Starting phenix.real_space_refine on Sat Aug 23 10:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p23_17357/08_2025/8p23_17357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p23_17357/08_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_17357/08_2025/8p23_17357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p23_17357/08_2025/8p23_17357.map" model { file = "/net/cci-nas-00/data/ceres_data/8p23_17357/08_2025/8p23_17357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p23_17357/08_2025/8p23_17357.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.22, per 1000 atoms: 0.28 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: 1.03 Conformation dependent library (CDL) restraints added in 574.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.36 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: 1.83 Time building geometry restraints manager: 1.34 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 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: 1.730 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- 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 : 5.87 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (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 ARG 0.006 0.000 ARG A 381 TYR 0.026 0.001 TYR B 371 PHE 0.010 0.001 PHE A 224 TRP 0.005 0.001 TRP A 720 HIS 0.003 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00358 (11625) covalent geometry : angle 0.69248 (15714) hydrogen bonds : bond 0.16120 ( 444) hydrogen bonds : angle 5.93029 ( 1278) metal coordination : bond 0.00079 ( 3) *********************** 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 : 0.516 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: 0.1367 time to fit residues: 71.1526 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 : 0.465 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 0.0770 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 242 ASN A 300 ASN A 395 GLN A 506 ASN A 676 ASN B 78 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 548 GLN B 572 ASN B 652 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114279 restraints weight = 16416.917| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.31 r_work: 0.3438 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1722 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= 0.132 Angle : 0.604 7.240 15714 Z= 0.318 Chirality : 0.044 0.261 1703 Planarity : 0.004 0.079 2015 Dihedral : 12.380 83.978 1741 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.61 % Favored : 93.03 % Rotamer: Outliers : 4.55 % Allowed : 13.55 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.24), residues: 1377 helix: 1.39 (0.22), residues: 633 sheet: 0.31 (0.52), residues: 113 loop : -2.84 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.012 0.001 TYR A 80 PHE 0.015 0.002 PHE A 383 TRP 0.010 0.001 TRP B 353 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00295 (11625) covalent geometry : angle 0.60385 (15714) hydrogen bonds : bond 0.04717 ( 444) hydrogen bonds : angle 4.22970 ( 1278) metal coordination : bond 0.00169 ( 3) *********************** 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 377 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 322 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8258 (mtpp) REVERT: A 21 MET cc_start: 0.6897 (mpt) cc_final: 0.6658 (mtp) REVERT: A 30 HIS cc_start: 0.8009 (m-70) cc_final: 0.7728 (m-70) REVERT: A 100 MET cc_start: 0.7380 (tmm) cc_final: 0.6979 (tmm) REVERT: A 117 MET cc_start: 0.6691 (mtp) cc_final: 0.6282 (mtp) REVERT: A 238 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 241 LYS cc_start: 0.8151 (tppp) cc_final: 0.7853 (ttmt) REVERT: A 244 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 264 GLU cc_start: 0.7681 (pm20) cc_final: 0.7447 (pm20) REVERT: A 313 SER cc_start: 0.7963 (p) cc_final: 0.7638 (m) REVERT: A 319 THR cc_start: 0.7858 (m) cc_final: 0.7312 (t) REVERT: A 342 ASN cc_start: 0.7766 (t0) cc_final: 0.7350 (t0) REVERT: A 352 ILE cc_start: 0.8612 (pp) cc_final: 0.8404 (pt) REVERT: A 360 ASN cc_start: 0.7850 (t0) cc_final: 0.7267 (t0) REVERT: A 462 MET cc_start: 0.7585 (ttm) cc_final: 0.7320 (ttp) REVERT: A 476 LYS cc_start: 0.8638 (tppp) cc_final: 0.8364 (tppt) REVERT: A 590 LYS cc_start: 0.7812 (mppt) cc_final: 0.7520 (mppt) REVERT: A 594 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 603 ASP cc_start: 0.7259 (t70) cc_final: 0.6989 (t0) REVERT: A 622 LEU cc_start: 0.8116 (mt) cc_final: 0.7810 (mt) REVERT: A 626 GLN cc_start: 0.8134 (mt0) cc_final: 0.7887 (mt0) REVERT: A 674 ASN cc_start: 0.7926 (m110) cc_final: 0.7683 (m-40) REVERT: A 719 ARG cc_start: 0.6738 (mtp180) cc_final: 0.6498 (mtp180) REVERT: A 725 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7680 (mt) REVERT: B 21 MET cc_start: 0.7714 (ptm) cc_final: 0.7312 (ptm) REVERT: B 24 ILE cc_start: 0.8463 (mm) cc_final: 0.8088 (mm) REVERT: B 28 MET cc_start: 0.6590 (mmm) cc_final: 0.6176 (mmm) REVERT: B 86 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 127 MET cc_start: 0.8585 (mmm) cc_final: 0.8375 (mmt) REVERT: B 145 GLU cc_start: 0.7874 (pm20) cc_final: 0.7595 (pm20) REVERT: B 148 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7589 (mtp85) REVERT: B 214 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 215 MET cc_start: 0.8273 (mtt) cc_final: 0.8039 (mtm) REVERT: B 239 GLU cc_start: 0.8307 (tp30) cc_final: 0.7583 (tp30) REVERT: B 292 MET cc_start: 0.7807 (tpp) cc_final: 0.7600 (mmt) REVERT: B 293 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7433 (tm-30) REVERT: B 299 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6721 (mpm) REVERT: B 372 LYS cc_start: 0.9003 (tppt) cc_final: 0.8564 (tppt) REVERT: B 376 LYS cc_start: 0.8076 (tppt) cc_final: 0.7793 (ttmm) REVERT: B 397 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8105 (tm-30) REVERT: B 429 THR cc_start: 0.8399 (t) cc_final: 0.8087 (p) REVERT: B 507 LEU cc_start: 0.7400 (pt) cc_final: 0.7040 (pp) REVERT: B 511 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6844 (tm-30) REVERT: B 560 ASP cc_start: 0.8111 (m-30) cc_final: 0.7778 (m-30) REVERT: B 603 ASP cc_start: 0.7716 (t0) cc_final: 0.7304 (t0) REVERT: B 623 