Starting phenix.real_space_refine on Wed May 14 07:14:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p23_17357/05_2025/8p23_17357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p23_17357/05_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_17357/05_2025/8p23_17357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p23_17357/05_2025/8p23_17357.map" model { file = "/net/cci-nas-00/data/ceres_data/8p23_17357/05_2025/8p23_17357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p23_17357/05_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-5687/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: 6.75, per 1000 atoms: 0.59 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: 1.15 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: 2.89 Time building geometry restraints manager: 3.19 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.000 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- 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 : 1.128 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: 0.2763 time to fit residues: 142.9815 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 : 1.247 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118089 restraints weight = 16239.713| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.28 r_work: 0.3499 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- 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 4.09859 ( 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 : 1.144 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: 0.6832 (mpt) cc_final: 0.6587 (mtp) REVERT: A 30 HIS cc_start: 0.7952 (m-70) cc_final: 0.7685 (m-70) REVERT: A 100 MET cc_start: 0.7300 (tmm) cc_final: 0.6914 (tmm) REVERT: A 117 MET cc_start: 0.6675 (mtp) cc_final: 0.6270 (mtp) REVERT: A 238 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 239 GLU cc_start: 0.7603 (tp30) cc_final: 0.7114 (mm-30) REVERT: A 241 LYS cc_start: 0.8070 (tppp) cc_final: 0.7760 (ttmt) REVERT: A 244 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 264 GLU cc_start: 0.7597 (pm20) cc_final: 0.7378 (pm20) REVERT: A 313 SER cc_start: 0.7894 (p) cc_final: 0.7584 (m) REVERT: A 316 ASN cc_start: 0.8048 (m-40) cc_final: 0.7776 (m-40) REVERT: A 319 THR cc_start: 0.7752 (m) cc_final: 0.7284 (t) REVERT: A 342 ASN cc_start: 0.7722 (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: 0.8245 (ttt90) cc_final: 0.7976 (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: 0.7713 (mppt) cc_final: 0.7441 (mppt) REVERT: A 594 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 603 ASP cc_start: 0.7209 (t70) cc_final: 0.6934 (t0) REVERT: A 642 TYR cc_start: 0.8128 (m-80) cc_final: 0.7563 (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: 0.8171 (OUTLIER) cc_final: 0.7680 (mt) REVERT: B 21 MET cc_start: 0.7618 (ptm) cc_final: 0.7210 (ptm) REVERT: B 24 ILE cc_start: 0.8441 (mm) cc_final: 0.8058 (mm) REVERT: B 28 MET cc_start: 0.6525 (mmm) cc_final: 0.6115 (mmm) REVERT: B 86 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 145 GLU cc_start: 0.7875 (pm20) cc_final: 0.7577 (pm20) REVERT: B 148 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7755 (mtp85) REVERT: B 214 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 239 GLU cc_start: 0.8229 (tp30) cc_final: 0.7655 (tp30) REVERT: B 293 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 299 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.5794 (mpm) REVERT: B 342 ASN cc_start: 0.7884 (t0) cc_final: 0.7652 (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: 0.8328 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 398 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8782 (mtmt) REVERT: B 429 THR cc_start: 0.8365 (t) cc_final: 0.8038 (p) REVERT: B 507 LEU cc_start: 0.7344 (pt) cc_final: 0.7003 (pp) REVERT: B 511 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6822 (tm-30) REVERT: B 560 ASP cc_start: 0.8069 (m-30) cc_final: 0.7768 (m-30) REVERT: B 603 ASP cc_start: 0.7577 (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: 0.8209 (pt) cc_final: 0.7989 (mt) REVERT: B 654 SER cc_start: 0.6091 (OUTLIER) cc_final: 0.5316 (p) REVERT: B 657 GLU cc_start: 0.7781 (tp30) cc_final: 0.7485 (tp30) REVERT: B 719 ARG cc_start: 0.8272 (mtp180) cc_final: 0.8041 (mtm110) outliers start: 51 outliers final: 29 residues processed: 343 average time/residue: 0.2640 time to fit residues: 122.3022 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 : 1.119 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 0.3980 chunk 66 optimal weight: 0.0000 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112601 restraints weight = 16458.884| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.31 r_work: 0.3400 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11628 Z= 0.178 Angle : 0.612 7.046 15714 Z= 0.326 Chirality : 0.046 0.274 1703 Planarity : 0.005 0.084 2015 Dihedral : 11.305 86.029 1714 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.97 % Favored : 92.67 % Rotamer: Outliers : 4.21 % Allowed : 15.45 % Favored : 80.33 % 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: -0.77 (0.23), residues: 1377 helix: 1.33 (0.21), residues: 635 sheet: 0.50 (0.53), residues: 107 loop : -2.80 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 399 HIS 0.012 0.001 HIS B 541 PHE 0.024 0.002 PHE A 526 TYR 0.015 0.002 TYR B 164 ARG 0.005 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.05599 ( 444) hydrogen bonds : angle 4.16217 ( 1278) metal coordination : bond 0.00236 ( 3) covalent geometry : bond 0.00408 (11625) covalent geometry : angle 0.61204 (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 379 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8285 (mtpp) REVERT: A 21 MET cc_start: 0.6938 (mpt) cc_final: 0.6196 (mtp) REVERT: A 25 ARG cc_start: 0.7861 (mpt-90) cc_final: 0.7417 (mpt-90) REVERT: A 30 HIS cc_start: 0.7991 (m-70) cc_final: 0.7767 (m-70) REVERT: A 45 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: A 55 MET cc_start: 0.6925 (mpp) cc_final: 0.6628 (tpp) REVERT: A 100 MET cc_start: 0.7504 (tmm) cc_final: 0.7124 (tmm) REVERT: A 117 MET cc_start: 0.6761 (mtp) cc_final: 0.6295 (mtp) REVERT: A 238 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7715 (mm-30) REVERT: A 241 LYS cc_start: 0.8223 (tppp) cc_final: 0.7931 (ttmt) REVERT: A 244 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 263 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 264 GLU cc_start: 0.7687 (pm20) cc_final: 0.7466 (pm20) REVERT: A 271 GLN cc_start: 0.8153 (pp30) cc_final: 0.7769 (pp30) REVERT: A 292 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7955 (mmm) REVERT: A 300 ASN cc_start: 0.8177 (t0) cc_final: 0.7942 (t0) REVERT: A 319 THR cc_start: 0.7943 (m) cc_final: 0.7361 (t) REVERT: A 334 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8000 (mp10) REVERT: A 342 ASN cc_start: 0.7804 (t0) cc_final: 0.7394 (t0) REVERT: A 352 ILE cc_start: 0.8620 (pp) cc_final: 0.8404 (pt) REVERT: A 360 ASN cc_start: 0.7896 (t0) cc_final: 0.7317 (t0) REVERT: A 364 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 380 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7792 (ttp80) REVERT: A 414 MET cc_start: 0.7116 (tmm) cc_final: 0.6762 (tmm) REVERT: A 462 MET cc_start: 0.7699 (ttm) cc_final: 0.7403 (ttp) REVERT: A 476 LYS cc_start: 0.8596 (tppp) cc_final: 0.8313 (tppt) REVERT: A 497 MET cc_start: 0.8285 (tpp) cc_final: 0.8083 (mpp) REVERT: A 590 LYS cc_start: 0.7882 (mppt) cc_final: 0.7635 (mppt) REVERT: A 594 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 603 ASP cc_start: 0.7270 (t70) cc_final: 0.6999 (t0) REVERT: A 719 ARG cc_start: 0.6763 (mtp180) cc_final: 0.6499 (mtp180) REVERT: A 725 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 21 MET cc_start: 0.7827 (ptm) cc_final: 0.7434 (ptm) REVERT: B 24 ILE cc_start: 0.8522 (mm) cc_final: 0.8058 (mm) REVERT: B 28 MET cc_start: 0.6946 (mmm) cc_final: 0.6437 (mmm) REVERT: B 86 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 148 ARG cc_start: 0.8106 (ttt-90) cc_final: 0.7635 (mtp85) REVERT: B 214 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 215 MET cc_start: 0.8217 (mtt) cc_final: 0.7935 (mtm) REVERT: B 239 GLU cc_start: 0.8352 (tp30) cc_final: 0.7669 (tp30) REVERT: B 293 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 372 LYS cc_start: 0.9009 (tppt) cc_final: 0.8546 (tppt) REVERT: B 376 LYS cc_start: 0.8008 (tppt) cc_final: 0.7728 (ttpp) REVERT: B 397 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8046 (tm-30) REVERT: B 429 THR cc_start: 0.8416 (t) cc_final: 0.8081 (p) REVERT: B 451 MET cc_start: 0.8142 (ttm) cc_final: 0.7796 (mtp) REVERT: B 507 LEU cc_start: 0.7440 (pt) cc_final: 0.7120 (pp) REVERT: B 511 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6912 (tm-30) REVERT: B 560 ASP cc_start: 0.8080 (m-30) cc_final: 0.7749 (m-30) REVERT: B 590 LYS cc_start: 0.7533 (mtmt) cc_final: 0.7321 (mttt) REVERT: B 603 ASP cc_start: 0.7812 (t0) cc_final: 0.7305 (t0) REVERT: B 611 ASN cc_start: 0.7640 (p0) cc_final: 0.7394 (p0) REVERT: B 654 SER cc_start: 0.6231 (OUTLIER) cc_final: 0.5579 (p) outliers start: 51 outliers final: 34 residues processed: 348 average time/residue: 0.2738 time to fit residues: 128.3835 Evaluate side-chains 348 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain A residue 292 MET 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 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 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 310 VAL 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: 0.0970 chunk 119 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.132948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114294 restraints weight = 16492.887| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.29 r_work: 0.3430 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2366 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= 0.120 Angle : 0.566 6.758 15714 Z= 0.301 Chirality : 0.043 0.278 1703 Planarity : 0.004 0.086 2015 Dihedral : 10.982 89.784 1711 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.17 % Favored : 93.46 % Rotamer: Outliers : 4.63 % Allowed : 17.19 % Favored : 78.18 % 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: -0.66 (0.23), residues: 1377 helix: 1.48 (0.21), residues: 632 sheet: 0.23 (0.54), residues: 102 loop : -2.71 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.002 0.001 HIS A 675 PHE 0.025 0.001 PHE B 463 TYR 0.010 0.001 TYR B 236 ARG 0.005 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 444) hydrogen bonds : angle 3.90509 ( 1278) metal coordination : bond 0.00119 ( 3) covalent geometry : bond 0.00264 (11625) covalent geometry : angle 0.56650 (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 364 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8278 (mtpp) REVERT: A 21 MET cc_start: 0.6943 (mpt) cc_final: 0.6175 (mtp) REVERT: A 25 ARG cc_start: 0.7888 (mpt-90) cc_final: 0.7406 (mpt-90) REVERT: A 30 HIS cc_start: 0.7978 (m-70) cc_final: 0.7774 (m-70) REVERT: A 45 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: A 100 MET cc_start: 0.7511 (tmm) cc_final: 0.7119 (tmm) REVERT: A 117 MET cc_start: 0.6676 (mtp) cc_final: 0.6158 (mtp) REVERT: A 241 LYS cc_start: 0.8140 (tppp) cc_final: 0.7849 (ttmt) REVERT: A 244 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 319 THR cc_start: 0.7804 (m) cc_final: 0.7245 (t) REVERT: A 334 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8057 (mp10) REVERT: A 342 ASN cc_start: 0.7773 (t0) cc_final: 0.7376 (t0) REVERT: A 352 ILE cc_start: 0.8549 (pp) cc_final: 0.8311 (pt) REVERT: A 360 ASN cc_start: 0.7796 (t0) cc_final: 0.7177 (t0) REVERT: A 364 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 380 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7858 (ttp80) REVERT: A 392 THR cc_start: 0.8503 (p) cc_final: 0.8296 (p) REVERT: A 414 MET cc_start: 0.6975 (tmm) cc_final: 0.6594 (tmm) REVERT: A 462 MET cc_start: 0.7531 (ttm) cc_final: 0.7247 (ttp) REVERT: A 497 MET cc_start: 0.8221 (tpp) cc_final: 0.7988 (mpp) REVERT: A 507 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7075 (pp) REVERT: A 590 LYS cc_start: 0.7832 (mppt) cc_final: 0.7617 (mppt) REVERT: A 594 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 603 ASP cc_start: 0.7226 (t70) cc_final: 0.6974 (t0) REVERT: A 617 TYR cc_start: 0.7733 (t80) cc_final: 0.7496 (t80) REVERT: A 719 ARG cc_start: 0.6840 (mtp180) cc_final: 0.6532 (mtp180) REVERT: A 725 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7647 (mt) REVERT: B 21 MET cc_start: 0.7721 (ptm) cc_final: 0.7340 (ptm) REVERT: B 24 ILE cc_start: 0.8516 (mm) cc_final: 0.8024 (mm) REVERT: B 28 MET cc_start: 0.6962 (mmm) cc_final: 0.6406 (mmm) REVERT: B 86 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 148 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7790 (mtp85) REVERT: B 214 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7703 (mt-10) REVERT: B 215 MET cc_start: 0.8270 (mtt) cc_final: 0.7944 (mtm) REVERT: B 219 GLN cc_start: 0.8473 (mp10) cc_final: 0.7764 (mp10) REVERT: B 239 GLU cc_start: 0.8302 (tp30) cc_final: 0.7700 (tp30) REVERT: B 293 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 327 CYS cc_start: 0.7592 (t) cc_final: 0.7222 (t) REVERT: B 376 LYS cc_start: 0.7964 (tppt) cc_final: 0.7709 (ttpp) REVERT: B 397 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 429 THR cc_start: 0.8353 (t) cc_final: 0.8005 (p) REVERT: B 451 MET cc_start: 0.8174 (ttm) cc_final: 0.7847 (mtp) REVERT: B 507 LEU cc_start: 0.7431 (pt) cc_final: 0.7072 (pp) REVERT: B 511 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7069 (tm-30) REVERT: B 560 ASP cc_start: 0.8076 (m-30) cc_final: 0.7727 (m-30) REVERT: B 578 THR cc_start: 0.8219 (m) cc_final: 0.7893 (p) REVERT: B 590 LYS cc_start: 0.7473 (mtmt) cc_final: 0.7272 (mttt) REVERT: B 603 ASP cc_start: 0.7690 (t0) cc_final: 0.7226 (t0) REVERT: B 611 ASN cc_start: 0.7693 (p0) cc_final: 0.7475 (p0) outliers start: 56 outliers final: 38 residues processed: 338 average time/residue: 0.2680 time to fit residues: 123.4292 Evaluate side-chains 351 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 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 178 VAL 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 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 310 VAL Chi-restraints excluded: chain B residue 420 VAL 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 639 HIS 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: 1.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111015 restraints weight = 16538.625| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.30 r_work: 0.3337 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11628 Z= 0.268 Angle : 0.682 8.060 15714 Z= 0.367 Chirality : 0.049 0.344 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.951 89.070 1708 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.22 % Favored : 90.41 % Rotamer: Outliers : 5.21 % Allowed : 17.44 % Favored : 77.36 % 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: -1.02 (0.23), residues: 1377 helix: 1.10 (0.21), residues: 634 sheet: 0.16 (0.50), residues: 113 loop : -2.89 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 720 HIS 0.007 0.001 HIS B 216 PHE 0.023 0.003 PHE A 526 TYR 0.018 0.002 TYR B 164 ARG 0.008 0.001 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.07360 ( 444) hydrogen bonds : angle 4.37768 ( 1278) metal coordination : bond 0.00383 ( 3) covalent geometry : bond 0.00623 (11625) covalent geometry : angle 0.68151 (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 378 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8399 (mtpt) REVERT: A 11 ARG cc_start: 0.7423 (mtt-85) cc_final: 0.7098 (mtt-85) REVERT: A 21 MET cc_start: 0.6987 (mpt) cc_final: 0.6542 (mtp) REVERT: A 25 ARG cc_start: 0.7956 (mpt-90) cc_final: 0.7482 (mpt-90) REVERT: A 30 HIS cc_start: 0.8044 (m-70) cc_final: 0.7829 (m-70) REVERT: A 45 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: A 55 MET cc_start: 0.7118 (tpp) cc_final: 0.6754 (tpp) REVERT: A 100 MET cc_start: 0.7645 (tmm) cc_final: 0.7259 (tmm) REVERT: A 114 ASN cc_start: 0.7298 (m-40) cc_final: 0.7096 (m-40) REVERT: A 117 MET cc_start: 0.6721 (mtp) cc_final: 0.6178 (mtp) REVERT: A 239 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7178 (tp30) REVERT: A 241 LYS cc_start: 0.8148 (tppp) cc_final: 0.7947 (ttmt) REVERT: A 243 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 244 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 319 THR cc_start: 0.7853 (m) cc_final: 0.7264 (p) REVERT: A 342 ASN cc_start: 0.7859 (t0) cc_final: 0.7437 (t0) REVERT: A 352 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (pt) REVERT: A 360 ASN cc_start: 0.7931 (t0) cc_final: 0.7351 (t0) REVERT: A 364 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 380 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7816 (ttp-170) REVERT: A 414 MET cc_start: 0.7268 (tmm) cc_final: 0.6874 (tmm) REVERT: A 462 MET cc_start: 0.8019 (ttm) cc_final: 0.7694 (ttp) REVERT: A 507 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7131 (pp) REVERT: A 510 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: A 529 LEU cc_start: 0.8813 (tm) cc_final: 0.8517 (tt) REVERT: A 594 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 603 ASP cc_start: 0.7298 (t70) cc_final: 0.7015 (t0) REVERT: A 606 TYR cc_start: 0.8609 (p90) cc_final: 0.8268 (p90) REVERT: A 645 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8040 (pp) REVERT: A 662 MET cc_start: 0.7510 (ttp) cc_final: 0.6983 (ptp) REVERT: A 719 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6521 (mtp180) REVERT: B 15 PHE cc_start: 0.7200 (t80) cc_final: 0.5874 (t80) REVERT: B 21 MET cc_start: 0.7923 (ptm) cc_final: 0.7556 (ptm) REVERT: B 24 ILE cc_start: 0.8577 (mm) cc_final: 0.8033 (mm) REVERT: B 28 MET cc_start: 0.7337 (mmm) cc_final: 0.6720 (mmm) REVERT: B 67 GLU cc_start: 0.7884 (tp30) cc_final: 0.7642 (tm-30) REVERT: B 86 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 113 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: B 132 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7551 (mm-30) REVERT: B 148 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.7894 (mtm110) REVERT: B 215 MET cc_start: 0.8348 (mtt) cc_final: 0.7958 (mtm) REVERT: B 219 GLN cc_start: 0.8548 (mp10) cc_final: 0.7689 (mm-40) REVERT: B 345 THR cc_start: 0.8350 (t) cc_final: 0.8102 (p) REVERT: B 376 LYS cc_start: 0.8037 (tppt) cc_final: 0.7824 (ttpp) REVERT: B 397 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8095 (tm-30) REVERT: B 429 THR cc_start: 0.8479 (t) cc_final: 0.8164 (t) REVERT: B 507 LEU cc_start: 0.7481 (pt) cc_final: 0.7138 (pp) REVERT: B 557 TYR cc_start: 0.8339 (t80) cc_final: 0.7974 (t80) REVERT: B 590 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7307 (mttt) REVERT: B 603 ASP cc_start: 0.7855 (t0) cc_final: 0.7375 (t0) REVERT: B 611 ASN cc_start: 0.8015 (p0) cc_final: 0.7722 (p0) outliers start: 63 outliers final: 46 residues processed: 342 average time/residue: 0.2655 time to fit residues: 122.9664 Evaluate side-chains 365 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU 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 178 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 242 ASN 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 352 ILE Chi-restraints excluded: chain A residue 448 ILE 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 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 674 ASN 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 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 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 408 LYS Chi-restraints excluded: chain B residue 420 VAL 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 541 HIS Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 639 HIS 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: 3.9990 chunk 9 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 126 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3775 r_free = 0.3775 target = 0.132420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113862 restraints weight = 16754.105| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.34 r_work: 0.3385 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11628 Z= 0.143 Angle : 0.619 8.426 15714 Z= 0.330 Chirality : 0.044 0.356 1703 Planarity : 0.005 0.090 2015 Dihedral : 10.614 84.746 1708 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.39 % Favored : 93.25 % Rotamer: Outliers : 4.88 % Allowed : 18.93 % Favored : 76.20 % 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: -0.83 (0.23), residues: 1377 helix: 1.39 (0.21), residues: 634 sheet: 0.05 (0.57), residues: 94 loop : -2.82 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 399 HIS 0.003 0.001 HIS B 216 PHE 0.025 0.002 PHE A 526 TYR 0.012 0.001 TYR A 262 ARG 0.004 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.05122 ( 444) hydrogen bonds : angle 3.98684 ( 1278) metal coordination : bond 0.00156 ( 3) covalent geometry : bond 0.00325 (11625) covalent geometry : angle 0.61862 (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 383 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8387 (mtpt) REVERT: A 11 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.7080 (mtt-85) REVERT: A 21 MET cc_start: 0.6998 (mpt) cc_final: 0.6449 (mtp) REVERT: A 25 ARG cc_start: 0.7941 (mpt-90) cc_final: 0.7476 (mpt-90) REVERT: A 45 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: A 55 MET cc_start: 0.6890 (tpp) cc_final: 0.6575 (tpp) REVERT: A 100 MET cc_start: 0.7602 (tmm) cc_final: 0.7222 (tmm) REVERT: A 114 ASN cc_start: 0.7299 (m-40) cc_final: 0.7096 (m-40) REVERT: A 117 MET cc_start: 0.6722 (mtp) cc_final: 0.6516 (mtp) REVERT: A 239 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 241 LYS cc_start: 0.8105 (tppp) cc_final: 0.7814 (mtpt) REVERT: A 244 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 293 GLU cc_start: 0.8236 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 319 THR cc_start: 0.7793 (m) cc_final: 0.7224 (t) REVERT: A 342 ASN cc_start: 0.7816 (t0) cc_final: 0.7391 (t0) REVERT: A 352 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8299 (pt) REVERT: A 360 ASN cc_start: 0.7831 (t0) cc_final: 0.7273 (t0) REVERT: A 364 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 414 MET cc_start: 0.7101 (tmm) cc_final: 0.6722 (tmm) REVERT: A 462 MET cc_start: 0.7739 (ttm) cc_final: 0.7444 (ttp) REVERT: A 507 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7046 (pp) REVERT: A 510 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7814 (pp20) REVERT: A 529 LEU cc_start: 0.8743 (tm) cc_final: 0.8423 (tt) REVERT: A 590 LYS