Starting phenix.real_space_refine on Wed Mar 4 03:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5u_30093/03_2026/6m5u_30093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5u_30093/03_2026/6m5u_30093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m5u_30093/03_2026/6m5u_30093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5u_30093/03_2026/6m5u_30093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m5u_30093/03_2026/6m5u_30093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5u_30093/03_2026/6m5u_30093.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 6703 2.51 5 N 1893 2.21 5 O 1897 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4482 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 29, 'TRANS': 555} Chain breaks: 7 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5208 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 636} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 825 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5415 SG CYS B 121 28.952 52.885 52.444 1.00 47.42 S ATOM 10277 SG CYS C 101 27.583 53.204 55.790 1.00 59.52 S ATOM 6010 SG CYS B 197 51.114 57.002 49.253 1.00 43.06 S ATOM 6028 SG CYS B 200 52.928 58.057 52.017 1.00 41.30 S Time building chain proxies: 2.59, per 1000 atoms: 0.25 Number of scatterers: 10549 At special positions: 0 Unit cell: (108.324, 108.324, 118.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 47 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1897 8.00 N 1893 7.00 C 6703 6.00 Be 1 4.00 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: 0.89 Conformation dependent library (CDL) restraints added in 582.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 801 " - pdb=" SG CYS C 101 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 200 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 197 " 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 53.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 73 through 81 removed outlier: 4.299A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.539A pdb=" N PHE A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 129 through 149 removed outlier: 3.731A pdb=" N GLN A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.741A pdb=" N ASP A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 203 through 221 removed outlier: 4.173A pdb=" N LEU A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.674A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.710A pdb=" N VAL A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 365 through 373 removed outlier: 4.179A pdb=" N ILE A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 549 through 569 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.613A pdb=" N VAL B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 74 through 101 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.597A pdb=" N PHE B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 removed outlier: 3.633A pdb=" N VAL B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 180 removed outlier: 3.818A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.788A pdb=" N SER B 191 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.786A pdb=" N PHE B 201 " --> pdb=" O CYS B 197 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.525A pdb=" N TYR B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.103A pdb=" N GLN B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 355 Processing helix chain 'B' and resid 374 through 381 removed outlier: 3.763A pdb=" N ILE B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.868A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.554A pdb=" N CYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 510 removed outlier: 3.557A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.542A pdb=" N MET B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 560 removed outlier: 3.741A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 removed outlier: 3.937A pdb=" N ALA B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 595 through 608 removed outlier: 4.314A pdb=" N HIS B 601 " --> pdb=" O PRO B 597 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 606 " --> pdb=" O ARG B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 633 removed outlier: 3.911A pdb=" N SER B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.643A pdb=" N GLU B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B 643 " --> pdb=" O HIS B 639 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 700 removed outlier: 3.533A pdb=" N GLN B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 772 removed outlier: 3.700A pdb=" N LEU B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.633A pdb=" N LEU C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 80 removed outlier: 3.628A pdb=" N LEU C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 128 removed outlier: 3.676A pdb=" N GLU C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 386 removed outlier: 7.623A pdb=" N THR A 254 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER A 384 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 256 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR A 386 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 258 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 255 " --> pdb=" O ASN A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.656A