (ttp) REVERT: A 492 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8222 (mm-40) REVERT: A 496 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7172 (mp) REVERT: A 507 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7112 (pp) REVERT: A 510 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 529 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 594 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 603 ASP cc_start: 0.7333 (t70) cc_final: 0.7054 (t0) REVERT: A 606 TYR cc_start: 0.8459 (p90) cc_final: 0.8137 (p90) REVERT: A 642 TYR cc_start: 0.8126 (m-80) cc_final: 0.7642 (t80) REVERT: A 645 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 719 ARG cc_start: 0.6934 (mtp180) cc_final: 0.6589 (mtp180) REVERT: B 21 MET cc_start: 0.7808 (ptm) cc_final: 0.7444 (ptm) REVERT: B 24 ILE cc_start: 0.8512 (mm) cc_final: 0.7916 (mm) REVERT: B 28 MET cc_start: 0.7390 (mmm) cc_final: 0.6717 (mmm) REVERT: B 86 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 132 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7551 (mm-30) REVERT: B 148 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7863 (mtm110) REVERT: B 162 ASP cc_start: 0.7520 (p0) cc_final: 0.7210 (p0) REVERT: B 214 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 219 GLN cc_start: 0.8456 (mp10) cc_final: 0.8184 (mm-40) REVERT: B 238 GLU cc_start: 0.7837 (tp30) cc_final: 0.7549 (tp30) REVERT: B 239 GLU cc_start: 0.8377 (tp30) cc_final: 0.7700 (tp30) REVERT: B 243 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 292 MET cc_start: 0.7819 (mmp) cc_final: 0.7564 (mmt) REVERT: B 293 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 345 THR cc_start: 0.8395 (t) cc_final: 0.8193 (p) REVERT: B 397 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 429 THR cc_start: 0.8365 (t) cc_final: 0.8033 (p) REVERT: B 451 MET cc_start: 0.8195 (ttm) cc_final: 0.7863 (mtp) REVERT: B 507 LEU cc_start: 0.7465 (pt) cc_final: 0.7048 (pp) REVERT: B 537 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6550 (mt) REVERT: B 557 TYR cc_start: 0.8117 (t80) cc_final: 0.7715 (t80) REVERT: B 560 ASP cc_start: 0.8097 (m-30) cc_final: 0.7833 (m-30) REVERT: B 570 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7293 (t70) REVERT: B 578 THR cc_start: 0.8180 (m) cc_final: 0.7842 (p) REVERT: B 603 ASP cc_start: 0.7757 (t0) cc_final: 0.7386 (t0) outliers start: 65 outliers final: 46 residues processed: 335 average time/residue: 0.5129 time to fit residues: 232.2683 Evaluate side-chains 350 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 118 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 chunk 52 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.114441 restraints weight = 16675.320| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.34 r_work: 0.3391 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11628 Z= 0.147 Angle : 0.625 8.417 15714 Z= 0.333 Chirality : 0.045 0.268 1703 Planarity : 0.005 0.092 2015 Dihedral : 9.960 86.963 1703 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.59 % Rotamer: Outliers : 5.54 % Allowed : 19.92 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1377 helix: 1.55 (0.21), residues: 634 sheet: 0.41 (0.51), residues: 103 loop : -2.80 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.018 0.001 PHE A 526 TYR 0.012 0.001 TYR B 236 ARG 0.006 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 444) hydrogen bonds : angle 3.83236 ( 1278) metal coordination : bond 0.00168 ( 3) covalent geometry : bond 0.00335 (11625) covalent geometry : angle 0.62471 (15714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8327 (mmmt) REVERT: A 11 ARG cc_start: 0.7536 (mtt-85) cc_final: 0.7103 (mtt-85) REVERT: A 17 GLU cc_start: 0.7569 (pp20) cc_final: 0.7140 (pp20) REVERT: A 25 ARG cc_start: 0.7929 (mpt-90) cc_final: 0.7630 (mpt-90) REVERT: A 45 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: A 55 MET cc_start: 0.6876 (tpp) cc_final: 0.6537 (tpp) REVERT: A 100 MET cc_start: 0.7616 (tmm) cc_final: 0.7247 (tmm) REVERT: A 117 MET cc_start: 0.6646 (mtp) cc_final: 0.6145 (mtp) REVERT: A 241 LYS cc_start: 0.8150 (tppp) cc_final: 0.7892 (mtmt) REVERT: A 264 GLU cc_start: 0.7691 (pm20) cc_final: 0.7401 (pm20) REVERT: A 292 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7922 (mmm) REVERT: A 