cc_start: 0.7922 (mppt) cc_final: 0.7720 (mppt) REVERT: A 594 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 603 ASP cc_start: 0.7262 (t70) cc_final: 0.6996 (t0) REVERT: A 606 TYR cc_start: 0.8510 (p90) cc_final: 0.8143 (p90) REVERT: A 642 TYR cc_start: 0.8099 (m-80) cc_final: 0.7584 (t80) REVERT: A 645 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 21 MET cc_start: 0.7839 (ptm) cc_final: 0.7475 (ptm) REVERT: B 24 ILE cc_start: 0.8572 (mm) cc_final: 0.7941 (mm) REVERT: B 28 MET cc_start: 0.7233 (mmm) cc_final: 0.6581 (mmm) REVERT: B 86 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 132 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7460 (mm-30) REVERT: B 148 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7836 (mtm110) REVERT: B 214 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 215 MET cc_start: 0.8289 (mtt) cc_final: 0.7929 (mtm) REVERT: B 219 GLN cc_start: 0.8445 (mp10) cc_final: 0.7633 (mm-40) REVERT: B 238 GLU cc_start: 0.7839 (tp30) cc_final: 0.7549 (tp30) REVERT: B 239 GLU cc_start: 0.8376 (tp30) cc_final: 0.7650 (tp30) REVERT: B 376 LYS cc_start: 0.8040 (tppt) cc_final: 0.7785 (ttpp) REVERT: B 397 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 429 THR cc_start: 0.8390 (t) cc_final: 0.8044 (p) REVERT: B 499 TYR cc_start: 0.8052 (m-80) cc_final: 0.7705 (m-80) REVERT: B 507 LEU cc_start: 0.7456 (pt) cc_final: 0.7116 (pp) REVERT: B 537 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6361 (mt) REVERT: B 578 THR cc_start: 0.8230 (m) cc_final: 0.7887 (p) REVERT: B 603 ASP cc_start: 0.7725 (t0) cc_final: 0.7318 (t0) REVERT: B 611 ASN cc_start: 0.7968 (p0) cc_final: 0.7679 (p0) outliers start: 59 outliers final: 45 residues processed: 353 average time/residue: 0.2705 time to fit residues: 129.3731 Evaluate side-chains 361 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 507 LEU Chi-restraints excluded: chain A residue 510 GLU 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 602 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 663 MET Chi-restraints excluded: chain A residue 674 ASN 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 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 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 663 MET 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: 0.8980 chunk 39 optimal weight: 0.7980 chunk 131 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 HIS ** 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 612 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113120 restraints weight = 16718.751| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.33 r_work: 0.3418 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11628 Z= 0.125 Angle : 0.604 10.813 15714 Z= 0.320 Chirality : 0.043 0.326 1703 Planarity : 0.005 0.090 2015 Dihedral : 10.252 80.220 1706 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.10 % Rotamer: Outliers : 4.55 % Allowed : 20.00 % Favored : 75.45 % 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: 1.56 (0.21), residues: 633 sheet: 0.27 (0.56), residues: 93 loop : -2.73 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.007 0.001 HIS B 612 PHE 0.025 0.001 PHE A 526 TYR 0.010 0.001 TYR B 371 ARG 0.005 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 444) hydrogen bonds : angle 3.80199 ( 1278) metal coordination : bond 0.00113 ( 3) covalent geometry : bond 0.00279 (11625) covalent geometry : angle 0.60353 (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 370 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8366 (mtpt) REVERT: A 11 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7032 (mtt-85) REVERT: A 21 MET cc_start: 0.7095 (mpt) cc_final: 0.6528 (mtp) REVERT: A 25 ARG cc_start: 0.7910 (mpt-90) cc_final: 0.7444 (mpt-90) REVERT: A 45 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: A 55 MET cc_start: 0.6755 (tpp) cc_final: 0.6473 (tpp) REVERT: A 100 MET cc_start: 0.7555 (tmm) cc_final: 0.7184 (tmm) REVERT: A 117 MET cc_start: 0.6727 (mtp) cc_final: 0.6204 (mtp) REVERT: A 239 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7038 (tp30) REVERT: A 319 THR cc_start: 0.7767 (m) cc_final: 0.7216 (t) REVERT: A 342 ASN cc_start: 0.7778 (t0) cc_final: 0.7348 (t0) REVERT: A 360 ASN cc_start: 0.7856 (t0) cc_final: 0.7251 (t0) REVERT: A 364 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 414 MET cc_start: 0.7048 (tmm) cc_final: 0.6706 (tmm) REVERT: A 462 MET cc_start: 0.7560 (ttm) cc_final: 0.7265 (ttp) REVERT: A 492 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: A 507 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7025 (pp) REVERT: A 510 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: A 529 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8426 (tt) REVERT: A 590 LYS cc_start: 0.7923 (mppt) cc_final: 0.7710 (mppt) REVERT: A 594 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 603 ASP cc_start: 0.7305 (t70) cc_final: 0.7043 (t0) REVERT: A 606 TYR cc_start: 0.8451 (p90) cc_final: 0.8080 (p90) REVERT: A 645 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7963 (pp) REVERT: A 719 ARG cc_start: 0.6841 (mtp180) cc_final: 0.6509 (mtp180) REVERT: A 725 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 21 MET cc_start: 0.7816 (ptm) cc_final: 0.7449 (ptm) REVERT: B 24 ILE cc_start: 0.8543 (mm) cc_final: 0.7925 (mm) REVERT: B 28 MET cc_start: 0.7275 (mmm) cc_final: 0.6601 (mmm) REVERT: B 67 GLU cc_start: 0.7779 (tp30) cc_final: 0.7483 (tm-30) REVERT: B 86 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 132 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7454 (mm-30) REVERT: B 148 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7832 (mtm110) REVERT: B 214 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 215 MET cc_start: 0.8231 (mtt) cc_final: 0.7926 (mtm) REVERT: B 219 GLN cc_start: 0.8439 (mp10) cc_final: 0.7823 (mm-40) REVERT: B 239 GLU cc_start: 0.8326 (tp30) cc_final: 0.7672 (tp30) REVERT: B 293 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 376 LYS cc_start: 0.8025 (tppt) cc_final: 0.7759 (ttpp) REVERT: B 397 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 429 THR cc_start: 0.8393 (t) cc_final: 0.8041 (p) REVERT: B 499 TYR cc_start: 0.8057 (m-80) cc_final: 0.7736 (m-80) REVERT: B 507 LEU cc_start: 0.7386 (pt) cc_final: 0.7015 (pp) REVERT: B 537 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6284 (mt) REVERT: B 578 THR cc_start: 0.8192 (m) cc_final: 0.7838 (p) REVERT: B 603 ASP cc_start: 0.7763 (t0) cc_final: 0.7351 (t0) REVERT: B 611 ASN cc_start: 0.7780 (p0) cc_final: 0.7463 (p0) outliers start: 55 outliers final: 41 residues processed: 342 average time/residue: 0.2848 time to fit residues: 130.9298 Evaluate side-chains 348 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 254 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 492 GLN 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 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 663 MET 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 178 VAL 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 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 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 639 HIS Chi-restraints excluded: chain B residue 663 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** 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 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111969 restraints weight = 16564.254| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.31 r_work: 0.3396 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11628 Z= 0.152 Angle : 0.623 9.621 15714 Z= 0.332 Chirality : 0.044 0.256 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.211 79.314 1706 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.33 % Favored : 92.30 % Rotamer: Outliers : 4.96 % Allowed : 20.25 % 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: -0.61 (0.23), residues: 1377 helix: 1.54 (0.21), residues: 634 sheet: 0.37 (0.52), residues: 103 loop : -2.75 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.004 0.001 HIS A 30 PHE 0.014 0.002 PHE B 463 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 444) hydrogen bonds : angle 3.88188 ( 1278) metal coordination : bond 0.00189 ( 3) covalent geometry : bond 0.00350 (11625) covalent geometry : angle 0.62295 (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 358 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8337 (mmmt) REVERT: A 11 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7077 (mtt-85) REVERT: A 21 MET cc_start: 0.7152 (mpt) cc_final: 0.6653 (mtp) REVERT: A 25 ARG cc_start: 0.7931 (mpt-90) cc_final: 0.7490 (mpt-90) REVERT: A 45 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: A 55 MET cc_start: 0.6811 (tpp) cc_final: 0.6519 (tpp) REVERT: A 100 MET cc_start: 0.7595 (tmm) cc_final: 0.7221 (tmm) REVERT: A 117 MET cc_start: 0.6622 (mtp) cc_final: 0.6104 (mtp) REVERT: A 292 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: A 293 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 319 THR cc_start: 0.7711 (m) cc_final: 0.7161 (t) REVERT: A 342 ASN cc_start: 0.7767 (t0) cc_final: 0.7333 (t0) REVERT: A 360 ASN cc_start: 0.7764 (t0) cc_final: 0.7191 (t0) REVERT: A 364 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 380 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7877 (ttp-170) REVERT: A 414 MET cc_start: 0.6940 (tmm) cc_final: 0.6667 (tmm) REVERT: A 462 MET cc_start: 0.7698 (ttm) cc_final: 0.7413 (ttp) REVERT: A 492 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: A 507 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7073 (pp) REVERT: A 510 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: A 529 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 594 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 603 ASP cc_start: 0.7321 (t70) cc_final: 0.7047 (t0) REVERT: A 606 TYR cc_start: 0.8475 (p90) cc_final: 0.8108 (p90) REVERT: A 645 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 719 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6511 (mtp180) REVERT: A 725 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7646 (mt) REVERT: B 21 MET cc_start: 0.7838 (ptm) cc_final: 0.7473 (ptm) REVERT: B 24 ILE cc_start: 0.8533 (mm) cc_final: 0.7922 (mm) REVERT: B 28 MET cc_start: 0.7270 (mmm) cc_final: 0.6631 (mmm) REVERT: B 86 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 132 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7461 (mm-30) REVERT: B 148 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7881 (mtm110) REVERT: B 215 MET cc_start: 0.8290 (mtt) cc_final: 0.7932 (mtm) REVERT: B 219 GLN cc_start: 0.8466 (mp10) cc_final: 0.7868 (mm-40) REVERT: B 293 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 376 LYS cc_start: 0.8017 (tppt) cc_final: 0.7758 (ttpp) REVERT: B 397 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 429 THR cc_start: 0.8407 (t) cc_final: 0.8047 (p) REVERT: B 499 TYR cc_start: 0.8088 (m-80) cc_final: 0.7750 (m-80) REVERT: B 507 LEU cc_start: 0.7457 (pt) cc_final: 0.7092 (pp) REVERT: B 537 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6417 (mt) REVERT: B 578 THR cc_start: 0.8203 (m) cc_final: 0.7857 (p) REVERT: B 603 ASP cc_start: 0.7753 (t0) cc_final: 0.7358 (t0) REVERT: B 611 ASN cc_start: 0.7995 (p0) cc_final: 0.7730 (p0) outliers start: 60 outliers final: 42 residues processed: 