pdb=" N SER A 332 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 619 removed outlier: 6.120A pdb=" N VAL A 576 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 504 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA A 579 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 506 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 503 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG A 528 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR A 521 " --> pdb=" O HIS A 540 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 540 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 523 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 538 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 525 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 659 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 535 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 661 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 537 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 663 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 539 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA7, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.363A pdb=" N ILE B 567 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 738 " --> pdb=" O TYR B 728 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1691 1.30 - 1.43: 2871 1.43 - 1.56: 6133 1.56 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 10776 Sorted by residual: bond pdb=" F3 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" F1 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" F2 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C ALA A 482 " pdb=" O ALA A 482 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.17e-02 7.31e+03 3.05e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 10771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 14166 2.16 - 4.32: 413 4.32 - 6.48: 49 6.48 - 8.64: 11 8.64 - 10.80: 4 Bond angle restraints: 14643 Sorted by residual: angle pdb=" C CYS A 125 " pdb=" N ALA A 126 " pdb=" CA ALA A 126 " ideal model delta sigma weight residual 122.52 130.41 -7.89 1.16e+00 7.43e-01 4.62e+01 angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 110.36 115.77 -5.41 1.05e+00 9.07e-01 2.65e+01 angle pdb=" N CYS A 125 " pdb=" CA CYS A 125 " pdb=" C CYS A 125 " ideal model delta sigma weight residual 108.42 116.07 -7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" N ARG B 59 " pdb=" CA ARG B 59 " pdb=" C ARG B 59 " ideal model delta sigma weight residual 114.56 108.46 6.10 1.27e+00 6.20e-01 2.31e+01 angle pdb=" N SER A 481 " pdb=" CA SER A 481 " pdb=" C SER A 481 " ideal model delta sigma weight residual 111.07 106.37 4.70 1.07e+00 8.73e-01 1.93e+01 ... (remaining 14638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 5926 23.49 - 46.98: 417 46.98 - 70.47: 62 70.47 - 93.95: 12 93.95 - 117.44: 2 Dihedral angle restraints: 6419 sinusoidal: 2471 harmonic: 3948 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 57.44 -117.44 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" CA CYS B 223 " pdb=" C CYS B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 37.48 -97.48 1 2.00e+01 2.50e-03 2.71e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1474 0.074 - 0.147: 181 0.147 - 0.221: 21 0.221 - 0.294: 4 0.294 - 0.368: 1 Chirality restraints: 1681 Sorted by residual: chirality pdb=" CA VAL A 558 " pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CB VAL A 558 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA HIS B 535 " pdb=" N HIS B 535 " pdb=" C HIS B 535 " pdb=" CB HIS B 535 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1678 not shown) Planarity restraints: 1892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 242 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C TYR B 242 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR B 242 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 243 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 534 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C VAL B 534 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 534 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS B 535 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 724 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 725 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " 0.030 5.00e-02 4.00e+02 ... (remaining 1889 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1398 2.75 - 3.29: 10590 3.29 - 3.82: 17408 3.82 - 4.36: 20207 4.36 - 4.90: 34862 Nonbonded interactions: 84465 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb=" ND1 HIS B 225 " model vdw 2.210 3.120 nonbonded pdb=" O CYS C 101 " pdb=" N GLY C 104 " model vdw 2.224 3.120 nonbonded pdb=" NE2 HIS B 157 " pdb=" O ASN B 608 " model vdw 2.269 3.120 nonbonded pdb=" O SER B 713 " pdb=" OG SER B 713 " model vdw 2.279 3.040 nonbonded pdb=" O GLY A 654 " pdb=" NH1 ARG C 120 " model vdw 2.281 3.120 ... (remaining 84460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.010 0.639 10780 Z= 0.468 Angle : 0.862 10.800 14643 Z= 0.537 Chirality : 0.051 0.368 1681 Planarity : 0.005 0.055 1892 Dihedral : 16.072 117.442 3853 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.03 % Favored : 90.82 % Rotamer: Outliers : 5.59 % Allowed : 16.68 % Favored : 77.73 