293 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 319 THR cc_start: 0.7785 (m) cc_final: 0.7225 (t) REVERT: A 342 ASN cc_start: 0.7807 (t0) cc_final: 0.7384 (t0) REVERT: A 352 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8273 (pt) REVERT: A 360 ASN cc_start: 0.7858 (t0) cc_final: 0.7223 (t0) REVERT: A 364 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 414 MET cc_start: 0.7096 (tmm) cc_final: 0.6560 (tmm) REVERT: A 462 MET cc_start: 0.7666 (ttm) cc_final: 0.7384 (ttp) REVERT: A 492 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8215 (mm-40) REVERT: A 496 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 507 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7117 (pp) REVERT: A 510 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: A 529 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 594 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 603 ASP cc_start: 0.7346 (t70) cc_final: 0.7066 (t0) REVERT: A 606 TYR cc_start: 0.8446 (p90) cc_final: 0.8124 (p90) REVERT: A 645 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 719 ARG cc_start: 0.6933 (mtp180) cc_final: 0.6589 (mtp180) REVERT: B 21 MET cc_start: 0.7846 (ptm) cc_final: 0.7492 (ptm) REVERT: B 24 ILE cc_start: 0.8511 (mm) cc_final: 0.7908 (mm) REVERT: B 28 MET cc_start: 0.7405 (mmm) cc_final: 0.6755 (mmm) REVERT: B 86 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 113 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: B 132 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7543 (mm-30) REVERT: B 148 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.7876 (mtm110) REVERT: B 162 ASP cc_start: 0.7538 (p0) cc_final: 0.7212 (p0) REVERT: B 219 GLN cc_start: 0.8410 (mp10) cc_final: 0.8203 (mm-40) REVERT: B 243 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 293 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 372 LYS cc_start: 0.8942 (tptt) cc_final: 0.8551 (tppt) REVERT: B 397 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 429 THR cc_start: 0.8371 (t) cc_final: 0.8051 (p) REVERT: B 507 LEU cc_start: 0.7442 (pt) cc_final: 0.7051 (pp) REVERT: B 537 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6654 (mt) REVERT: B 557 TYR cc_start: 0.8138 (t80) cc_final: 0.7746 (t80) REVERT: B 560 ASP cc_start: 0.8101 (m-30) cc_final: 0.7840 (m-30) REVERT: B 570 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7334 (t70) REVERT: B 578 THR cc_start: 0.8180 (m) cc_final: 0.7842 (p) REVERT: B 603 ASP cc_start: 0.7814 (t0) cc_final: 0.7441 (t0) outliers start: 67 outliers final: 51 residues processed: 337 average time/residue: 0.3475 time to fit residues: 159.2616 Evaluate side-chains 362 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 298 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 4 optimal weight: 4.9990 chunk 124 optimal weight: 0.0010 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114816 restraints weight = 16555.769| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.34 r_work: 0.3395 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11628 Z= 0.145 Angle : 0.637 8.743 15714 Z= 0.339 Chirality : 0.044 0.268 1703 Planarity : 0.005 0.092 2015 Dihedral : 9.849 87.291 1703 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.68 % Favored : 92.96 % Rotamer: Outliers : 5.45 % Allowed : 19.75 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 (0.23), residues: 1377 helix: 1.61 (0.21), residues: 634 sheet: 0.50 (0.51), residues: 103 loop : -2.80 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.006 0.001 HIS A 612 PHE 0.013 0.001 PHE A 393 TYR 0.015 0.001 TYR B 371 ARG 0.007 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 444) hydrogen bonds : angle 3.79889 ( 1278) metal coordination : bond 0.00162 ( 3) covalent geometry : bond 0.00328 (11625) covalent geometry : angle 0.63699 (15714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8333 (mmmt) REVERT: A 11 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.7110 (mtt-85) REVERT: A 17 GLU cc_start: 0.7545 (pp20) cc_final: 0.7099 (pp20) REVERT: A 25 ARG cc_start: 0.7913 (mpt-90) cc_final: 0.7625 (mpt-90) REVERT: A 45 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: A 100 MET cc_start: 0.7635 (tmm) cc_final: 0.7266 (tmm) REVERT: A 117 MET cc_start: 0.6654 (mtp) cc_final: 0.6147 (mtp) REVERT: A 241 LYS cc_start: 0.8157 (tppp) cc_final: 0.7897 (mtmt) REVERT: A 264 GLU cc_start: 0.7675 (pm20) cc_final: 0.7381 (pm20) REVERT: A 274 GLU cc_start: 0.7680 (pt0) cc_final: 0.7453 (pt0) REVERT: A 292 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7920 (mmm) REVERT: A 293 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 319 THR cc_start: 0.7754 (m) cc_final: 0.7200 (t) REVERT: A 342 ASN cc_start: 0.7811 (t0) cc_final: 0.7383 (t0) REVERT: A 352 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8251 (pt) REVERT: A 360 ASN cc_start: 0.7810 (t0) cc_final: 0.7208 (t0) REVERT: A 364 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 414 MET cc_start: 0.7083 (tmm) cc_final: 0.6544 (tmm) REVERT: A 462 MET cc_start: 0.7644 (ttm) cc_final: 0.7368 (ttp) REVERT: A 492 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8248 (mm-40) REVERT: A 496 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7143 (mp) REVERT: A 507 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7129 (pp) REVERT: A 510 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: A 529 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 594 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 603 ASP cc_start: 0.7353 (t70) cc_final: 0.7075 (t0) REVERT: A 606 TYR cc_start: 0.8436 (p90) cc_final: 0.8112 (p90) REVERT: A 642 TYR cc_start: 0.8121 (m-80) cc_final: 0.7658 (t80) REVERT: A 645 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7934 (pp) REVERT: A 719 ARG cc_start: 0.6931 (mtp180) cc_final: 0.6588 (mtp180) REVERT: A 725 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7653 (mt) REVERT: B 21 MET cc_start: 0.7819 (ptm) cc_final: 0.7463 (ptm) REVERT: B 24 ILE cc_start: 0.8501 (mm) cc_final: 0.7915 (mm) REVERT: B 28 MET cc_start: 0.7388 (mmm) cc_final: 0.6739 (mmm) REVERT: B 86 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 109 ASP cc_start: 0.7821 (t70) cc_final: 0.7435 (t0) REVERT: B 113 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: B 132 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7549 (mm-30) REVERT: B 148 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7867 (mtm110) REVERT: B 162 ASP cc_start: 0.7518 (p0) cc_final: 0.7201 (p0) REVERT: B 238 GLU cc_start: 0.7867 (tp30) cc_final: 0.7573 (tp30) REVERT: B 243 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 293 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 397 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 429 THR cc_start: 0.8363 (t) cc_final: 0.8041 (p) REVERT: B 507 LEU cc_start: 0.7417 (pt) cc_final: 0.7032 (pp) REVERT: B 537 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6647 (mt) REVERT: B 560 ASP cc_start: 0.8085 (m-30) cc_final: 0.7820 (m-30) REVERT: B 570 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7321 (t70) REVERT: B 578 THR cc_start: 0.8178 (m) cc_final: 0.7851 (p) REVERT: B 603 ASP cc_start: 0.7785 (t0) cc_final: 0.7476 (t0) outliers start: 66 outliers final: 48 residues processed: 331 average time/residue: 0.2896 time to fit residues: 129.4958 Evaluate side-chains 365 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 570 HIS Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 131 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114665 restraints weight = 16486.355| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.32 r_work: 0.3399 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11628 Z= 0.143 Angle : 0.652 9.419 15714 Z= 0.346 Chirality : 0.046 0.467 1703 Planarity : 0.005 0.097 2015 Dihedral : 9.720 84.637 1703 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.32 % Favored : 93.32 % Rotamer: Outliers : 4.96 % Allowed : 20.58 % Favored : 74.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.52 (0.23), residues: 1377 helix: 1.65 (0.21), residues: 634 sheet: 0.33 (0.49), residues: 115 loop : -2.78 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.019 0.001 PHE A 526 TYR 0.023 0.001 TYR B 371 ARG 0.007 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 444) hydrogen bonds : angle 3.74190 ( 1278) metal coordination : bond 0.00160 ( 3) covalent geometry : bond 0.00326 (11625) covalent geometry : angle 0.65202 (15714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7568.17 seconds wall clock time: 137 minutes 40.04 seconds (8260.04 seconds total)