Starting phenix.real_space_refine on Sat Nov 16 16:41:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/11_2024/8p23_17357.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/11_2024/8p23_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/11_2024/8p23_17357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/11_2024/8p23_17357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/11_2024/8p23_17357.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p23_17357/11_2024/8p23_17357.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 S 71 5.16 5 C 7126 2.51 5 N 2000 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11399 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5510 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 665} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5735 Classifications: {'peptide': 715} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 693} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' ZN': 1, 'ATP': 2, 'CTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10830 SG CYS B 683 16.674 87.785 61.025 1.00102.46 S ATOM 10921 SG CYS B 695 14.070 86.300 63.500 1.00104.69 S ATOM 10943 SG CYS B 698 14.686 84.344 61.636 1.00105.10 S Time building chain proxies: 7.05, per 1000 atoms: 0.62 Number of scatterers: 11399 At special positions: 0 Unit cell: (82.422, 137.948, 118.861, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 71 16.00 P 15 15.00 O 2186 8.00 N 2000 7.00 C 7126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 698 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 695 " 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 50.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 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: 3.72 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1921 1.31 - 1.43: 3075 1.43 - 1.56: 6483 1.56 - 1.68: 25 1.68 - 1.81: 121 Bond restraints: 11625 Sorted by residual: bond pdb=" C TYR B 371 " pdb=" O TYR B 371 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.15e-02 7.56e+03 2.19e+01 bond pdb=" C VAL B 659 " pdb=" O VAL B 659 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.19e-02 7.06e+03 1.97e+01 bond pdb=" C ALA B 374 " pdb=" O ALA B 374 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.26e-02 6.30e+03 1.57e+01 bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.531 1.477 0.053 1.37e-02 5.33e+03 1.52e+01 bond pdb=" N ILE B 735 " pdb=" CA ILE B 735 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.30e-02 5.92e+03 1.34e+01 ... (remaining 11620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 15518 2.82 - 5.64: 165 5.64 - 8.46: 25 8.46 - 11.28: 5 11.28 - 14.10: 1 Bond angle restraints: 15714 Sorted by residual: angle pdb=" N GLN B 212 " pdb=" CA GLN B 212 " pdb=" C GLN B 212 " ideal model delta sigma weight residual 112.57 98.47 14.10 1.13e+00 7.83e-01 1.56e+02 angle pdb=" N HIS B 734 " pdb=" CA HIS B 734 " pdb=" C HIS B 734 " ideal model delta sigma weight residual 110.24 100.41 9.83 1.47e+00 4.63e-01 4.47e+01 angle pdb=" C ARG B 305 " pdb=" CA ARG B 305 " pdb=" CB ARG B 305 " ideal model delta sigma weight residual 109.80 99.24 10.56 1.61e+00 3.86e-01 4.30e+01 angle pdb=" N ASN B 213 " pdb=" CA ASN B 213 " pdb=" C ASN B 213 " ideal model delta sigma weight residual 112.54 103.50 9.04 1.51e+00 4.39e-01 3.59e+01 angle pdb=" N THR B 650 " pdb=" CA THR B 650 " pdb=" C THR B 650 " ideal model delta sigma weight residual 113.38 106.21 7.17 1.23e+00 6.61e-01 3.40e+01 ... (remaining 15709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6559 17.25 - 34.50: 354 34.50 - 51.75: 112 51.75 - 69.00: 40 69.00 - 86.25: 13 Dihedral angle restraints: 7078 sinusoidal: 2991 harmonic: 4087 Sorted by residual: dihedral pdb=" C CYS B 327 " pdb=" N CYS B 327 " pdb=" CA CYS B 327 " pdb=" CB CYS B 327 " ideal model delta harmonic sigma weight residual -122.60 -108.55 -14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C ARG B 305 " pdb=" N ARG B 305 " pdb=" CA ARG B 305 " pdb=" CB ARG B 305 " ideal model delta harmonic sigma weight residual -122.60 -109.48 -13.12 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CA VAL B 714 " pdb=" C VAL B 714 " pdb=" N GLY B 715 " pdb=" CA GLY B 715 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1582 0.091 - 0.182: 98 0.182 - 0.273: 11 0.273 - 0.363: 11 0.363 - 0.454: 1 Chirality restraints: 1703 Sorted by residual: chirality pdb=" CA LYS B 33 " pdb=" N LYS B 33 " pdb=" C LYS B 33 " pdb=" CB LYS B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA CYS B 327 " pdb=" N CYS B 327 " pdb=" C CYS B 327 " pdb=" CB CYS B 327 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA HIS B 734 " pdb=" N HIS B 734 " pdb=" C HIS B 734 " pdb=" CB HIS B 734 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1700 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 302 " -0.031 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C ILE B 302 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 302 " -0.040 2.00e-02 2.50e+03 pdb=" N HIS B 303 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 326 " -0.394 9.50e-02 1.11e+02 1.77e-01 1.91e+01 pdb=" NE ARG B 326 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 326 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 326 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 403 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO B 404 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " -0.041 5.00e-02 4.00e+02 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 254 2.65 - 3.21: 11071 3.21 - 3.78: 16233 3.78 - 4.34: 22097 4.34 - 4.90: 36886 Nonbonded interactions: 86541 Sorted by model distance: nonbonded pdb=" N CYS B 698 " pdb="ZN ZN B 804 " model vdw 2.090 2.310 nonbonded pdb=" O ALA A 391 " pdb=" OG1 THR A 392 " model vdw 2.139 3.040 nonbonded pdb=" O PHE B 526 " pdb=" OG SER B 610 " model vdw 2.155 3.040 