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7784 (ttpp) REVERT: B 654 SER cc_start: 0.6166 (OUTLIER) cc_final: 0.5513 (p) REVERT: B 657 GLU cc_start: 0.7780 (tp30) cc_final: 0.7486 (tp30) REVERT: B 719 ARG cc_start: 0.8263 (mtp180) cc_final: 0.8032 (mtm180) outliers start: 55 outliers final: 32 residues processed: 354 average time/residue: 0.1337 time to fit residues: 64.1664 Evaluate side-chains 345 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 310 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 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS 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 508 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 639 HIS 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 109 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 298 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 541 HIS B 611 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112216 restraints weight = 16539.109| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.28 r_work: 0.3403 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2085 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= 0.164 Angle : 0.602 7.353 15714 Z= 0.322 Chirality : 0.045 0.281 1703 Planarity : 0.004 0.084 2015 Dihedral : 11.501 85.744 1719 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.97 % Favored : 92.67 % Rotamer: Outliers : 4.71 % Allowed : 14.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.23), residues: 1377 helix: 1.34 (0.22), residues: 634 sheet: 0.36 (0.52), residues: 113 loop : -2.82 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 406 TYR 0.013 0.001 TYR B 236 PHE 0.026 0.002 PHE A 526 TRP 0.007 0.001 TRP B 399 HIS 0.013 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00374 (11625) covalent geometry : angle 0.60219 (15714) hydrogen bonds : bond 0.05373 ( 444) hydrogen bonds : angle 4.15312 ( 1278) metal coordination : bond 0.00203 ( 3) *********************** 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 374 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8341 (mtpp) REVERT: A 21 MET cc_start: 0.6974 (mpt) cc_final: 0.6239 (mtp) REVERT: A 25 ARG cc_start: 0.7873 (mpt-90) cc_final: 0.7411 (mpt-90) REVERT: A 30 HIS cc_start: 0.8021 (m-70) cc_final: 0.7806 (m-70) REVERT: A 45 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: A 55 MET cc_start: 0.6895 (mpp) cc_final: 0.6628 (tpp) REVERT: A 100 MET cc_start: 0.7524 (tmm) cc_final: 0.7139 (tmm) REVERT: A 117 MET cc_start: 0.6695 (mtp) cc_final: 0.6200 (mtp) REVERT: A 238 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 241 LYS cc_start: 0.8193 (tppp) cc_final: 0.7912 (ttmt) REVERT: A 244 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 263 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7932 (mp) REVERT: A 264 GLU cc_start: 0.7673 (pm20) cc_final: 0.7465 (pm20) REVERT: A 292 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7884 (mmm) REVERT: A 319 THR cc_start: 0.7952 (m) cc_final: 0.7338 (t) REVERT: A 342 ASN cc_start: 0.7790 (t0) cc_final: 0.7376 (t0) REVERT: A 352 ILE cc_start: 0.8633 (pp) cc_final: 0.8341 (pt) REVERT: A 360 ASN cc_start: 0.7936 (t0) cc_final: 0.7305 (t0) REVERT: A 380 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7875 (ttp80) REVERT: A 414 MET cc_start: 0.7150 (tmm) cc_final: 0.6764 (tmm) REVERT: A 462 MET cc_start: 0.7697 (ttm) cc_final: 0.7410 (ttp) REVERT: A 476 LYS cc_start: 0.8593 (tppp) cc_final: 0.8321 (tppt) REVERT: A 590 LYS cc_start: 0.7872 (mppt) cc_final: 0.7608 (mppt) REVERT: A 594 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 603 ASP cc_start: 0.7274 (t70) cc_final: 0.7007 (t0) REVERT: A 674 ASN cc_start: 0.7965 (m110) cc_final: 0.7755 (m-40) REVERT: A 719 ARG cc_start: 0.6756 (mtp180) cc_final: 0.6489 (mtp180) REVERT: A 725 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7707 (mt) REVERT: B 21 MET cc_start: 0.7775 (ptm) cc_final: 0.7394 (ptm) REVERT: B 24 ILE cc_start: 0.8525 (mm) cc_final: 0.8068 (mm) REVERT: B 28 MET cc_start: 0.6893 (mmm) cc_final: 0.6359 (mmm) REVERT: B 86 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8012 (tm-30) REVERT: B 127 MET cc_start: 0.8583 (mmm) cc_final: 0.8375 (mmt) REVERT: B 145 GLU cc_start: 0.7895 (pm20) cc_final: 0.7639 (pm20) REVERT: B 148 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7838 (mtm110) REVERT: B 214 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 215 MET cc_start: 0.8301 (mtt) cc_final: 0.8047 (mtt) REVERT: B 239 GLU cc_start: 0.8349 (tp30) cc_final: 0.7695 (tp30) REVERT: B 292 MET cc_start: 0.7837 (tpp) cc_final: 0.7582 (mpp) REVERT: B 293 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 299 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6891 (mpm) REVERT: B 372 LYS cc_start: 0.8972 (tppt) cc_final: 0.8514 (tppt) REVERT: B 376 LYS cc_start: 0.8048 (tppt) cc_final: 0.7755 (ttpp) REVERT: B 380 ARG cc_start: 0.8531 (tpt-90) cc_final: 0.8032 (ttt-90) REVERT: B 397 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 429 THR cc_start: 0.8395 (t) cc_final: 0.8094 (p) REVERT: B 451 MET cc_start: 0.8157 (ttm) cc_final: 0.7899 (mtp) REVERT: B 507 LEU cc_start: 0.7429 (pt) cc_final: 0.7073 (pp) REVERT: B 511 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6969 (tm-30) REVERT: B 557 TYR cc_start: 0.8213 (t80) cc_final: 0.7790 (t80) REVERT: B 560 ASP cc_start: 0.8068 (m-30) cc_final: 0.7734 (m-30) REVERT: B 603 ASP cc_start: 0.7711 (t0) cc_final: 0.7231 (t0) REVERT: B 611 ASN cc_start: 0.7666 (p0) cc_final: 0.7448 (p0) REVERT: B 654 SER cc_start: 0.6247 (OUTLIER) cc_final: 0.5541 (p) outliers start: 57 outliers final: 40 residues processed: 343 average time/residue: 0.1356 time to fit residues: 63.4578 Evaluate side-chains 354 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 300 ASN 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 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 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 408 LYS 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 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 76 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 38 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.0570 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** 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 = 0.3794 r_free = 0.3794 target = 0.132688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114074 restraints weight = 16521.043| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.31 r_work: 0.3435 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2355 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= 0.117 Angle : 0.558 6.885 15714 Z= 0.297 Chirality : 0.043 0.285 1703 Planarity : 0.004 0.086 2015 Dihedral : 10.859 89.965 1718 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.03 % Favored : 93.61 % Rotamer: Outliers : 5.12 % Allowed : 16.