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.21), residues: 1329 helix: -1.01 (0.18), residues: 692 sheet: -1.77 (0.52), residues: 92 loop : -3.41 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 528 TYR 0.019 0.002 TYR A 507 PHE 0.023 0.002 PHE A 634 TRP 0.011 0.001 TRP A 308 HIS 0.009 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00745 (10776) covalent geometry : angle 0.86205 (14643) hydrogen bonds : bond 0.13153 ( 499) hydrogen bonds : angle 5.74664 ( 1452) metal coordination : bond 0.32793 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 0.389 Fit side-chains REVERT: A 165 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8454 (tp40) REVERT: A 372 PHE cc_start: 0.7409 (m-80) cc_final: 0.6876 (m-80) REVERT: B 222 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 529 MET cc_start: 0.8909 (tpp) cc_final: 0.8704 (tpt) REVERT: B 617 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8910 (m170) REVERT: C 50 MET cc_start: 0.7759 (mtp) cc_final: 0.7558 (mtp) REVERT: C 54 GLU cc_start: 0.8239 (mp0) cc_final: 0.7640 (mp0) outliers start: 61 outliers final: 41 residues processed: 265 average time/residue: 0.1208 time to fit residues: 42.7428 Evaluate side-chains 202 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 617 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 211 HIS A 224 HIS A 374 ASN A 377 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN A 670 GLN B 68 GLN B 124 HIS B 210 GLN B 237 ASN B 323 GLN B 621 GLN B 624 ASN B 679 GLN C 119 ASN C 126 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.132963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.112618 restraints weight = 15298.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.114845 restraints weight = 10619.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.116429 restraints weight = 8210.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117370 restraints weight = 6839.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118203 restraints weight = 6048.232| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10780 Z= 0.147 Angle : 0.677 9.511 14643 Z= 0.335 Chirality : 0.042 0.179 1681 Planarity : 0.005 0.049 1892 Dihedral : 8.660 127.653 1564 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.86 % Allowed : 19.43 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.23), residues: 1329 helix: 0.27 (0.20), residues: 681 sheet: -1.66 (0.50), residues: 102 loop : -2.66 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.011 0.001 TYR A 533 PHE 0.019 0.001 PHE A 633 TRP 0.014 0.001 TRP A 308 HIS 0.006 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00334 (10776) covalent geometry : angle 0.67715 (14643) hydrogen bonds : bond 0.03718 ( 499) hydrogen bonds : angle 4.13518 ( 1452) metal coordination : bond 0.00736 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.340 Fit side-chains REVERT: A 141 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 165 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8469 (tp40) REVERT: A 240 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 709 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6275 (ttp) REVERT: B 222 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8309 (mm) REVERT: B 241 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8112 (mtp85) REVERT: B 714 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8253 (mtt-85) REVERT: B 722 ARG cc_start: 0.8681 (ptp90) cc_final: 0.8454 (ptp90) outliers start: 53 outliers final: 28 residues processed: 211 average time/residue: 0.0945 time to fit residues: 28.0248 Evaluate side-chains 187 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 237 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112377 restraints weight = 15311.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114587 restraints weight = 10626.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.116094 restraints weight = 8212.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.116983 restraints weight = 6901.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.117737 restraints weight = 6124.362| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10780 Z= 0.137 Angle : 0.623 7.838 14643 Z= 0.310 Chirality : 0.041 0.214 1681 Planarity : 0.004 0.044 1892 Dihedral : 7.015 130.911 1525 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 5.04 % Allowed : 20.99 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1329 helix: 0.89 (0.20), residues: 681 sheet: -1.01 (0.60), residues: 74 loop : -2.37 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 250 TYR 0.008 0.001 TYR B 132 PHE 0.020 0.001 PHE A 541 TRP 0.009 0.001 TRP A 308 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00315 (10776) covalent geometry : angle 0.62284 (14643) hydrogen bonds : bond 0.03411 ( 499) hydrogen bonds : angle 3.83047 ( 1452) metal coordination : bond 0.00254 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6638 (pm20) REVERT: A 141 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8068 (mp) REVERT: A 165 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8404 (tp40) REVERT: A 240 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8400 (pp) REVERT: A 541 PHE cc_start: 0.7482 (t80) cc_final: 0.7148 (t80) REVERT: B 21 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: B 222 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8353 (mm) REVERT: B 582 MET cc_start: 0.8562 (tpp) cc_final: 0.8160 (tpp) REVERT: B 714 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8179 (mtt-85) outliers start: 55 outliers final: 30 residues processed: 211 average time/residue: 0.0993 time to fit residues: 29.4194 Evaluate side-chains 186 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 8 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 134 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.133817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.113483 restraints weight = 15328.