nonbonded pdb=" O ASP B 403 " pdb=" N GLU B 405 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP B 633 " pdb=" NH2 ARG B 636 " model vdw 2.207 3.120 ... (remaining 86536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 33 or resid 36 through 49 or resid 55 through 71 \ or resid 75 through 735 or resid 801)) selection = (chain 'B' and (resid 2 through 184 or resid 193 through 303 or resid 310 throug \ h 676 or (resid 705 and (name N or name CA or name C or name O or name CB )) or \ resid 706 through 707 or (resid 708 and (name N or name CA or name C or name O o \ r name CB )) or resid 713 through 735 or resid 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.050 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- 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 11625 Z= 0.247 Angle : 0.692 14.103 15714 Z= 0.426 Chirality : 0.051 0.454 1703 Planarity : 0.006 0.177 2015 Dihedral : 13.197 86.251 4442 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.81 % Favored : 93.68 % Rotamer: Outliers : 4.71 % Allowed : 7.77 % Favored : 87.52 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1377 helix: 1.35 (0.22), residues: 627 sheet: 0.03 (0.52), residues: 113 loop : -2.99 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 720 HIS 0.003 0.001 HIS B 303 PHE 0.010 0.001 PHE A 224 TYR 0.026 0.001 TYR B 371 ARG 0.006 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 1.336 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: 0.2951 time to fit residues: 152.0024 Evaluate side-chains 337 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.0040 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.0010 chunk 108 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 0.0970 overall best weight: 0.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 114 ASN A 182 HIS A 278 GLN A 300 ASN A 395 GLN A 506 ASN A 675 HIS A 676 ASN B 78 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 541 HIS B 572 ASN B 652 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11625 Z= 0.165 Angle : 0.585 7.432 15714 Z= 0.307 Chirality : 0.043 0.266 1703 Planarity : 0.004 0.076 2015 Dihedral : 12.303 86.484 1741 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.74 % Favored : 93.90 % Rotamer: Outliers : 4.21 % Allowed : 13.64 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1377 helix: 1.55 (0.22), residues: 628 sheet: -0.02 (0.53), residues: 106 loop : -2.72 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS A 182 PHE 0.015 0.001 PHE A 383 TYR 0.010 0.001 TYR A 80 ARG 0.004 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8085 (mtpp) REVERT: A 30 HIS cc_start: 0.7758 (m-70) cc_final: 0.7477 (m-70) REVERT: A 100 MET cc_start: 0.6576 (tmm) cc_final: 0.6308 (tmm) REVERT: A 117 MET cc_start: 0.6105 (mtp) cc_final: 0.5792 (mtp) REVERT: A 238 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6793 (mm-30) REVERT: A 239 GLU cc_start: 0.6804 (tp30) cc_final: 0.6376 (mm-30) REVERT: A 241 LYS cc_start: 0.7550 (tppp) cc_final: 0.7264 (ttmt) REVERT: A 244 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 264 GLU cc_start: 0.6848 (pm20) cc_final: 0.6613 (pm20) REVERT: A 313 SER cc_start: 0.7626 (p) cc_final: 0.7353 (m) REVERT: A 316 ASN cc_start: 0.7775 (m-40) cc_final: 0.7445 (m-40) REVERT: A 319 THR cc_start: 0.7009 (m) cc_final: 0.6576 (t) REVERT: A 342 ASN cc_start: 0.7234 (t0) cc_final: 0.6869 (t0) REVERT: A 352 ILE cc_start: 0.8520 (pp) cc_final: 0.8260 (pt) REVERT: A 357 ARG cc_start: 0.7781 (ttt90) cc_final: 0.7458 (ttt180) REVERT: A 360 ASN cc_start: 0.7457 (t0) cc_final: 0.6857 (t0) REVERT: A 380 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7993 (ttp80) REVERT: A 450 CYS cc_start: 0.7756 (m) cc_final: 0.7418 (m) REVERT: A 462 MET cc_start: 0.6309 (ttm) cc_final: 0.5996 (ttp) REVERT: A 590 LYS cc_start: 0.7394 (mppt) cc_final: 0.7118 (mppt) REVERT: A 594 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6937 (tm-30) REVERT: A 603 ASP cc_start: 0.6918 (t70) cc_final: 0.6653 (t0) REVERT: A 642 TYR cc_start: 0.7424 (m-80) cc_final: 0.6782 (t80) REVERT: A 674 ASN cc_start: 0.7413 (m110) cc_final: 0.6954 (m-40) REVERT: A 725 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7762 (mt) REVERT: B 21 MET cc_start: 0.7039 (ptm) cc_final: 0.6669 (ptm) REVERT: B 24 ILE cc_start: 0.8213 (mm) cc_final: 0.7714 (mm) REVERT: B 28 MET cc_start: 0.6039 (mmm) cc_final: 0.5642 (mmm) REVERT: B 86 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 145 GLU cc_start: 0.7456 (pm20) cc_final: 0.7209 (pm20) REVERT: B 214 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 239 GLU cc_start: 0.7932 (tp30) cc_final: 0.7416 (tp30) REVERT: B 299 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.4989 (mpm) REVERT: B 342 ASN cc_start: 0.7563 (t0) cc_final: 0.7341 (t0) REVERT: B 372 LYS cc_start: 0.8680 (tppt) cc_final: 0.8100 (tppt) REVERT: B 397 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7202 (tm-30) REVERT: B 398 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8475 (mtmt) REVERT: B 429 THR cc_start: 0.8141 (t) cc_final: 0.7829 (p) REVERT: B 435 ASN cc_start: 0.7794 (t0) cc_final: 0.7594 (t0) REVERT: B 511 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6506 (tm-30) REVERT: B 560 ASP cc_start: 0.7457 (m-30) cc_final: 0.7114 (m-30) REVERT: B 603 ASP cc_start: 0.7112 (t0) cc_final: 0.6709 (t0) REVERT: B 623 LYS cc_start: 0.7616 (ttpp) cc_final: 0.7408 (ttmm) REVERT: B 654 SER cc_start: 0.5740 (OUTLIER) cc_final: 0.5069 (p) REVERT: B 657 GLU cc_start: 0.7173 (tp30) cc_final: 0.6884 (tp30) REVERT: B 719 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7774 (mtm110) outliers start: 51 outliers final: 29 residues processed: 343 average time/residue: 0.2878 time to fit residues: 132.7293 Evaluate side-chains 334 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 675 