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1377 helix: 1.52 (0.21), residues: 633 sheet: 0.04 (0.54), residues: 105 loop : -2.70 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.010 0.001 TYR B 80 PHE 0.028 0.001 PHE A 382 TRP 0.006 0.001 TRP B 353 HIS 0.003 0.000 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00255 (11625) covalent geometry : angle 0.55791 (15714) hydrogen bonds : bond 0.04108 ( 444) hydrogen bonds : angle 3.91104 ( 1278) metal coordination : bond 0.00107 ( 3) *********************** 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 369 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8292 (mtpp) REVERT: A 21 MET cc_start: 0.6898 (mpt) cc_final: 0.6140 (mtp) REVERT: A 25 ARG cc_start: 0.7917 (mpt-90) cc_final: 0.7442 (mpt-90) REVERT: A 45 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: A 100 MET cc_start: 0.7536 (tmm) cc_final: 0.7147 (tmm) REVERT: A 117 MET cc_start: 0.6674 (mtp) cc_final: 0.6194 (mtp) REVERT: A 241 LYS cc_start: 0.8122 (tppp) cc_final: 0.7851 (ttmt) REVERT: A 244 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 300 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.6971 (t0) REVERT: A 319 THR cc_start: 0.7810 (m) cc_final: 0.7234 (t) REVERT: A 334 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8004 (mp10) REVERT: A 342 ASN cc_start: 0.7769 (t0) cc_final: 0.7355 (t0) REVERT: A 360 ASN cc_start: 0.7824 (t0) cc_final: 0.7197 (t0) REVERT: A 364 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 380 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7833 (ttp-170) REVERT: A 414 MET cc_start: 0.7069 (tmm) cc_final: 0.6687 (tmm) REVERT: A 450 CYS cc_start: 0.8581 (m) cc_final: 0.8308 (m) REVERT: A 462 MET cc_start: 0.7567 (ttm) cc_final: 0.7210 (ttp) REVERT: A 507 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6913 (pp) REVERT: A 590 LYS cc_start: 0.7847 (mppt) cc_final: 0.7613 (mppt) REVERT: A 594 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 603 ASP cc_start: 0.7243 (t70) cc_final: 0.6990 (t0) REVERT: A 617 TYR cc_start: 0.7725 (t80) cc_final: 0.7511 (t80) REVERT: A 662 MET cc_start: 0.7282 (ttp) cc_final: 0.6943 (ptm) REVERT: A 719 ARG cc_start: 0.6707 (mtp180) cc_final: 0.6407 (mtp180) REVERT: A 725 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7651 (mt) REVERT: B 7 LYS cc_start: 0.8338 (mtmp) cc_final: 0.7726 (mtpp) REVERT: B 21 MET cc_start: 0.7690 (ptm) cc_final: 0.7307 (ptm) REVERT: B 24 ILE cc_start: 0.8519 (mm) cc_final: 0.8026 (mm) REVERT: B 28 MET cc_start: 0.6951 (mmm) cc_final: 0.6359 (mmm) REVERT: B 86 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 127 MET cc_start: 0.8584 (mmm) cc_final: 0.8349 (mmt) REVERT: B 132 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7483 (mm-30) REVERT: B 148 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7645 (mtp85) REVERT: B 214 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7807 (mt-10) REVERT: B 238 GLU cc_start: 0.7814 (tp30) cc_final: 0.7516 (tp30) REVERT: B 239 GLU cc_start: 0.8338 (tp30) cc_final: 0.7705 (tp30) REVERT: B 292 MET cc_start: 0.7804 (tpp) cc_final: 0.7578 (mpp) REVERT: B 293 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 299 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6003 (mpm) REVERT: B 376 LYS cc_start: 0.8004 (tppt) cc_final: 0.7725 (ttpp) REVERT: B 397 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 429 THR cc_start: 0.8361 (t) cc_final: 0.8021 (p) REVERT: B 451 MET cc_start: 0.8190 (ttm) cc_final: 0.7939 (mtp) REVERT: B 507 LEU cc_start: 0.7368 (pt) cc_final: 0.7031 (pp) REVERT: B 511 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7030 (tm-30) REVERT: B 560 ASP cc_start: 0.8067 (m-30) cc_final: 0.7713 (m-30) REVERT: B 578 THR cc_start: 0.8227 (m) cc_final: 0.7902 (p) REVERT: B 603 ASP cc_start: 0.7683 (t0) cc_final: 0.7233 (t0) REVERT: B 654 SER cc_start: 0.6175 (OUTLIER) cc_final: 0.5423 (p) REVERT: B 719 ARG cc_start: 0.8248 (mtp180) cc_final: 0.8000 (mtm180) outliers start: 62 outliers final: 39 residues processed: 338 average time/residue: 0.1268 time to fit residues: 58.4660 Evaluate side-chains 342 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 292 MET Chi-restraints excluded: chain A residue 300 ASN 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 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 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 242 ASN Chi-restraints excluded: chain B residue 254 LEU 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 489 MET 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 639 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 316 ASN ** 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 = 0.3788 r_free = 0.3788 target = 0.133329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114835 restraints weight = 16605.815| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.32 r_work: 0.3402 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2501 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= 0.145 Angle : 0.584 6.850 15714 Z= 0.314 Chirality : 0.044 0.303 1703 Planarity : 0.004 0.088 2015 Dihedral : 10.519 85.408 1715 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.90 % Favored : 92.74 % Rotamer: Outliers : 4.88 % Allowed : 17.52 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1377 helix: 1.52 (0.21), residues: 634 sheet: 0.51 (0.55), residues: 95 loop : -2.77 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.011 0.001 TYR B 164 PHE 0.027 0.002 PHE A 526 TRP 0.006 0.001 TRP B 399 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00331 (11625) covalent