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.115686 restraints weight = 10604.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.117254 restraints weight = 8183.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118101 restraints weight = 6843.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119038 restraints weight = 6081.882| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10780 Z= 0.121 Angle : 0.609 7.792 14643 Z= 0.302 Chirality : 0.040 0.215 1681 Planarity : 0.004 0.048 1892 Dihedral : 6.724 130.085 1520 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.32 % Allowed : 21.36 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1329 helix: 1.16 (0.20), residues: 683 sheet: -0.73 (0.62), residues: 74 loop : -2.20 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.008 0.001 TYR B 721 PHE 0.018 0.001 PHE A 633 TRP 0.010 0.001 TRP A 308 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00274 (10776) covalent geometry : angle 0.60863 (14643) hydrogen bonds : bond 0.03200 ( 499) hydrogen bonds : angle 3.70653 ( 1452) metal coordination : bond 0.00143 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7337 (ttm170) cc_final: 0.6810 (ttm170) REVERT: A 141 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 165 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8352 (tp40) REVERT: A 240 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8275 (pp) REVERT: A 541 PHE cc_start: 0.7495 (t80) cc_final: 0.7132 (t80) REVERT: B 222 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 582 MET cc_start: 0.8517 (tpp) cc_final: 0.8103 (tpp) REVERT: B 608 ASN cc_start: 0.8295 (t0) cc_final: 0.7886 (t0) REVERT: B 714 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8128 (mtt-85) outliers start: 58 outliers final: 39 residues processed: 210 average time/residue: 0.0929 time to fit residues: 28.0418 Evaluate side-chains 194 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 61 optimal weight: 0.0670 chunk 96 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS B 237 ASN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.134243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114155 restraints weight = 15139.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.116308 restraints weight = 10544.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.117827 restraints weight = 8174.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118912 restraints weight = 6827.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119374 restraints weight = 6012.770| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10780 Z= 0.120 Angle : 0.602 7.851 14643 Z= 0.295 Chirality : 0.040 0.173 1681 Planarity : 0.004 0.048 1892 Dihedral : 6.554 129.355 1519 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.22 % Allowed : 23.19 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1329 helix: 1.34 (0.21), residues: 689 sheet: -0.90 (0.56), residues: 86 loop : -2.16 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.008 0.001 TYR B 721 PHE 0.017 0.001 PHE A 633 TRP 0.011 0.001 TRP A 308 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00271 (10776) covalent geometry : angle 0.60172 (14643) hydrogen bonds : bond 0.03106 ( 499) hydrogen bonds : angle 3.58561 ( 1452) metal coordination : bond 0.00144 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7325 (ttm170) cc_final: 0.6900 (ttm170) REVERT: A 141 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7944 (mp) REVERT: A 165 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8247 (tp40) REVERT: A 240 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 541 PHE cc_start: 0.7655 (t80) cc_final: 0.7050 (t80) REVERT: B 582 MET cc_start: 0.8511 (tpp) cc_final: 0.8128 (tpp) REVERT: B 608 ASN cc_start: 0.8311 (t0) cc_final: 0.7984 (t0) REVERT: B 714 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8109 (mtt-85) outliers start: 46 outliers final: 38 residues processed: 204 average time/residue: 0.0894 time to fit residues: 26.2819 Evaluate side-chains 196 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 127 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 chunk 29 optimal weight: 0.0370 chunk 128 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.115874 restraints weight = 15155.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.118011 restraints weight = 10474.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.119552 restraints weight = 8101.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120460 restraints weight = 6781.