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 282 ASN B 541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11625 Z= 0.228 Angle : 0.591 6.866 15714 Z= 0.315 Chirality : 0.044 0.272 1703 Planarity : 0.004 0.084 2015 Dihedral : 11.234 85.553 1714 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.46 % Favored : 93.17 % Rotamer: Outliers : 4.30 % Allowed : 15.21 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1377 helix: 1.42 (0.22), residues: 635 sheet: 0.57 (0.53), residues: 107 loop : -2.78 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 720 HIS 0.014 0.001 HIS B 541 PHE 0.025 0.002 PHE A 526 TYR 0.013 0.001 TYR B 164 ARG 0.004 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8113 (mtpp) REVERT: A 21 MET cc_start: 0.6494 (mtp) cc_final: 0.5900 (mtp) REVERT: A 25 ARG cc_start: 0.7500 (mpt-90) cc_final: 0.7080 (mpt-90) REVERT: A 30 HIS cc_start: 0.7786 (m-70) cc_final: 0.7542 (m-70) REVERT: A 45 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6771 (m-30) REVERT: A 100 MET cc_start: 0.6676 (tmm) cc_final: 0.6420 (tmm) REVERT: A 238 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6827 (mm-30) REVERT: A 241 LYS cc_start: 0.7634 (tppp) cc_final: 0.7373 (ttmt) REVERT: A 244 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6936 (tm-30) REVERT: A 263 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 264 GLU cc_start: 0.6908 (pm20) cc_final: 0.6670 (pm20) REVERT: A 271 GLN cc_start: 0.7592 (pp30) cc_final: 0.7215 (pp30) REVERT: A 292 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7570 (mmm) REVERT: A 319 THR cc_start: 0.7204 (m) cc_final: 0.6668 (t) REVERT: A 334 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7349 (mp10) REVERT: A 342 ASN cc_start: 0.7291 (t0) cc_final: 0.6917 (t0) REVERT: A 352 ILE cc_start: 0.8551 (pp) cc_final: 0.8320 (pt) REVERT: A 360 ASN cc_start: 0.7626 (t0) cc_final: 0.6982 (t0) REVERT: A 364 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6786 (tm-30) REVERT: A 380 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7693 (ttp-170) REVERT: A 414 MET cc_start: 0.6784 (tmm) cc_final: 0.6466 (tmm) REVERT: A 450 CYS cc_start: 0.7812 (m) cc_final: 0.7378 (m) REVERT: A 462 MET cc_start: 0.6688 (ttm) cc_final: 0.6263 (ttp) REVERT: A 476 LYS cc_start: 0.7981 (tppp) cc_final: 0.7631 (tppt) REVERT: A 590 LYS cc_start: 0.7554 (mppt) cc_final: 0.7303 (mppt) REVERT: A 594 GLN cc_start: 0.7391 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 603 ASP cc_start: 0.6966 (t70) cc_final: 0.6709 (t0) REVERT: A 719 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6329 (mtp180) REVERT: A 725 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7756 (mt) REVERT: B 7 LYS cc_start: 0.7537 (mtmp) cc_final: 0.6760 (mtpp) REVERT: B 21 MET cc_start: 0.7173 (ptm) cc_final: 0.6811 (ptm) REVERT: B 24 ILE cc_start: 0.8283 (mm) cc_final: 0.7661 (mm) REVERT: B 28 MET cc_start: 0.6296 (mmm) cc_final: 0.5817 (mmm) REVERT: B 86 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7719 (tm-30) REVERT: B 214 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 239 GLU cc_start: 0.8007 (tp30) cc_final: 0.7380 (tp30) REVERT: B 372 LYS cc_start: 0.8652 (tppt) cc_final: 0.8130 (tppt) REVERT: B 397 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 398 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8537 (mtmt) REVERT: B 429 THR cc_start: 0.8187 (t) cc_final: 0.7849 (p) REVERT: B 435 ASN cc_start: 0.7762 (t0) cc_final: 0.7553 (t0) REVERT: B 437 SER cc_start: 0.7999 (p) cc_final: 0.7649 (m) REVERT: B 511 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6585 (tm-30) REVERT: B 560 ASP cc_start: 0.7457 (m-30) cc_final: 0.7103 (m-30) REVERT: B 603 ASP cc_start: 0.7195 (t0) cc_final: 0.6791 (t0) REVERT: B 611 ASN cc_start: 0.7107 (p0) cc_final: 0.6871 (p0) REVERT: B 654 SER cc_start: 0.5946 (OUTLIER) cc_final: 0.5482 (p) REVERT: B 657 GLU cc_start: 0.7207 (tp30) cc_final: 0.7001 (mm-30) outliers start: 52 outliers final: 31 residues processed: 349 average time/residue: 0.2894 time to fit residues: 135.9389 Evaluate side-chains 343 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 489 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 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 124 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 298 ASN B 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11625 Z= 0.308 Angle : 0.634 6.870 15714 Z= 0.341 Chirality : 0.046 0.292 1703 Planarity : 0.005 0.088 2015 Dihedral : 11.309 89.333 1711 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.28 % Favored : 91.36 % Rotamer: Outliers : 5.04 % Allowed : 17.52 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1377 helix: 1.31 (0.21), residues: 630 sheet: 0.23 (0.56), residues: 96 loop : -2.79 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 720 HIS 0.005 0.001 HIS B 216 PHE 0.020 0.002 PHE B 463 TYR 0.016 0.002 TYR B 164 ARG 0.006 0.001 ARG A 406 *********************** 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 385 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8141 (mtpt) REVERT: A 25 ARG cc_start: 0.7553 (mpt-90) cc_final: 0.7160 (mpt-90) REVERT: A 30 HIS cc_start: 0.7815 (m-70) cc_final: 0.7572 (m-70) REVERT: A 45 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: A 100 MET cc_start: 0.6757 (tmm) cc_final: 0.6489 (tmm) REVERT: A 114 ASN cc_start: 0.7228 (m-40) cc_final: 0.7009 (m-40) REVERT: A 214 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7445 (mp0) REVERT: A 241 LYS cc_start: 0.7590 (tppp) cc_final: 0.7362 (ttmt) REVERT: A 244 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6935 (tm-30) REVERT: A 287 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7735 (mmm160) REVERT: A 316 ASN cc_start: 0.7848 (m-40) cc_final: 0.7578 (m-40) REVERT: A 319 THR cc_start: 0.7221 (m) cc_final: 0.6665 (t) REVERT: A 334 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7372 (mp10) REVERT: A 342 ASN cc_start: 0.7353 (t0) cc_final: 0.6954 (t0) REVERT: A 352 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8274 (pt) REVERT: A 360 ASN cc_start: 0.7520 (t0) cc_final: 0.6862 (t0) REVERT: A 364 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6862 (tm-30) REVERT: A 380 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7531 (ttp-170) REVERT: A 392 THR cc_start: 0.8419 (p) cc_final: 0.8212 (p) REVERT: A 407 TYR cc_start: 0.8074 (p90) cc_final: 0.7858 (p90) REVERT: A 414 MET cc_start: 0.6834 (tmm) cc_final: 0.6537 (tmm) REVERT: A 462 MET cc_start: 0.7039 (ttm) cc_final: 0.6758 (ttp) REVERT: A 476 LYS cc_start: 0.7905 (tppp) cc_final: 0.7608 (tppt) REVERT: A 507 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6723 (pp) REVERT: A 594 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 603 ASP cc_start: 0.6957 (t70) cc_final: 0.6695 (t0) REVERT: A 662 MET cc_start: 0.6978 (ttp) cc_final: 0.6531 (ptp) REVERT: A 719 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6369 (mtp180) REVERT: A 725 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7770 (mt) REVERT: B 15 PHE cc_start: 0.6818 (t80) cc_final: 0.5205 (t80) REVERT: B 21 MET cc_start: 0.7293 (ptm) cc_final: 0.6924 (ptm) REVERT: B 24 ILE cc_start: 0.8336 (mm) cc_final: 0.7644 (mm) REVERT: B 28 MET cc_start: 0.6613 (mmm) cc_final: 0.6055 (mmm) REVERT: B 86 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 154 ASN cc_start: 0.7419 (t0) cc_final: 0.7186 (t0) REVERT: B 219 GLN cc_start: 0.8235 (mp10) cc_final: 0.7680 (mp10) REVERT: B 345 THR cc_start: 0.7970 (t) cc_final: 0.7718 (p) REVERT: B 397 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 398 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8509 (mtmt) REVERT: B 429 THR cc_start: 0.8233 (t) cc_final: 0.7790 (t) REVERT: B 557 TYR cc_start: 0.8040 (t80) cc_final: 0.7628 (t80) REVERT: B 560 ASP cc_start: 0.7449 (m-30) cc_final: 0.7207 (m-30) REVERT: B 578 THR cc_start: 0.8046 (m) cc_final: 0.7671 (p) REVERT: B 603 ASP cc_start: 0.7276 (t0) cc_final: 0.6898 (t0) REVERT: B 611 ASN cc_start: 0.7527 (p0) cc_final: 0.7225 (p0) REVERT: B 654 SER cc_start: 0.5943 (OUTLIER) cc_final: 0.5355 (p) outliers start: 61 outliers final: 41 residues processed: 353 average time/residue: 0.2925 time to fit residues: 138.4057 Evaluate side-chains 362 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 352 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 719 ARG 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 121 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 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 111 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11625 Z= 0.200 Angle : 0.596 7.492 15714 Z= 0.319 Chirality : 0.044 0.315 1703 Planarity : 0.004 0.088 2015 Dihedral : 10.758 87.886 1709 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.90 % Favored : 92.74 % Rotamer: Outliers : 4.38 % Allowed : 18.60 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1377 helix: 1.45 (0.21), residues: 634 sheet: 0.55 (0.52), residues: 106 loop : -2.80 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 675 PHE 0.020 0.002 PHE B 15 TYR 0.011 0.001 TYR A 262 ARG 0.005 0.000 ARG A 433 *********************** 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 376 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 323 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8103 (mtpp) REVERT: A 17 GLU cc_start: 0.7578 (pp20) cc_final: 0.7133 (pp20) REVERT: A 25 ARG cc_start: 0.7544 (mpt-90) cc_final: 0.7153 (mpt-90) REVERT: A 45 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: A 100 MET cc_start: 0.6748 (tmm) cc_final: 0.6501 (tmm) REVERT: A 215 MET cc_start: 0.7902 (mtm) cc_final: 0.7343 (mtm) REVERT: A 244 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 292 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7567 (mmm) REVERT: A 316 ASN cc_start: 0.7819 (m-40) cc_final: 0.7587 (m-40) REVERT: A 319 THR cc_start: 0.7203 (m) cc_final: 0.6651 (t) REVERT: A 342 ASN cc_start: 0.7339 (t0) cc_final: 0.6934 (t0) REVERT: A 352 ILE cc_start: 0.8558 (pp) cc_final: 0.8261 (pt) REVERT: A 360 ASN cc_start: 0.7553 (t0) cc_final: 0.6908 (t0) REVERT: A 364 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6822 (tm-30) REVERT: A 380 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7613 (ttp80) REVERT: A 414 MET cc_start: 0.6747 (tmm) cc_final: 0.6431 (tmm) REVERT: A 462 MET cc_start: 0.6800 (ttm) cc_final: 0.6572 (ttp) REVERT: A 496 LEU cc_start: 0.7182 (tt) cc_final: 0.6914 (mp) REVERT: A 497 MET cc_start: 0.7849 (tpp) cc_final: 0.7553 (mpp) REVERT: A 507 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6689 (pp) REVERT: A 594 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 603 ASP cc_start: 0.6932 (t70) cc_final: 0.6686 (t0) REVERT: A 606 TYR cc_start: 0.8208 (p90) cc_final: 0.7880 (p90) REVERT: A 642 TYR cc_start: 0.7327 (m-80) cc_final: 0.6731 (t80) REVERT: A 719 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6406 (mtp180) REVERT: A 725 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7768 (mt) REVERT: B 21 MET cc_start: 0.7224 (ptm) cc_final: 0.6869 (ptm) REVERT: B 24 ILE cc_start: 0.8314 (mm) cc_final: 0.7586 (mm) REVERT: B 28 MET cc_start: 0.6665 (mmm) cc_final: 0.6117 (mmm) REVERT: B 67 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 86 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 148 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7842 (mtp85) REVERT: B 154 ASN cc_start: 0.7461 (t0) cc_final: 0.7185 (t0) REVERT: B 214 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 215 MET cc_start: 0.7812 (mpp) cc_final: 0.7579 (mtm) REVERT: B 219 GLN cc_start: 0.8213 (mp10) cc_final: 0.7709 (mp10) REVERT: B 225 ASP cc_start: 0.7420 (p0) cc_final: 0.7196 (p0) REVERT: B 238 GLU cc_start: 0.6863 (tp30) cc_final: 0.6652 (tp30) REVERT: B 239 GLU cc_start: 0.8053 (tp30) cc_final: 0.7378 (tp30) REVERT: B 345 THR cc_start: 0.7983 (t) cc_final: 0.7768 (p) REVERT: B 397 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 429 THR cc_start: 0.8188 (t) cc_final: 0.7847 (p) REVERT: B 537 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5877 (mt) REVERT: B 560 ASP cc_start: 0.7496 (m-30) cc_final: 0.7205 (m-30) REVERT: B 578 THR cc_start: 0.8066 (m) cc_final: 0.7703 (p) REVERT: B 603 ASP cc_start: 0.7195 (t0) cc_final: 0.6894 (t0) REVERT: B 611 ASN cc_start: 0.7481 (p0) cc_final: 0.7189 (p0) REVERT: B 654 SER cc_start: 0.5899 (OUTLIER) cc_final: 0.5378 (p) outliers start: 53 outliers final: 34 residues processed: 348 average time/residue: 0.2930 time to fit residues: 136.9161 Evaluate side-chains 349 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 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 639 HIS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 691 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11625 Z= 0.193 Angle : 0.592 8.571 15714 Z= 0.316 Chirality : 0.043 0.295 1703 Planarity : 0.004 0.090 2015 Dihedral : 10.443 83.001 1709 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.54 % Favored : 93.10 % Rotamer: Outliers : 4.55 % Allowed : 19.50 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1377 helix: 1.55 (0.21), residues: 634 sheet: 0.64 (0.51), residues: 106 loop : -2.80 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 399 HIS 0.004 0.001 HIS A 30 PHE 0.028 0.002 PHE A 526 TYR 0.010 0.001 TYR B 236 ARG 0.005 0.000 ARG A 406 *********************** 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 356 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8096 (mtpp) REVERT: A 25 ARG cc_start: 0.7505 (mpt-90) cc_final: 0.7215 (mpt-90) REVERT: A 45 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: A 100 MET cc_start: 0.6760 (tmm) cc_final: 0.6508 (tmm) REVERT: A 215 MET cc_start: 0.7894 (mtm) cc_final: 0.7338 (mtm) REVERT: A 244 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6837 (tm-30) REVERT: A 292 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7568 (mmm) REVERT: A 316 ASN cc_start: 0.7818 (m-40) cc_final: 0.7557 (m-40) REVERT: A 319 THR cc_start: 0.7155 (m) cc_final: 0.6600 (t) REVERT: A 342 ASN cc_start: 0.7340 (t0) cc_final: 0.6949 (t0) REVERT: A 352 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8270 (pt) REVERT: A 360 ASN cc_start: 0.7538 (t0) cc_final: 0.6919 (t0) REVERT: A 364 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6789 (tm-30) REVERT: A 380 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7575 (ttp-170) REVERT: A 414 MET cc_start: 0.6736 (tmm) cc_final: 0.6387 (tmm) REVERT: A 462 MET cc_start: 0.6713 (ttm) cc_final: 0.6486 (ttp) REVERT: A 507 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6753 (pp) REVERT: A 529 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8320 (tt) REVERT: A 594 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 603 ASP cc_start: 0.6957 (t70) cc_final: 0.6706 (t0) REVERT: A 606 TYR cc_start: 0.8186 (p90) cc_final: 0.7872 (p90) REVERT: A 719 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6422 (mtp180) REVERT: A 725 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7757 (mt) REVERT: B 21 MET cc_start: 0.7246 (ptm) cc_final: 0.6885 (ptm) REVERT: B 24 ILE cc_start: 0.8353 (mm) cc_final: 0.7623 (mm) REVERT: B 28 MET cc_start: 0.6709 (mmm) cc_final: 0.6110 (mmm) REVERT: B 67 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 86 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 113 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: B 132 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6789 (mm-30) REVERT: B 154 ASN cc_start: 0.7531 (t0) cc_final: 0.7188 (t0) REVERT: B 215 MET cc_start: 0.7797 (mpp) cc_final: 0.7540 (mtm) REVERT: B 219 GLN cc_start: 0.8186 (mp10) cc_final: 0.7818 (mm-40) REVERT: B 225 ASP cc_start: 0.7427 (p0) cc_final: 0.7178 (p0) REVERT: B 292 MET cc_start: 0.7513 (mmp) cc_final: 0.7181 (mmt) REVERT: B 316 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: B 397 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 429 THR cc_start: 0.8174 (t) cc_final: 0.7827 (p) REVERT: B 537 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5910 (mt) REVERT: B 560 ASP cc_start: 0.7502 (m-30) cc_final: 0.7182 (m-30) REVERT: B 578 THR cc_start: 0.7998 (m) cc_final: 0.7634 (p) REVERT: B 603 ASP cc_start: 0.7193 (t0) cc_final: 0.6913 (t0) REVERT: B 611 ASN cc_start: 0.7512 (p0) cc_final: 0.7232 (p0) outliers start: 55 outliers final: 40 residues processed: 330 average time/residue: 0.3040 time to fit residues: 134.7572 Evaluate side-chains 355 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 292 MET Chi-restraints excluded: chain A residue 352 ILE 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 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 602 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 663 MET Chi-restraints excluded: chain A residue 719 ARG 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 47 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 16 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS B 612 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11625 Z= 0.212 Angle : 0.595 8.278 15714 Z= 0.319 Chirality : 0.044 0.288 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.316 80.645 1706 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.81 % Rotamer: Outliers : 4.63 % Allowed : 20.00 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1377 helix: 1.59 (0.21), residues: 634 sheet: 0.59 (0.52), residues: 107 loop : -2.82 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.008 0.001 HIS B 612 PHE 0.025 0.002 PHE A 526 TYR 0.012 0.001 TYR B 236 ARG 0.005 0.000 ARG A 406 *********************** 