geometry : angle 0.58405 (15714) hydrogen bonds : bond 0.04922 ( 444) hydrogen bonds : angle 3.92433 ( 1278) metal coordination : bond 0.00178 ( 3) *********************** 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 382 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8324 (mtpp) REVERT: A 21 MET cc_start: 0.6955 (mpt) cc_final: 0.6458 (mtp) REVERT: A 25 ARG cc_start: 0.7952 (mpt-90) cc_final: 0.7468 (mpt-90) REVERT: A 45 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: A 55 MET cc_start: 0.6824 (tpp) cc_final: 0.6522 (tpp) REVERT: A 100 MET cc_start: 0.7563 (tmm) cc_final: 0.7175 (tmm) REVERT: A 117 MET cc_start: 0.6714 (mtp) cc_final: 0.6221 (mtp) REVERT: A 215 MET cc_start: 0.8452 (mtm) cc_final: 0.8017 (mtm) REVERT: A 219 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7582 (mm110) REVERT: A 239 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7002 (tp30) REVERT: A 292 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: A 300 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7252 (p0) REVERT: A 319 THR cc_start: 0.7828 (m) cc_final: 0.7250 (t) REVERT: A 342 ASN cc_start: 0.7805 (t0) cc_final: 0.7379 (t0) REVERT: A 360 ASN cc_start: 0.7868 (t0) cc_final: 0.7265 (t0) REVERT: A 364 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 380 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7814 (ttp-170) REVERT: A 414 MET cc_start: 0.7026 (tmm) cc_final: 0.6752 (tmm) REVERT: A 450 CYS cc_start: 0.8649 (m) cc_final: 0.8351 (m) REVERT: A 462 MET cc_start: 0.7684 (ttm) cc_final: 0.7333 (ttp) REVERT: A 496 LEU cc_start: 0.7512 (tt) cc_final: 0.7240 (mp) REVERT: A 497 MET cc_start: 0.8178 (tpp) cc_final: 0.7928 (mpp) REVERT: A 498 LYS cc_start: 0.7863 (tppt) cc_final: 0.7661 (tppt) REVERT: A 507 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7044 (pp) REVERT: A 510 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7732 (pp20) REVERT: A 594 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 603 ASP cc_start: 0.7280 (t70) cc_final: 0.7007 (t0) REVERT: A 645 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7954 (pp) REVERT: A 662 MET cc_start: 0.7375 (ttp) cc_final: 0.7034 (ptm) REVERT: A 719 ARG cc_start: 0.6785 (mtp180) cc_final: 0.6465 (mtp180) REVERT: A 725 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7654 (mt) REVERT: B 21 MET cc_start: 0.7764 (ptm) cc_final: 0.7386 (ptm) REVERT: B 24 ILE cc_start: 0.8544 (mm) cc_final: 0.8035 (mm) REVERT: B 28 MET cc_start: 0.7190 (mmm) cc_final: 0.6582 (mmm) REVERT: B 67 GLU cc_start: 0.7851 (tp30) cc_final: 0.7627 (tm-30) REVERT: B 86 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7976 (tm-30) REVERT: B 132 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7500 (mm-30) REVERT: B 148 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7850 (mtm110) REVERT: B 214 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 219 GLN cc_start: 0.8495 (mp10) cc_final: 0.7968 (mm-40) REVERT: B 239 GLU cc_start: 0.8362 (tp30) cc_final: 0.7680 (tp30) REVERT: B 292 MET cc_start: 0.7796 (tpp) cc_final: 0.7592 (mpp) REVERT: B 376 LYS cc_start: 0.8047 (tppt) cc_final: 0.7802 (ttpp) REVERT: B 397 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 429 THR cc_start: 0.8393 (t) cc_final: 0.8086 (p) REVERT: B 453 ILE cc_start: 0.6092 (mt) cc_final: 0.5699 (mt) REVERT: B 507 LEU cc_start: 0.7437 (pt) cc_final: 0.7064 (pp) REVERT: B 511 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7095 (tm-30) REVERT: B 537 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6111 (mt) REVERT: B 560 ASP cc_start: 0.8099 (m-30) cc_final: 0.7758 (m-30) REVERT: B 578 THR cc_start: 0.8245 (m) cc_final: 0.7893 (p) REVERT: B 590 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7270 (mttt) REVERT: B 603 ASP cc_start: 0.7731 (t0) cc_final: 0.7281 (t0) outliers start: 59 outliers final: 40 residues processed: 350 average time/residue: 0.1324 time to fit residues: 62.8502 Evaluate side-chains 359 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 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 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU 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 489 MET Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 136 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 612 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111447 restraints weight = 16671.443| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.30 r_work: 0.3392 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11628 Z= 0.164 Angle : 0.604 8.497 15714 Z= 0.324 Chirality : 0.044 0.291 1703 Planarity : 0.005 0.090 2015 Dihedral : 10.451 82.929 1714 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.12 % Favored : 92.52 % Rotamer: Outliers : 5.04 % Allowed : 18.68 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.23), residues: 1377 helix: 1.53 (0.21), residues: 634 sheet: 0.51 (0.51), residues: 106 loop : -2.78 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 380 TYR 0.015 0.001 TYR A 262 PHE 0.017 0.002 PHE B 463 TRP 0.007 0.001 TRP B 399 HIS 0.010 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00380 (11625) covalent geometry : angle 0.60393 (15714) hydrogen bonds : bond 0.05420 ( 444) hydrogen bonds : angle 3.96335 ( 1278) metal coordination : bond 0.00209 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8404 (mtpt) REVERT: A 11 ARG cc_start: 0.7408 (mtt-85) cc_final: 0.6998 (mtt-85) REVERT: A 21 MET cc_start: 0.7016 (mpt) cc_final: 0.6463 (mtp) REVERT: A 25 ARG cc_start: 0.7964 (mpt-90) cc_final: 0.7494 (mpt-90) REVERT: A 45 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: A 55 MET cc_start: 0.6889 (tpp) cc_final: 0.6590 (tpp) REVERT: A 100 MET cc_start: 0.7628 (tmm) cc_final: 0.7251 (tmm) REVERT: A 117 MET cc_start: 0.6776 (mtp) cc_final: 0.6234 (mtp) REVERT: A 215 MET cc_start: 0.8463 (mtm) cc_final: 0.8074 (mtm) REVERT: A 219 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7488 (mm110) REVERT: A 239 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7086 (tp30) REVERT: A 244 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 292 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: A 319 THR cc_start: 0.7799 (m) cc_final: 0.7181 (t) REVERT: A 342 ASN cc_start: 0.7833 (t0) cc_final: 0.7404 (t0) REVERT: A 360 ASN cc_start: 0.7766 (t0) cc_final: 0.7220 (t0) REVERT: A 364 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 380 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7878 (ttp-170) REVERT: A 462 MET cc_start: 0.7754 (ttm) cc_final: 0.7465 (ttp) REVERT: A 507 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7002 (pp) REVERT: A 510 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: A 529 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 590 LYS cc_start: 0.7966 (mppt) cc_final: 0.7757 (mppt) REVERT: A 594 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 603 ASP cc_start: 0.7286 (t70) cc_final: 0.7017 (t0) REVERT: A 606 TYR cc_start: 0.8519 (p90) cc_final: 0.8158 (p90) REVERT: A 645 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7953 (pp) REVERT: A 719 ARG cc_start: 0.6840 (mtp180) cc_final: 0.6513 (mtp180) REVERT: A 725 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 21 MET cc_start: 0.7785 (ptm) cc_final: 0.7400 (ptm) REVERT: B 24 ILE cc_start: 0.8591 (mm) cc_final: 0.8050 (mm) REVERT: B 28 MET cc_start: 0.7271 (mmm) cc_final: 0.6628 (mmm) REVERT: B 86 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 132 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7477 (mm-30) REVERT: B 148 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7908 (mtm110) REVERT: B 162 ASP cc_start: 0.7572 (p0) cc_final: 0.7359 (p0) REVERT: B 214 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 239 GLU cc_start: 0.8388 (tp30) cc_final: 0.7662 (tp30) REVERT: B 292 MET cc_start: 0.7806 (tpp) cc_final: 0.7559 (mpp) REVERT: B 293 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 376 LYS cc_start: 0.8036 (tppt) cc_final: 0.7800 (ttpp) REVERT: B 397 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 429 THR cc_start: 0.8415 (t) cc_final: 0.8077 (t) REVERT: B 453 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5726 (mt) REVERT: B 507 LEU cc_start: 0.7441 (pt) cc_final: 0.7083 (pp) REVERT: B 511 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7134 (tm-30) REVERT: B 537 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6356 (mt) REVERT: B 557 TYR cc_start: 0.8201 (t80) cc_final: 0.7787 (t80) REVERT: B 560 ASP cc_start: 0.8088 (m-30) cc_final: 0.7773 (m-30) REVERT: B 578 THR cc_start: 0.8172 (m) cc_final: 0.7847 (p) REVERT: B 603 ASP cc_start: 0.7738 (t0) cc_final: 0.7310 (t0) outliers start: 61 outliers final: 44 residues processed: 345 average time/residue: 0.1375 time to fit residues: 64.7678 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 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 451 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 489 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 612 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112550 restraints weight = 16553.163| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.32 r_work: 0.3407 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2722 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= 0.136 Angle : 0.594 8.300 15714 Z= 0.317 Chirality : 0.043 0.294 1703 Planarity : 0.004 0.091 2015 Dihedral : 10.228 79.936 1710 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.75 % Favored : 92.88 % Rotamer: Outliers : 5.04 % Allowed : 19.42 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.23), residues: 1377 helix: 1.62 (0.21), residues: 634 sheet: 0.41 (0.51), residues: 108 loop : -2.77 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 561 TYR 0.012 0.001 TYR A 262 PHE 0.018 0.001 PHE B 463 TRP 0.007 0.001 TRP B 399 HIS 0.009 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00309 (11625) covalent geometry : angle 0.59441 (15714) hydrogen bonds : bond 0.04678 ( 444) hydrogen bonds : angle 3.83136 ( 1278) metal coordination : bond 0.00147 ( 3) *********************** 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 372 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8385 (mtpt) REVERT: A 11 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.7058 (mtt-85) REVERT: A 21 MET cc_start: 0.7027 (mpt) cc_final: 0.6391 (mtp) REVERT: A 25 ARG cc_start: 0.7951 (mpt-90) cc_final: 0.7473 (mpt-90) REVERT: A 45 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: A 55 MET cc_start: 0.6746 (tpp) cc_final: 0.6466 (tpp) REVERT: A 100 MET cc_start: 0.7628 (tmm) cc_final: 0.7244 (tmm) REVERT: A 117 MET cc_start: 0.6804 (mtp) cc_final: 0.6277 (mtp) REVERT: A 219 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7682 (mm110) REVERT: A 239 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7002 (tp30) REVERT: A 244 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 319 THR cc_start: 0.7761 (m) cc_final: 0.7158 (t) REVERT: A 342 ASN cc_start: 0.7809 (t0) cc_final: 0.7378 (t0) REVERT: A 360 ASN cc_start: 0.7814 (t0) cc_final: 0.7209 (t0) REVERT: A 364 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 380 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7921 (ttp-170) REVERT: A 406 ARG cc_start: 0.7692 (tpp80) cc_final: 0.7360 (tpp80) REVERT: A 462 MET cc_start: 0.7682 (ttm) cc_final: 0.7409 (ttp) REVERT: A 507 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6973 (pp) REVERT: A 510 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7718 (pp20) REVERT: A 529 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 590 LYS cc_start: 0.7962 (mppt) cc_final: 0.7748 (mppt) REVERT: A 594 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 603 ASP cc_start: 0.7304 (t70) cc_final: 0.7023 (t0) REVERT: A 606 TYR cc_start: 0.8480 (p90) cc_final: 0.8118 (p90) REVERT: A 645 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7956 (pp) REVERT: A 662 MET cc_start: 0.7393 (ttp) cc_final: 0.7047 (ptm) REVERT: A 719 ARG cc_start: 0.6883 (mtp180) cc_final: 0.6545 (mtp180) REVERT: A 725 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7646 (mt) REVERT: B 15 PHE cc_start: 0.7110 (t80) cc_final: 0.6178 (t80) REVERT: B 21 MET cc_start: 0.7772 (ptm) cc_final: 0.7386 (ptm) REVERT: B 24 ILE cc_start: 0.8549 (mm) cc_final: 0.7960 (mm) REVERT: B 28 MET cc_start: 0.7314 (mmm) cc_final: 0.6635 (mmm) REVERT: B 86 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 132 