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121218 restraints weight = 6007.602| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10780 Z= 0.110 Angle : 0.595 8.303 14643 Z= 0.291 Chirality : 0.040 0.234 1681 Planarity : 0.004 0.051 1892 Dihedral : 6.380 127.818 1517 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.12 % Allowed : 24.20 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1329 helix: 1.51 (0.21), residues: 689 sheet: -0.72 (0.56), residues: 86 loop : -2.20 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.009 0.001 TYR B 721 PHE 0.017 0.001 PHE B 72 TRP 0.028 0.002 TRP B 658 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00242 (10776) covalent geometry : angle 0.59499 (14643) hydrogen bonds : bond 0.02958 ( 499) hydrogen bonds : angle 3.55336 ( 1452) metal coordination : bond 0.00136 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.318 Fit side-chains REVERT: A 96 ARG cc_start: 0.7351 (ttm170) cc_final: 0.6844 (ttm170) REVERT: A 124 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 141 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 165 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8095 (tp40) REVERT: A 541 PHE cc_start: 0.7552 (t80) cc_final: 0.7082 (t80) REVERT: B 113 GLU cc_start: 0.7899 (tp30) cc_final: 0.7668 (tp30) REVERT: B 582 MET cc_start: 0.8478 (tpp) cc_final: 0.8093 (tpp) REVERT: B 714 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8083 (mtt-85) outliers start: 45 outliers final: 36 residues processed: 198 average time/residue: 0.0926 time to fit residues: 26.4757 Evaluate side-chains 192 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 540 HIS B 21 GLN B 237 ASN B 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.133904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.113958 restraints weight = 15169.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116065 restraints weight = 10613.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117486 restraints weight = 8268.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.118583 restraints weight = 6944.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.118950 restraints weight = 6137.676| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10780 Z= 0.126 Angle : 0.600 7.635 14643 Z= 0.293 Chirality : 0.040 0.209 1681 Planarity : 0.004 0.055 1892 Dihedral : 6.355 127.349 1517 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.49 % Allowed : 23.83 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1329 helix: 1.60 (0.21), residues: 688 sheet: -0.70 (0.56), residues: 86 loop : -2.12 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 722 TYR 0.007 0.001 TYR B 721 PHE 0.019 0.001 PHE B 72 TRP 0.018 0.002 TRP B 658 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00291 (10776) covalent geometry : angle 0.59984 (14643) hydrogen bonds : bond 0.03050 ( 499) hydrogen bonds : angle 3.52790 ( 1452) metal coordination : bond 0.00166 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.309 Fit side-chains REVERT: A 96 ARG cc_start: 0.7333 (ttm170) cc_final: 0.6877 (ttm170) REVERT: A 124 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: A 165 GLN cc_start: 0.8315 (tp-100) cc_final: 0.8082 (tp40) REVERT: A 240 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 541 PHE cc_start: 0.7535 (t80) cc_final: 0.7059 (t80) REVERT: B 113 GLU cc_start: 0.7795 (tp30) cc_final: 0.7539 (tp30) REVERT: B 582 MET cc_start: 0.8548 (tpp) cc_final: 0.8202 (tpp) REVERT: B 608 ASN cc_start: 0.8536 (t0) cc_final: 0.8281 (t0) REVERT: B 714 ARG cc_start: 0.8337 (mtp85) cc_final: 0.8017 (mtt-85) outliers start: 49 outliers final: 37 residues processed: 204 average time/residue: 0.0928 time to fit residues: 27.4434 Evaluate side-chains 198 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111097 restraints weight = 15155.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113178 restraints weight = 10722.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.114486 restraints weight = 8405.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115513 restraints weight = 7124.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116415 restraints weight = 6298.704| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10780 Z= 0.163 Angle : 0.629 7.966 14643 Z= 0.311 Chirality : 0.041 0.184 1681 Planarity : 0.004 0.057 1892 Dihedral : 6.316 128.087 1514 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.67 % Allowed : 24.84 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1329 helix: 1.53 (0.20), residues: 687 sheet: -0.99 (0.54), residues: 94 loop : -2.20 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.009 0.001 TYR A 533 PHE 0.023 0.001 PHE B 72 TRP 0.017 0.002 TRP B 658 HIS 0.016 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00389 (10776) covalent geometry : angle 0.62876 (14643) hydrogen bonds : bond 0.03228 ( 499) hydrogen bonds : angle 3.58900 ( 1452) metal coordination : bond 0.00253 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.256 Fit side-chains REVERT: A 96 ARG cc_start: 0.7340 (ttm170) cc_final: 0.6858 (ttm170) REVERT: A 165 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8096 (tp40) REVERT: A 240 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 287 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 113 GLU cc_start: 0.7913 (tp30) cc_final: 0.7628 (tp30) REVERT: B 582 MET cc_start: 0.8449 (tpp) cc_final: 0.8124 (tpp) REVERT: B 608 ASN cc_start: 0.8562 (t0) cc_final: 0.8282 (t0) REVERT: B 714 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8056 (mtt-85) outliers start: 51 outliers final: 41 residues processed: 200 average time/residue: 0.0903 time to fit residues: 25.9100 Evaluate side-chains 201 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 0.0870 chunk 117 optimal weight: 0.0870 chunk 106 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 540 HIS B 231 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115354 restraints weight = 15111.