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 364 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8132 (mtpt) REVERT: A 25 ARG cc_start: 0.7520 (mpt-90) cc_final: 0.7249 (mpt-90) REVERT: A 45 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: A 100 MET cc_start: 0.6766 (tmm) cc_final: 0.6505 (tmm) REVERT: A 215 MET cc_start: 0.7868 (mtm) cc_final: 0.7293 (mtm) REVERT: A 219 GLN cc_start: 0.7452 (mm110) cc_final: 0.7040 (mm110) REVERT: A 244 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 292 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7604 (mmm) REVERT: A 316 ASN cc_start: 0.7814 (m-40) cc_final: 0.7559 (m-40) REVERT: A 319 THR cc_start: 0.7134 (m) cc_final: 0.6616 (t) REVERT: A 334 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7502 (mp10) REVERT: A 342 ASN cc_start: 0.7349 (t0) cc_final: 0.6952 (t0) REVERT: A 352 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8254 (pt) REVERT: A 360 ASN cc_start: 0.7574 (t0) cc_final: 0.6905 (t0) REVERT: A 364 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6765 (tm-30) REVERT: A 410 GLU cc_start: 0.7782 (pt0) cc_final: 0.7475 (pt0) REVERT: A 414 MET cc_start: 0.6754 (tmm) cc_final: 0.6394 (tmm) REVERT: A 462 MET cc_start: 0.6789 (ttm) cc_final: 0.6574 (ttp) REVERT: A 492 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: A 507 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6799 (pp) REVERT: A 529 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 590 LYS cc_start: 0.7645 (mppt) cc_final: 0.7429 (mppt) REVERT: A 594 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 603 ASP cc_start: 0.6960 (t70) cc_final: 0.6707 (t0) REVERT: A 606 TYR cc_start: 0.8188 (p90) cc_final: 0.7910 (p90) REVERT: A 719 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6423 (mtp180) REVERT: A 725 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7754 (mt) REVERT: B 21 MET cc_start: 0.7252 (ptm) cc_final: 0.6900 (ptm) REVERT: B 24 ILE cc_start: 0.8369 (mm) cc_final: 0.7569 (mm) REVERT: B 28 MET cc_start: 0.6708 (mmm) cc_final: 0.6119 (mmm) REVERT: B 67 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 86 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 132 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6771 (mm-30) REVERT: B 148 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7713 (mtp85) REVERT: B 154 ASN cc_start: 0.7568 (t0) cc_final: 0.7208 (t0) REVERT: B 214 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 219 GLN cc_start: 0.8198 (mp10) cc_final: 0.7814 (mm-40) REVERT: B 225 ASP cc_start: 0.7417 (p0) cc_final: 0.7209 (p0) REVERT: B 239 GLU cc_start: 0.8054 (tp30) cc_final: 0.7379 (tp30) REVERT: B 292 MET cc_start: 0.7511 (mmp) cc_final: 0.7146 (mmt) REVERT: B 316 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: B 397 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 398 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8488 (mtmm) REVERT: B 429 THR cc_start: 0.8176 (t) cc_final: 0.7845 (p) REVERT: B 537 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5935 (mt) REVERT: B 560 ASP cc_start: 0.7495 (m-30) cc_final: 0.7191 (m-30) REVERT: B 578 THR cc_start: 0.8061 (m) cc_final: 0.7690 (p) REVERT: B 603 ASP cc_start: 0.7215 (t0) cc_final: 0.6959 (t0) REVERT: B 611 ASN cc_start: 0.7455 (p0) cc_final: 0.7152 (p0) REVERT: B 657 GLU cc_start: 0.7331 (tp30) cc_final: 0.7125 (mm-30) outliers start: 56 outliers final: 37 residues processed: 336 average time/residue: 0.2946 time to fit residues: 132.9958 Evaluate side-chains 348 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 352 ILE 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 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 5 VAL 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 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11625 Z= 0.210 Angle : 0.599 8.061 15714 Z= 0.321 Chirality : 0.044 0.280 1703 Planarity : 0.005 0.091 2015 Dihedral : 10.145 78.524 1706 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.90 % Favored : 92.74 % Rotamer: Outliers : 4.55 % Allowed : 20.66 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1377 helix: 1.62 (0.21), residues: 634 sheet: 0.66 (0.52), residues: 106 loop : -2.79 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.023 0.002 PHE A 526 TYR 0.012 0.001 TYR B 236 ARG 0.006 0.000 ARG A 406 *********************** 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 356 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8125 (mtpt) REVERT: A 25 ARG cc_start: 0.7517 (mpt-90) cc_final: 0.7251 (mpt-90) REVERT: A 45 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6745 (m-30) REVERT: A 100 MET cc_start: 0.6764 (tmm) cc_final: 0.6504 (tmm) REVERT: A 215 MET cc_start: 0.7887 (mtm) cc_final: 0.7337 (mtm) REVERT: A 219 GLN cc_start: 0.7437 (mm110) cc_final: 0.7134 (mm110) REVERT: A 244 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6863 (tm-30) REVERT: A 292 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7614 (mmm) REVERT: A 316 ASN cc_start: 0.7821 (m-40) cc_final: 0.7560 (m-40) REVERT: A 319 THR cc_start: 0.7106 (m) cc_final: 0.6592 (t) REVERT: A 334 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7489 (mp10) REVERT: A 342 ASN cc_start: 0.7349 (t0) cc_final: 0.6939 (t0) REVERT: A 352 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8231 (pt) REVERT: A 360 ASN cc_start: 0.7554 (t0) cc_final: 0.6960 (t0) REVERT: A 364 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 410 GLU cc_start: 0.7798 (pt0) cc_final: 0.7459 (pt0) REVERT: A 414 MET cc_start: 0.6752 (tmm) cc_final: 0.6367 (tmm) REVERT: A 462 MET cc_start: 0.6775 (ttm) cc_final: 0.6562 (ttp) REVERT: A 492 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: A 507 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6796 (pp) REVERT: A 529 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 594 