Starting phenix.real_space_refine on Mon Jun 9 13:13:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5u_30093/06_2025/6m5u_30093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5u_30093/06_2025/6m5u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m5u_30093/06_2025/6m5u_30093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5u_30093/06_2025/6m5u_30093.map" model { file = "/net/cci-nas-00/data/ceres_data/6m5u_30093/06_2025/6m5u_30093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5u_30093/06_2025/6m5u_30093.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} 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: {'ARG:plan': 1, 'ASP:plan': 4} 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: 7.01, per 1000 atoms: 0.66 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: 2.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.00 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: 3.19 Time building geometry restraints manager: 3.17 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.120 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.670 ------------------------------------------------------------------------------- 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 : 18.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP A 308 HIS 0.009 0.001 HIS A 540 PHE 0.023 0.002 PHE A 634 TYR 0.019 0.002 TYR A 507 ARG 0.005 0.000 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.13153 ( 499) hydrogen bonds : angle 5.74664 ( 1452) metal coordination : bond 0.32793 ( 4) covalent geometry : bond 0.00745 (10776) covalent geometry : angle 0.86205 (14643) *********************** 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 : 1.099 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: 0.8481 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 529 MET cc_start: 0.8908 (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: 0.2748 time to fit residues: 97.5454 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 : 1.154 ------------------------------------------------------------------------------- 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 113 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 = 0.3421 r_free = 0.3421 target = 0.134150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.113830 restraints weight = 15211.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116099 restraints weight = 10534.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117690 restraints weight = 8110.993| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10780 Z= 0.135 Angle : 0.671 9.503 14643 Z= 0.332 Chirality : 0.041 0.209 1681 Planarity : 0.005 0.053 1892 Dihedral : 8.550 129.024 1564 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.58 % Allowed : 19.62 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1329 helix: 0.31 (0.20), residues: 683 sheet: -1.61 (0.50), residues: 102 loop : -2.62 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 308 HIS 0.006 0.001 HIS A 569 PHE 0.017 0.001 PHE A 633 TYR 0.010 0.001 TYR B 721 ARG 0.005 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 499) hydrogen bonds : angle 4.09622 ( 1452) metal coordination : bond 0.01586 ( 4) covalent geometry : bond 0.00296 (10776) covalent geometry : angle 0.67149 (14643) *********************** 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: 50 poor density : 177 time to evaluate : 1.081 Fit side-chains REVERT: A 141 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8161 (mp) REVERT: A 165 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8486 (tp40) REVERT: A 240 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8385 (pp) REVERT: A 304 CYS cc_start: 0.8200 (p) cc_final: 0.7763 (p) REVERT: A 709 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6264 (ttp) REVERT: B 375 MET cc_start: 0.8306 (tpp) cc_final: 0.7995 (tpp) REVERT: B 582 MET cc_start: 0.8577 (tpp) cc_final: 0.8149 (tpp) REVERT: B 646 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: B 714 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8198 (mtt-85) outliers start: 50 outliers final: 25 residues processed: 212 average time/residue: 0.2284 time to fit residues: 67.7593 Evaluate side-chains 184 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 MET 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 374 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 495 ASP 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 116 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 86 ASN B 21 GLN B 125 GLN B 237 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106188 restraints weight = 15597.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.108263 restraints weight = 11001.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.109663 restraints weight = 8635.503| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 10780 Z= 0.249 Angle : 0.722 10.773 14643 Z= 0.361 Chirality : 0.045 0.212 1681 Planarity : 0.005 0.052 1892 Dihedral : 7.357 132.761 1521 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.31 % Favored : 89.62 % Rotamer: Outliers : 6.87 % Allowed : 20.44 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1329 helix: 0.55 (0.20), residues: 687 sheet: -1.59 (0.53), residues: 94 loop : -2.58 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 308 HIS 0.007 0.001 HIS A 560 PHE 0.024 0.002 PHE A 633 TYR 0.010 0.001 TYR B 25 ARG 0.005 0.000 ARG B 506 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 499) hydrogen bonds : angle 4.08462 ( 1452) metal coordination : bond 0.00588 ( 4) covalent geometry : bond 0.00599 (10776) covalent geometry : angle 0.72217 (14643) *********************** 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 231 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 156 time to evaluate : 1.207 Fit side-chains REVERT: A 115 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8114 (mtp85) REVERT: A 124 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: A 149 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7023 (ptp-110) REVERT: A 165 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8481 (tp40) REVERT: A 240 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8547 (pp) REVERT: B 21 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: B 72 PHE cc_start: 0.8625 (t80) cc_final: 0.8421 (t80) REVERT: B 617 HIS cc_start: 0.9161 (OUTLIER) cc_final: 0.8942 (m170) REVERT: B 646 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: B 714 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8229 (mtt-85) outliers start: 75 outliers final: 50 residues processed: 212 average time/residue: 0.2324 time to fit residues: 70.1164 Evaluate side-chains 200 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL 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 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 409 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 B residue 21 GLN 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 182 SER Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 CYS 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 386 THR 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 496 VAL 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 617 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 730 THR 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 98 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.112153 restraints weight = 15093.