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7489 (mm-30) REVERT: B 148 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7871 (mtm110) REVERT: B 219 GLN cc_start: 0.8486 (mp10) cc_final: 0.8235 (mm-40) REVERT: B 292 MET cc_start: 0.7787 (tpp) cc_final: 0.7553 (mpp) REVERT: B 293 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 376 LYS cc_start: 0.8028 (tppt) cc_final: 0.7770 (ttpp) REVERT: B 397 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 429 THR cc_start: 0.8385 (t) cc_final: 0.8033 (p) REVERT: B 451 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: B 507 LEU cc_start: 0.7446 (pt) cc_final: 0.7093 (pp) REVERT: B 537 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6346 (mt) REVERT: B 557 TYR cc_start: 0.8165 (t80) cc_final: 0.7751 (t80) REVERT: B 560 ASP cc_start: 0.8077 (m-30) cc_final: 0.7743 (m-30) REVERT: B 578 THR cc_start: 0.8172 (m) cc_final: 0.7840 (p) REVERT: B 603 ASP cc_start: 0.7760 (t0) cc_final: 0.7359 (t0) REVERT: B 654 SER cc_start: 0.6057 (OUTLIER) cc_final: 0.5639 (p) outliers start: 61 outliers final: 42 residues processed: 338 average time/residue: 0.1297 time to fit residues: 59.9442 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 529 LEU 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 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 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 26 LYS Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU 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 451 MET 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 654 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 122 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 174 HIS B 612 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114648 restraints weight = 16577.736| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.33 r_work: 0.3401 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11628 Z= 0.148 Angle : 0.616 8.041 15714 Z= 0.328 Chirality : 0.044 0.285 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.167 78.462 1710 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.04 % Favored : 92.59 % Rotamer: Outliers : 5.12 % Allowed : 20.17 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.23), residues: 1377 helix: 1.64 (0.21), residues: 633 sheet: 0.42 (0.51), residues: 108 loop : -2.77 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.012 0.001 TYR B 164 PHE 0.020 0.002 PHE B 15 TRP 0.007 0.001 TRP B 399 HIS 0.009 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00341 (11625) covalent geometry : angle 0.61582 (15714) hydrogen bonds : bond 0.04956 ( 444) hydrogen bonds : angle 3.83190 ( 1278) metal coordination : bond 0.00166 ( 3) *********************** 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 369 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8275 (mmmm) REVERT: A 11 ARG cc_start: 0.7477 (mtt-85) cc_final: 0.7099 (mtt-85) REVERT: A 21 MET cc_start: 0.7097 (mpt) cc_final: 0.6538 (mtp) REVERT: A 25 ARG cc_start: 0.7957 (mpt-90) cc_final: 0.7505 (mpt-90) REVERT: A 45 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: A 55 MET cc_start: 0.6823 (tpp) cc_final: 0.6522 (tpp) REVERT: A 100 MET cc_start: 0.7611 (tmm) cc_final: 0.7227 (tmm) REVERT: A 117 MET cc_start: 0.6769 (mtp) cc_final: 0.6250 (mtp) REVERT: A 215 MET cc_start: 0.8492 (mpp) cc_final: 0.7495 (mtm) REVERT: A 219 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7350 (mm110) REVERT: A 244 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 319 THR cc_start: 0.7751 (m) cc_final: 0.7141 (t) REVERT: A 342 ASN cc_start: 0.7807 (t0) cc_final: 0.7381 (t0) REVERT: A 360 ASN cc_start: 0.7748 (t0) cc_final: 0.7192 (t0) REVERT: A 364 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 380 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7936 (ttp-170) REVERT: A 406 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7418 (tpp80) REVERT: A 462 MET cc_start: 0.7731 (ttm) cc_final: 0.7454 (ttp) REVERT: A 492 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: A 498 LYS cc_start: 0.7588 (tppt) cc_final: 0.7360 (tppt) REVERT: A 507 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7046 (pp) REVERT: A 510 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7726 (pp20) REVERT: A 529 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 590 LYS cc_start: 0.7990 (mppt) cc_final: 0.7758 (mppt) REVERT: A 594 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 603 ASP cc_start: 0.7319 (t70) cc_final: 0.7037 (t0) REVERT: A 606 TYR cc_start: 0.8478 (p90) cc_final: 0.8113 (p90) REVERT: A 645 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7960 (pp) REVERT: A 719 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6497 (mtp180) REVERT: A 725 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7630 (mt) REVERT: B 21 MET cc_start: 0.7793 (ptm) cc_final: 0.7405 (ptm) REVERT: B 24 ILE cc_start: 0.8546 (mm) cc_final: 0.7960 (mm) REVERT: B 28 MET cc_start: 0.7309 (mmm) cc_final: 0.6648 (mmm) REVERT: B 86 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 132 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7488 (mm-30) REVERT: B 148 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7857 (mtm110) REVERT: B 214 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 239 GLU cc_start: 0.8355 (tp30) cc_final: 0.7664 (tp30) REVERT: B 292 MET cc_start: 0.7756 (tpp) cc_final: 0.7528 (mpp) REVERT: B 293 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 345 THR cc_start: 0.8367 (t) cc_final: 0.8164 (p) REVERT: B 376 LYS cc_start: 0.8040 (tppt) cc_final: 0.7786 (ttpp) REVERT: B 397 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 429 THR cc_start: 0.8403 (t) cc_final: 0.8049 (p) REVERT: B 451 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7948 (mtp) REVERT: B 507 LEU cc_start: 0.7433 (pt) cc_final: 0.7085 (pp) REVERT: B 537 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6424 (mt) REVERT: B 557 TYR cc_start: 0.8163 (t80) cc_final: 0.7758 (t80) REVERT: B 560 ASP cc_start: 0.8078 (m-30) cc_final: 0.7743 (m-30) REVERT: B 578 THR cc_start: 0.8191 (m) cc_final: 0.7866 (p) REVERT: B 603 ASP cc_start: 0.7737 (t0) cc_final: 0.7312 (t0) outliers start: 62 outliers final: 42 residues processed: 337 average