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117515 restraints weight = 10563.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119048 restraints weight = 8222.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119949 restraints weight = 6873.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120827 restraints weight = 6086.922| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10780 Z= 0.112 Angle : 0.599 7.910 14643 Z= 0.295 Chirality : 0.040 0.174 1681 Planarity : 0.004 0.052 1892 Dihedral : 6.146 126.039 1514 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.57 % Allowed : 26.12 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1329 helix: 1.66 (0.20), residues: 689 sheet: -0.54 (0.58), residues: 86 loop : -2.15 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.008 0.001 TYR B 721 PHE 0.019 0.001 PHE B 72 TRP 0.019 0.001 TRP B 658 HIS 0.004 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00243 (10776) covalent geometry : angle 0.59940 (14643) hydrogen bonds : bond 0.02934 ( 499) hydrogen bonds : angle 3.51961 ( 1452) metal coordination : bond 0.00138 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.412 Fit side-chains REVERT: A 96 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6864 (ttm170) REVERT: A 240 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8314 (pp) REVERT: B 225 HIS cc_start: 0.7645 (m90) cc_final: 0.7436 (m90) REVERT: B 582 MET cc_start: 0.8501 (tpp) cc_final: 0.8221 (tpp) REVERT: B 608 ASN cc_start: 0.8501 (t0) cc_final: 0.8248 (t0) REVERT: B 714 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7970 (mtt-85) outliers start: 39 outliers final: 37 residues processed: 188 average time/residue: 0.0933 time to fit residues: 25.1919 Evaluate side-chains 194 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 0.0050 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 624 ASN B 770 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113994 restraints weight = 15003.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116107 restraints weight = 10538.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.117432 restraints weight = 8183.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.118700 restraints weight = 6897.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119284 restraints weight = 6022.154| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10780 Z= 0.128 Angle : 0.610 8.318 14643 Z= 0.299 Chirality : 0.040 0.175 1681 Planarity : 0.004 0.052 1892 Dihedral : 6.131 125.951 1514 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.76 % Allowed : 26.03 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1329 helix: 1.69 (0.20), residues: 691 sheet: -0.52 (0.58), residues: 85 loop : -2.10 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.008 0.001 TYR B 721 PHE 0.019 0.001 PHE B 72 TRP 0.019 0.002 TRP B 658 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00301 (10776) covalent geometry : angle 0.60997 (14643) hydrogen bonds : bond 0.03002 ( 499) hydrogen bonds : angle 3.51209 ( 1452) metal coordination : bond 0.00162 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.379 Fit side-chains REVERT: A 96 ARG cc_start: 0.7312 (ttm170) cc_final: 0.6841 (ttm170) REVERT: A 240 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8327 (pp) REVERT: B 225 HIS cc_start: 0.7735 (m90) cc_final: 0.7516 (m90) REVERT: B 582 MET cc_start: 0.8491 (tpp) cc_final: 0.8201 (tpp) REVERT: B 714 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7926 (mtt-85) outliers start: 41 outliers final: 35 residues processed: 196 average time/residue: 0.0949 time to fit residues: 26.5129 Evaluate side-chains 196 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.115078 restraints weight = 15103.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.117207 restraints weight = 10587.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.118768 restraints weight = 8215.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119626 restraints weight = 6829.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120397 restraints weight = 6084.433| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10780 Z= 0.126 Angle : 0.625 13.632 14643 Z= 0.306 Chirality : 0.041 0.270 1681 Planarity : 0.004 0.049 1892 Dihedral : 6.083 125.814 1513 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.39 % Allowed : 26.76 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1329 helix: 1.68 (0.20), residues: 691 sheet: -0.46 (0.59), residues: 85 loop : -2.05 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 115 TYR 0.008 0.001 TYR B 766 PHE 0.020 0.001 PHE B 72 TRP 0.019 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00295 (10776) covalent geometry : angle 0.62484 (14643) hydrogen bonds : bond 0.02997 ( 499) hydrogen bonds : angle 3.56751 ( 1452) metal coordination : bond 0.00161 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.00 seconds wall clock time: 27 minutes 54.37 seconds (1674.37 seconds total)