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 603 ASP cc_start: 0.7006 (t70) cc_final: 0.6729 (t0) REVERT: A 606 TYR cc_start: 0.8191 (p90) cc_final: 0.7914 (p90) REVERT: A 719 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6457 (mtp180) REVERT: A 725 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7755 (mt) REVERT: B 21 MET cc_start: 0.7259 (ptm) cc_final: 0.6896 (ptm) REVERT: B 24 ILE cc_start: 0.8349 (mm) cc_final: 0.7525 (mm) REVERT: B 28 MET cc_start: 0.6697 (mmm) cc_final: 0.6149 (mmm) REVERT: B 67 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 86 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 109 ASP cc_start: 0.7126 (t70) cc_final: 0.6767 (t0) REVERT: B 113 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: B 132 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6763 (mm-30) REVERT: B 148 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7673 (mtp85) REVERT: B 154 ASN cc_start: 0.7595 (t0) cc_final: 0.7204 (t0) REVERT: B 219 GLN cc_start: 0.8161 (mp10) cc_final: 0.7818 (mm-40) REVERT: B 225 ASP cc_start: 0.7416 (p0) cc_final: 0.7214 (p0) REVERT: B 238 GLU cc_start: 0.6873 (tp30) cc_final: 0.6653 (tp30) REVERT: B 292 MET cc_start: 0.7475 (mmp) cc_final: 0.7121 (mmt) REVERT: B 316 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: B 397 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7202 (tm-30) REVERT: B 429 THR cc_start: 0.8168 (t) cc_final: 0.7830 (p) REVERT: B 537 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.6030 (mt) REVERT: B 560 ASP cc_start: 0.7495 (m-30) cc_final: 0.7192 (m-30) REVERT: B 578 THR cc_start: 0.8058 (m) cc_final: 0.7683 (p) REVERT: B 603 ASP cc_start: 0.7213 (t0) cc_final: 0.6961 (t0) REVERT: B 611 ASN cc_start: 0.7567 (p0) cc_final: 0.7304 (p0) REVERT: B 657 GLU cc_start: 0.7326 (tp30) cc_final: 0.7122 (mm-30) outliers start: 55 outliers final: 39 residues processed: 328 average time/residue: 0.2945 time to fit residues: 129.1276 Evaluate side-chains 351 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 352 ILE 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 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 719 ARG 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 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 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 128 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 173 GLN B 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11625 Z= 0.199 Angle : 0.601 7.907 15714 Z= 0.321 Chirality : 0.043 0.281 1703 Planarity : 0.005 0.092 2015 Dihedral : 9.870 81.984 1703 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.25 % Favored : 93.39 % Rotamer: Outliers : 4.63 % Allowed : 20.17 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1377 helix: 1.65 (0.21), residues: 635 sheet: 0.62 (0.53), residues: 101 loop : -2.77 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.023 0.001 PHE A 526 TYR 0.011 0.001 TYR A 80 ARG 0.004 0.000 ARG A 406 *********************** 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 352 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8072 (mmmt) REVERT: A 25 ARG cc_start: 0.7501 (mpt-90) cc_final: 0.7245 (mpt-90) REVERT: A 45 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: A 100 MET cc_start: 0.6769 (tmm) cc_final: 0.6501 (tmm) REVERT: A 215 MET cc_start: 0.7888 (mtm) cc_final: 0.7352 (mtm) REVERT: A 219 GLN cc_start: 0.7450 (mm110) cc_final: 0.7172 (mm110) REVERT: A 244 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6858 (tm-30) REVERT: A 316 ASN cc_start: 0.7825 (m-40) cc_final: 0.7565 (m-40) REVERT: A 319 THR cc_start: 0.7070 (m) cc_final: 0.6568 (t) REVERT: A 342 ASN cc_start: 0.7352 (t0) cc_final: 0.6952 (t0) REVERT: A 352 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8217 (pt) REVERT: A 360 ASN cc_start: 0.7551 (t0) cc_final: 0.6976 (t0) REVERT: A 364 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 410 GLU cc_start: 0.7792 (pt0) cc_final: 0.7420 (pt0) REVERT: A 414 MET cc_start: 0.6755 (tmm) cc_final: 0.6374 (tmm) REVERT: A 462 MET cc_start: 0.6733 (ttm) cc_final: 0.6471 (ttp) REVERT: A 492 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: A 507 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6782 (pp) REVERT: A 529 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 594 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7149 (tm-30) REVERT: A 603 ASP cc_start: 0.6982 (t70) cc_final: 0.6723 (t0) REVERT: A 606 TYR cc_start: 0.8169 (p90) cc_final: 0.7887 (p90) REVERT: A 719 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6456 (mtp180) REVERT: A 725 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 21 MET cc_start: 0.7256 (ptm) cc_final: 0.6895 (ptm) REVERT: B 24 ILE cc_start: 0.8316 (mm) cc_final: 0.7489 (mm) REVERT: B 28 MET cc_start: 0.6778 (mmm) cc_final: 0.6217 (mmm) REVERT: B 67 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7650 (tm-30) REVERT: B 86 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 154 ASN cc_start: 0.7584 (t0) cc_final: 0.7204 (t0) REVERT: B 214 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 219 GLN cc_start: 0.8112 (mp10) cc_final: 0.7814 (mm-40) REVERT: B 225 ASP cc_start: 0.7423 (p0) cc_final: 0.7199 (p0) REVERT: B 238 GLU cc_start: 0.6869 (tp30) cc_final: 0.6646 (tp30) REVERT: B 239 GLU cc_start: 0.8026 (tp30) cc_final: 0.7398 (tp30) REVERT: B 292 MET cc_start: 0.7423 (mmp) cc_final: 0.7072 (mmt) REVERT: B 316 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: B 397 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 429 THR cc_start: 0.8153 (t) cc_final: 0.7829 (p) REVERT: B 537 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6118 (mt) REVERT: B 560 ASP cc_start: 0.7492 (m-30) cc_final: 0.7184 (m-30) REVERT: B 578 THR cc_start: 0.8049 (m) cc_final: 0.7683 (p) REVERT: B 603 ASP cc_start: 0.7233 (t0) cc_final: 0.6996 (t0) REVERT: B 611 ASN cc_start: 0.7593 (p0) cc_final: 0.7321 (p0) outliers start: 56 outliers final: 40 residues processed: 328 average time/residue: 0.2918 time to fit residues: 128.9834 Evaluate side-chains 341 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 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 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 719 ARG 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 39 LEU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 67 optimal weight: 0.0270 chunk 87 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11625 Z= 0.175 Angle : 0.599 8.082 15714 Z= 0.318 Chirality : 0.043 0.274 1703 Planarity : 0.004 0.092 2015 Dihedral : 9.478 83.406 1703 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.95 % Favored : 93.68 % Rotamer: Outliers : 3.88 % Allowed : 21.