330 average time/residue: 0.2806 time to fit residues: 125.3832 Evaluate side-chains 348 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 492 GLN 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 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 663 MET 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 79 LYS Chi-restraints excluded: chain B residue 92 LYS 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 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 574 SER 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: 2.9990 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 119 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 16 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113463 restraints weight = 16672.062| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.32 r_work: 0.3418 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11628 Z= 0.129 Angle : 0.618 9.174 15714 Z= 0.327 Chirality : 0.043 0.263 1703 Planarity : 0.005 0.092 2015 Dihedral : 9.951 79.061 1706 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.10 % Rotamer: Outliers : 4.46 % Allowed : 20.74 % 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: -0.52 (0.23), residues: 1377 helix: 1.65 (0.21), residues: 635 sheet: 0.58 (0.55), residues: 93 loop : -2.74 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.019 0.001 PHE A 526 TYR 0.010 0.001 TYR B 371 ARG 0.003 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 444) hydrogen bonds : angle 3.77274 ( 1278) metal coordination : bond 0.00126 ( 3) covalent geometry : bond 0.00292 (11625) covalent geometry : angle 0.61829 (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 356 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8353 (mmmt) REVERT: A 11 ARG cc_start: 0.7439 (mtt-85) cc_final: 0.7077 (mtt-85) REVERT: A 21 MET cc_start: 0.7147 (mpt) cc_final: 0.6609 (mtp) REVERT: A 25 ARG cc_start: 0.7902 (mpt-90) cc_final: 0.7479 (mpt-90) REVERT: A 45 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: A 55 MET cc_start: 0.6719 (tpp) cc_final: 0.6444 (tpp) REVERT: A 100 MET cc_start: 0.7598 (tmm) cc_final: 0.7228 (tmm) REVERT: A 117 MET cc_start: 0.6726 (mtp) cc_final: 0.6218 (mtp) REVERT: A 293 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 319 THR cc_start: 0.7691 (m) cc_final: 0.7174 (t) REVERT: A 342 ASN cc_start: 0.7768 (t0) cc_final: 0.7349 (t0) REVERT: A 360 ASN cc_start: 0.7784 (t0) cc_final: 0.7212 (t0) REVERT: A 364 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 380 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7904 (ttp-170) REVERT: A 462 MET cc_start: 0.7562 (ttm) cc_final: 0.7298 (ttp) REVERT: A 492 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8215 (mm-40) REVERT: A 507 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7109 (pp) REVERT: A 510 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7735 (pp20) REVERT: A 590 LYS cc_start: 0.7984 (mppt) cc_final: 0.7774 (mppt) REVERT: A 594 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 603 ASP cc_start: 0.7365 (t70) cc_final: 0.7086 (t0) REVERT: A 606 TYR cc_start: 0.8429 (p90) cc_final: 0.8064 (p90) REVERT: A 645 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7972 (pp) REVERT: A 719 ARG cc_start: 0.6819 (mtp180) cc_final: 0.6497 (mtp180) REVERT: A 725 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7668 (mt) REVERT: B 21 MET cc_start: 0.7811 (ptm) cc_final: 0.7453 (ptm) REVERT: B 24 ILE cc_start: 0.8532 (mm) cc_final: 0.7907 (mm) REVERT: B 28 MET cc_start: 0.7317 (mmm) cc_final: 0.6668 (mmm) REVERT: B 86 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 109 ASP cc_start: 0.7821 (t70) cc_final: 0.7437 (t0) REVERT: B 126 MET cc_start: 0.8840 (mmm) cc_final: 0.8554 (tpp) REVERT: B 132 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7450 (mm-30) REVERT: B 148 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7874 (mtm110) REVERT: B 215 MET cc_start: 0.8224 (mtt) cc_final: 0.7951 (mtm) REVERT: B 219 GLN cc_start: 0.8435 (mp10) cc_final: 0.7829 (mm-40) REVERT: B 376 LYS cc_start: 0.7989 (tppt) cc_final: 0.7760 (ttpp) REVERT: B 397 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 429 THR cc_start: 0.8399 (t) cc_final: 0.8043 (p) REVERT: B 449 GLU cc_start: 0.7808 (tt0) cc_final: 0.7411 (mt-10) REVERT: B 499 TYR cc_start: 0.8056 (m-80) cc_final: 0.7711 (m-80) REVERT: B 507 LEU cc_start: 0.7399 (pt) cc_final: 0.7032 (pp) REVERT: B 537 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6445 (mt) REVERT: B 578 THR cc_start: 0.8171 (m) cc_final: 0.7832 (p) REVERT: B 603 ASP cc_start: 0.7745 (t0) cc_final: 0.7359 (t0) REVERT: B 611 ASN cc_start: 0.7922 (p0) cc_final: 0.7623 (p0) outliers start: 54 outliers final: 44 residues processed: 326 average time/residue: 0.2676 time to fit residues: 118.1469 Evaluate side-chains 351 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 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 292 MET Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 492 GLN 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 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 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 663 MET 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 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 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET 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 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: 0.9990 chunk 59 optimal weight: 0.0770 chunk 11 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 16 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115727 restraints weight = 16490.598| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.33 