time/residue: 0.1279 time to fit residues: 58.8593 Evaluate side-chains 354 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 316 ASN 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 529 LEU 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 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 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 26 LYS 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 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 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 451 MET 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 53 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 124 optimal weight: 0.0170 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 0.0770 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118509 restraints weight = 16342.049| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.31 r_work: 0.3454 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11628 Z= 0.117 Angle : 0.595 9.211 15714 Z= 0.314 Chirality : 0.043 0.278 1703 Planarity : 0.004 0.091 2015 Dihedral : 9.577 83.430 1710 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.37 % Favored : 94.26 % Rotamer: Outliers : 3.97 % Allowed : 21.16 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.23), residues: 1377 helix: 1.81 (0.22), residues: 632 sheet: 0.56 (0.51), residues: 109 loop : -2.67 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 559 TYR 0.010 0.001 TYR B 407 PHE 0.018 0.001 PHE B 463 TRP 0.006 0.001 TRP B 399 HIS 0.004 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00257 (11625) covalent geometry : angle 0.59494 (15714) hydrogen bonds : bond 0.03345 ( 444) hydrogen bonds : angle 3.62378 ( 1278) metal coordination : bond 0.00031 ( 3) *********************** 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 359 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8185 (mmmt) REVERT: A 11 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.7021 (mtt-85) REVERT: A 21 MET cc_start: 0.7071 (mpt) cc_final: 0.6512 (mtp) REVERT: A 25 ARG cc_start: 0.7886 (mpt-90) cc_final: 0.7450 (mpt-90) REVERT: A 45 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: A 55 MET cc_start: 0.6587 (tpp) cc_final: 0.6318 (tpp) REVERT: A 100 MET cc_start: 0.7584 (tmm) cc_final: 0.7210 (tmm) REVERT: A 117 MET cc_start: 0.6767 (mtp) cc_final: 0.6275 (mtp) REVERT: A 215 MET cc_start: 0.8483 (mpp) cc_final: 0.7534 (mtm) REVERT: A 219 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7382 (mm110) REVERT: A 319 THR cc_start: 0.7702 (m) cc_final: 0.7133 (t) REVERT: A 342 ASN cc_start: 0.7752 (t0) cc_final: 0.7325 (t0) REVERT: A 360 ASN cc_start: 0.7765 (t0) cc_final: 0.7147 (t0) REVERT: A 364 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 406 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7439 (tpp80) REVERT: A 450 CYS cc_start: 0.8514 (m) cc_final: 0.7775 (m) REVERT: A 462 MET cc_start: 0.7438 (ttm) cc_final: 0.7041 (ttp) REVERT: A 492 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: A 505 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: A 506 ASN cc_start: 0.8087 (t0) cc_final: 0.7826 (t0) REVERT: A 507 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7027 (pp) REVERT: A 510 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: A 590 LYS cc_start: 0.7963 (mppt) cc_final: 0.7760 (mppt) REVERT: A 594 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 603 ASP cc_start: 0.7312 (t70) cc_final: 0.7048 (t0) REVERT: A 606 TYR cc_start: 0.8353 (p90) cc_final: 0.7965 (p90) REVERT: A 617 TYR cc_start: 0.7728 (t80) cc_final: 0.7516 (t80) REVERT: A 645 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7947 (pp) REVERT: A 719 ARG cc_start: 0.6863 (mtp180) cc_final: 0.6532 (mtp180) REVERT: A 725 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7647 (mt) REVERT: B 21 MET cc_start: 0.7745 (ptm) cc_final: 0.7365 (ptm) REVERT: B 24 ILE cc_start: 0.8506 (mm) cc_final: 0.7910 (mm) REVERT: B 28 MET cc_start: 0.7228 (mmm) cc_final: 0.6574 (mmm) REVERT: B 86 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 132 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7471 (mm-30) REVERT: B 148 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7685 (mtp85) REVERT: B 214 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7495 (mt-10) REVERT: B 238 GLU cc_start: 0.7887 (tp30) cc_final: 0.7587 (tp30) REVERT: B 239 GLU cc_start: 0.8282 (tp30) cc_final: 0.7785 (tp30) REVERT: B 292 MET cc_start: 0.7742 (tpp) cc_final: 0.7539 (mpp) REVERT: B 293 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 376 LYS cc_start: 0.7962 (tppt) cc_final: 0.7721 (ttpp) REVERT: B 397 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 429 THR cc_start: 0.8364 (t) cc_final: 0.7966 (p) REVERT: B 451 MET cc_start: 0.8284 (ttm) cc_final: 0.7968 (mtp) REVERT: B 507 LEU cc_start: 0.7400 (pt) cc_final: 0.7067 (pp) REVERT: B 537 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6400 (mt) REVERT: B 560 ASP cc_start: 0.8048 (m-30) cc_final: 0.7736 (m-30) REVERT: B 578 THR cc_start: 0.8121 (m) cc_final: 0.7812 (p) REVERT: B 603 ASP cc_start: 0.7745 (t0) cc_final: 0.7334 (t0) REVERT: B 606 TYR cc_start: 0.8634 (p90) cc_final: 0.8156 (p90) outliers start: 48 outliers final: 36 residues processed: 334 average time/residue: 0.1222 time to fit residues: 55.8399 Evaluate side-chains 351 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 316 ASN 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 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 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 26 LYS 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 242 ASN 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 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 489 MET 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 593 LYS Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 612 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116459 restraints weight = 16557.337| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.33 r_work: 0.3422 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2993 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= 0.135 Angle : 0.623 8.999 15714 Z= 0.329 Chirality : 0.044 0.273 1703 Planarity : 0.004 0.092 2015 Dihedral : 9.263 78.357 1704 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.61 % Favored : 93.03 % Rotamer: Outliers : 3.72 % Allowed : 21.82 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.23), residues: 1377 helix: 1.79 (0.21), residues: 633 sheet: 0.70 (0.52), residues: 102 loop : -2.68 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 719 TYR 0.010 0.001 TYR B 236 PHE 0.026 0.002 PHE A 641 TRP 0.007 0.001 TRP B 399 HIS 0.005 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00309 (11625) covalent geometry : angle 0.62276 (15714) hydrogen bonds : bond 0.04268 ( 444) hydrogen bonds : angle 3.69880 ( 1278) metal coordination : bond 0.00119 ( 3) ********************** 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 351 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8331 (mmmt) REVERT: A 11 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7118 (mtt-85) REVERT: A 21 MET cc_start: 0.7109 (mpt) cc_final: 0.6547 (mtp) REVERT: A 25 ARG cc_start: 0.7895 (mpt-90) cc_final: 0.7455 (mpt-90) REVERT: A 45 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: A 55 MET cc_start: 0.6699 (tpp) cc_final: 0.6415 (tpp) REVERT: A 100 MET cc_start: 0.7594 (tmm) cc_final: 0.7226 (tmm) REVERT: A 117 MET cc_start: 0.6748 (mtp) cc_final: 0.6213 (mtp) REVERT: A 215 MET cc_start: 0.8465 (mpp) cc_final: 0.7517 (mtm) REVERT: A 219 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7390 (mm110) REVERT: A 319 THR cc_start: 0.7707 (m) cc_final: 0.7126 (t) REVERT: A 342 ASN cc_start: 0.7761 (t0) cc_final: 0.7334 (t0) REVERT: A 360 ASN cc_start: 0.7735 (t0) cc_final: 0.7116 (t0) REVERT: A 364 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 406 ARG cc_start: 0.7714 (tpp80) cc_final: 0.7452 (tpp80) REVERT: A 462 MET cc_start: 0.7483 (ttm) cc_final: 0.7155 (ttp) REVERT: A 492 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8197 (mm-40) REVERT: A 507 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7107 (pp) REVERT: A 510 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: A 590 LYS cc_start: 0.7963 (mppt) cc_final: 0.7763 (mppt) REVERT: A 594 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 606 TYR cc_start: 0.8393 (p90) cc_final: 0.8010 (p90) REVERT: A 645 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7974 (pp) REVERT: A 719 ARG cc_start: 0.6850 (mtp180) cc_final: 0.6499 (mtp180) REVERT: A 725 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7632 (mt) REVERT: B 21 MET cc_start: 0.7787 (ptm) cc_final: 0.7400 (ptm) REVERT: B 24 ILE cc_start: 0.8482 (mm) cc_final: 0.7895 (mm) REVERT: B 28 MET cc_start: 0.7243 (mmm) cc_final: 0.6589 (mmm) REVERT: B 86 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 132 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7462 (mm-30) REVERT: B 148 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7717 (mtp85) REVERT: B 214 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 238 GLU cc_start: 0.7940 (tp30) cc_final: 0.7635 (tp30) REVERT: B 239 GLU cc_start: 0.8314 (tp30) cc_final: 0.7774 (tp30) REVERT: B 376 LYS cc_start: 0.7966 (tppt) cc_final: 0.7723 (ttpp) REVERT: B 397 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 429 THR cc_start: 0.8412 (t) cc_final: 0.8043 (p) REVERT: B 451 MET cc_start: 0.8332 (ttm) cc_final: 0.7981 (mtp) REVERT: B 537 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6427 (mt) REVERT: B 560 ASP cc_start: 0.8072 (m-30) cc_final: 0.7745 (m-30) REVERT: B 578 THR cc_start: 0.8107 (m) cc_final: 0.7798 (p) REVERT: B 603 ASP cc_start: 0.7778 (t0) cc_final: 0.7349 (t0) outliers start: 45 outliers final: 35 residues processed: 329 average time/residue: 0.1211 time to fit residues: 54.1578 Evaluate side-chains 342 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 316 ASN 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 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 626 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 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 178 VAL Chi-restraints excluded: chain B residue 242 ASN 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 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 489 MET 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 593 LYS Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9819 > 50: distance: 35 - 39: 34.222 distance: 39 - 40: 15.947 distance: 40 - 41: 59.247 distance: 40 - 43: 14.727 distance: 41 - 47: 39.823 distance: 43 - 44: 38.504 distance: 43 - 45: 56.630 distance: 47 - 48: 10.532 distance: 48 - 49: 39.635 distance: 49 - 50: 69.236 distance: 49 - 51: 40.050 distance: 51 - 52: 56.660 distance: 52 - 53: 55.289 distance: 52 - 55: 56.724 distance: 53 - 54: 56.009 distance: 53 - 60: 40.400 distance: 55 - 56: 56.299 distance: 56 - 57: 53.826 distance: 57 - 58: 47.209 distance: 58 - 59: 10.148 distance: 60 - 61: 38.571 distance: 61 - 64: 40.108 distance: 62 - 63: 56.470 distance: 65 - 66: 50.337 distance: 65 - 67: 57.152 distance: 66 - 68: 19.763 distance: 68 - 69: 45.606 distance: 71 - 72: 40.856 distance: 71 - 74: 57.131 distance: 72 - 80: 40.416 distance: 74 - 75: 57.280 distance: 75 - 76: 56.572 distance: 75 - 77: 57.228 distance: 76 - 78: 40.446 distance: 77 - 79: 69.301 distance: 81 - 82: 56.905 distance: 82 - 83: 39.503 distance: 82 - 84: 40.123 distance: 84 - 85: 69.373 distance: 85 - 86: 56.263 distance: 85 - 88: 38.538 distance: 86 - 87: 49.960 distance: 86 - 93: 69.203 distance: 88 - 89: 56.562 distance: 89 - 90: 55.392 distance: 90 - 91: 70.106 distance: 90 - 92: 39.740 distance: 93 - 94: 69.372 distance: 94 - 95: 55.270 distance: 94 - 97: 38.684 distance: 95 - 96: 40.506 distance: 95 - 99: 57.030 distance: 97 - 98: 55.768 distance: 99 - 100: 39.703 distance: 100 - 101: 56.312 distance: 100 - 103: 68.788 distance: 101 - 102: 55.923 distance: 101 - 108: 57.099 distance: 103 - 104: 57.974 distance: 104 - 105: 55.956 distance: 105 - 106: 40.136 distance: 105 - 107: 40.818 distance: 108 - 109: 57.479 distance: 109 - 110: 56.406 distance: 109 - 112: 40.441 distance: 110 - 111: 49.903 distance: 110 - 117: 33.339 distance: 111 - 136: 24.326 distance: 112 - 113: 39.910 distance: 113 - 114: 40.624 distance: 114 - 115: 39.732 distance: 115 - 116: 56.463