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1377 helix: 1.65 (0.22), residues: 637 sheet: 0.55 (0.52), residues: 103 loop : -2.71 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 399 HIS 0.003 0.000 HIS A 30 PHE 0.024 0.001 PHE A 526 TYR 0.010 0.001 TYR B 371 ARG 0.005 0.000 ARG A 406 ********************** 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 348 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8075 (mmmt) REVERT: A 25 ARG cc_start: 0.7484 (mpt-90) cc_final: 0.7247 (mpt-90) REVERT: A 45 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: A 100 MET cc_start: 0.6762 (tmm) cc_final: 0.6501 (tmm) REVERT: A 215 MET cc_start: 0.7832 (mtm) cc_final: 0.7273 (mtm) REVERT: A 316 ASN cc_start: 0.7838 (m-40) cc_final: 0.7567 (m-40) REVERT: A 319 THR cc_start: 0.6999 (m) cc_final: 0.6554 (t) REVERT: A 342 ASN cc_start: 0.7350 (t0) cc_final: 0.6959 (t0) REVERT: A 352 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8220 (pt) REVERT: A 360 ASN cc_start: 0.7537 (t0) cc_final: 0.6890 (t0) REVERT: A 364 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 410 GLU cc_start: 0.7777 (pt0) cc_final: 0.7418 (pt0) REVERT: A 414 MET cc_start: 0.6714 (tmm) cc_final: 0.6345 (tmm) REVERT: A 462 MET cc_start: 0.6562 (ttm) cc_final: 0.6343 (ttp) REVERT: A 492 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: A 507 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6796 (pp) REVERT: A 529 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 594 GLN cc_start: 0.7379 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 603 ASP cc_start: 0.7006 (t70) cc_final: 0.6742 (t0) REVERT: A 606 TYR cc_start: 0.8131 (p90) cc_final: 0.7847 (p90) REVERT: A 641 PHE cc_start: 0.8517 (t80) cc_final: 0.8240 (t80) REVERT: A 719 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6430 (mtp180) REVERT: A 725 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7755 (mt) REVERT: B 21 MET cc_start: 0.7226 (ptm) cc_final: 0.6865 (ptm) REVERT: B 24 ILE cc_start: 0.8291 (mm) cc_final: 0.7467 (mm) REVERT: B 28 MET cc_start: 0.6732 (mmm) cc_final: 0.6156 (mmm) REVERT: B 67 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 86 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 113 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: B 154 ASN cc_start: 0.7566 (t0) cc_final: 0.7205 (t0) REVERT: B 214 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7434 (mt-10) REVERT: B 215 MET cc_start: 0.7714 (mpp) cc_final: 0.6850 (mtm) REVERT: B 219 GLN cc_start: 0.8061 (mp10) cc_final: 0.7505 (mm-40) REVERT: B 225 ASP cc_start: 0.7423 (p0) cc_final: 0.7180 (p0) REVERT: B 238 GLU cc_start: 0.6904 (tp30) cc_final: 0.6671 (tp30) REVERT: B 239 GLU cc_start: 0.7972 (tp30) cc_final: 0.7438 (tp30) REVERT: B 316 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (m-40) REVERT: B 350 ILE cc_start: 0.7553 (mm) cc_final: 0.7294 (mt) REVERT: B 397 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 398 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8588 (mtmt) REVERT: B 429 THR cc_start: 0.8133 (t) cc_final: 0.7817 (p) REVERT: B 537 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6096 (mt) REVERT: B 560 ASP cc_start: 0.7517 (m-30) cc_final: 0.7214 (m-30) REVERT: B 578 THR cc_start: 0.8025 (m) cc_final: 0.7664 (p) REVERT: B 603 ASP cc_start: 0.7200 (t0) cc_final: 0.6984 (t0) REVERT: B 611 ASN cc_start: 0.7504 (p0) cc_final: 0.7232 (p0) outliers start: 47 outliers final: 35 residues processed: 328 average time/residue: 0.3061 time to fit residues: 134.2290 Evaluate side-chains 344 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 66 MET Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 352 ILE 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 529 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 639 HIS Chi-restraints excluded: chain A residue 719 ARG 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 39 LEU 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 254 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 VAL 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 Chi-restraints excluded: chain B residue 643 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116691 restraints weight = 16341.316| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.33 r_work: 0.3426 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11625 Z= 0.185 Angle : 0.607 8.660 15714 Z= 0.323 Chirality : 0.043 0.272 1703 Planarity : 0.005 0.093 2015 Dihedral : 9.303 80.536 1703 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.39 % Favored : 93.25 % Rotamer: Outliers : 4.05 % Allowed : 20.99 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1377 helix: 1.65 (0.21), residues: 634 sheet: 0.57 (0.52), residues: 103 loop : -2.71 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 399 HIS 0.003 0.001 HIS A 30 PHE 0.023 0.001 PHE A 526 TYR 0.011 0.001 TYR B 236 ARG 0.004 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.90 seconds wall clock time: 62 minutes 56.89 seconds (3776.89 seconds total)