r_work: 0.3411 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11628 Z= 0.133 Angle : 0.639 9.326 15714 Z= 0.336 Chirality : 0.043 0.261 1703 Planarity : 0.005 0.093 2015 Dihedral : 9.792 86.801 1706 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.68 % Favored : 92.96 % Rotamer: Outliers : 4.55 % Allowed : 21.82 % Favored : 73.64 % 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: -0.47 (0.23), residues: 1377 helix: 1.66 (0.21), residues: 635 sheet: 0.63 (0.52), residues: 102 loop : -2.72 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.034 0.001 PHE A 382 TYR 0.013 0.001 TYR B 371 ARG 0.006 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 444) hydrogen bonds : angle 3.76914 ( 1278) metal coordination : bond 0.00123 ( 3) covalent geometry : bond 0.00303 (11625) covalent geometry : angle 0.63894 (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 358 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8350 (mmmt) REVERT: A 11 ARG cc_start: 0.7448 (mtt-85) cc_final: 0.7070 (mtt-85) REVERT: A 21 MET cc_start: 0.7127 (mpt) cc_final: 0.6603 (mtp) REVERT: A 25 ARG cc_start: 0.7882 (mpt-90) cc_final: 0.7455 (mpt-90) REVERT: A 45 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: A 55 MET cc_start: 0.6709 (tpp) cc_final: 0.6432 (tpp) REVERT: A 100 MET cc_start: 0.7603 (tmm) cc_final: 0.7226 (tmm) REVERT: A 117 MET cc_start: 0.6714 (mtp) cc_final: 0.6181 (mtp) REVERT: A 293 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 319 THR cc_start: 0.7710 (m) cc_final: 0.7159 (t) REVERT: A 342 ASN cc_start: 0.7773 (t0) cc_final: 0.7352 (t0) REVERT: A 360 ASN cc_start: 0.7767 (t0) cc_final: 0.7189 (t0) REVERT: A 364 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 462 MET cc_start: 0.7584 (ttm) cc_final: 0.7253 (ttp) REVERT: A 492 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8272 (mm-40) REVERT: A 507 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7074 (pp) REVERT: A 510 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: A 594 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 603 ASP cc_start: 0.7333 (t70) cc_final: 0.7064 (t0) REVERT: A 606 TYR cc_start: 0.8416 (p90) cc_final: 0.8025 (p90) REVERT: A 645 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 719 ARG cc_start: 0.6822 (mtp180) cc_final: 0.6489 (mtp180) REVERT: A 725 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7651 (mt) REVERT: B 21 MET cc_start: 0.7830 (ptm) cc_final: 0.7471 (ptm) REVERT: B 24 ILE cc_start: 0.8521 (mm) cc_final: 0.7908 (mm) REVERT: B 28 MET cc_start: 0.7308 (mmm) cc_final: 0.6660 (mmm) REVERT: B 86 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 132 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7453 (mm-30) REVERT: B 148 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7685 (mtp85) REVERT: B 215 MET cc_start: 0.8253 (mtt) cc_final: 0.7966 (mtm) REVERT: B 219 GLN cc_start: 0.8451 (mp10) cc_final: 0.7846 (mm-40) REVERT: B 238 GLU cc_start: 0.7872 (tp30) cc_final: 0.7574 (tp30) REVERT: B 376 LYS cc_start: 0.7988 (tppt) cc_final: 0.7750 (ttpp) REVERT: B 397 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 429 THR cc_start: 0.8406 (t) cc_final: 0.8045 (p) REVERT: B 449 GLU cc_start: 0.7835 (tt0) cc_final: 0.7421 (mt-10) REVERT: B 451 MET cc_start: 0.8174 (ttm) cc_final: 0.7866 (mtp) REVERT: B 507 LEU cc_start: 0.7387 (pt) cc_final: 0.7026 (pp) REVERT: B 537 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6486 (mt) REVERT: B 578 THR cc_start: 0.8124 (m) cc_final: 0.7811 (p) REVERT: B 603 ASP cc_start: 0.7736 (t0) cc_final: 0.7409 (t0) REVERT: B 611 ASN cc_start: 0.7935 (p0) cc_final: 0.7641 (p0) outliers start: 55 outliers final: 44 residues processed: 328 average time/residue: 0.2846 time to fit residues: 127.1351 Evaluate side-chains 357 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 492 GLN 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 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 663 MET 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 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 261 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET 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 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: 2.9990 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 131 optimal weight: 0.0670 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 16 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 = 0.3787 r_free = 0.3787 target = 0.133510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114857 restraints weight = 16527.879| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.34 r_work: 0.3396 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3000 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= 0.149 Angle : 0.652 9.211 15714 Z= 0.342 Chirality : 0.044 0.267 1703 Planarity : 0.005 0.093 2015 Dihedral : 9.674 87.629 1706 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.75 % Favored : 92.88 % Rotamer: Outliers : 4.38 % Allowed : 22.40 % Favored : 73.22 % 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: -0.53 (0.23), residues: 1377 helix: 1.64 (0.21), residues: 635 sheet: 0.47 (0.54), residues: 94 loop : -2.72 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.014 0.001 PHE B 463 TYR 0.012 0.001 TYR B 164 ARG 0.005 0.000 ARG A 406 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 444) hydrogen bonds : angle 3.82191 ( 1278) metal coordination : bond 0.00149 ( 3) covalent geometry : bond 0.00342 (11625) covalent geometry : angle 0.65170 (15714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6559.64 seconds wall clock time: 114 minutes 1.33 seconds (6841.33 seconds total)