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114382 restraints weight = 10446.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115787 restraints weight = 8068.546| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10780 Z= 0.124 Angle : 0.627 8.217 14643 Z= 0.311 Chirality : 0.041 0.211 1681 Planarity : 0.004 0.047 1892 Dihedral : 6.691 131.359 1516 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.77 % Allowed : 22.82 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1329 helix: 0.99 (0.20), residues: 683 sheet: -0.81 (0.61), residues: 74 loop : -2.24 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 308 HIS 0.005 0.001 HIS B 402 PHE 0.020 0.001 PHE A 633 TYR 0.009 0.001 TYR B 132 ARG 0.004 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 499) hydrogen bonds : angle 3.80394 ( 1452) metal coordination : bond 0.00193 ( 4) covalent geometry : bond 0.00279 (10776) covalent geometry : angle 0.62708 (14643) *********************** 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 221 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6877 (ttm170) REVERT: A 141 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 165 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8390 (tp40) REVERT: A 240 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8377 (pp) REVERT: B 582 MET cc_start: 0.8536 (tpp) cc_final: 0.8153 (tpp) REVERT: B 714 ARG cc_start: 0.8547 (mtp85) cc_final: 0.8144 (mtt-85) outliers start: 52 outliers final: 37 residues processed: 207 average time/residue: 0.2329 time to fit residues: 67.3045 Evaluate side-chains 191 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 ILE 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 656 VAL Chi-restraints excluded: chain A residue 667 VAL 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 190 LEU Chi-restraints excluded: chain B residue 199 VAL 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 496 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 648 ILE 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 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 4 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.107054 restraints weight = 15366.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109106 restraints weight = 10859.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.110388 restraints weight = 8530.165| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10780 Z= 0.218 Angle : 0.694 9.656 14643 Z= 0.343 Chirality : 0.043 0.169 1681 Planarity : 0.005 0.055 1892 Dihedral : 6.777 132.007 1513 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.01 % Favored : 89.92 % Rotamer: Outliers : 5.87 % Allowed : 23.01 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1329 helix: 0.96 (0.20), residues: 686 sheet: -1.26 (0.53), residues: 94 loop : -2.38 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 308 HIS 0.006 0.001 HIS A 560 PHE 0.023 0.002 PHE A 633 TYR 0.012 0.001 TYR A 533 ARG 0.005 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 499) hydrogen bonds : angle 3.88382 ( 1452) metal coordination : bond 0.00382 ( 4) covalent geometry : bond 0.00522 (10776) covalent geometry : angle 0.69430 (14643) *********************** 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 225 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 161 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7362 (ttm170) cc_final: 0.6911 (ttm170) REVERT: A 144 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8310 (t80) REVERT: A 165 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8350 (tp40) REVERT: A 240 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8487 (pp) REVERT: B 646 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7566 (mtm-85) REVERT: B 714 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8220 (mtt-85) outliers start: 64 outliers final: 51 residues processed: 210 average time/residue: 0.2301 time to fit residues: 69.3767 Evaluate side-chains 207 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 144 PHE 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 287 THR 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 383 VAL Chi-restraints excluded: chain A residue 409 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 639 GLN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR 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 172 VAL Chi-restraints excluded: chain B residue 182 SER 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 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 496 VAL 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 631 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 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 65 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** B 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.131457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.111266 restraints weight = 15170.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.113353 restraints weight = 10631.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114944 restraints weight = 8281.835| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10780 Z= 0.125 Angle : 0.626 8.509 14643 Z= 0.306 Chirality : 0.041 0.301 1681 Planarity : 0.004 0.047 1892 Dihedral : 6.465 130.188 1513 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.86 % Allowed : 24.75 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1329 helix: 1.21 (0.21), residues: 687 sheet: -0.68 (0.62), residues: 74 loop : -2.30 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 308 HIS 0.005 0.001 HIS B 402 PHE 0.024 0.001 PHE A 541 TYR 0.009 0.001 TYR B 132 ARG 0.005 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 499) hydrogen bonds : angle 3.72605 ( 1452) metal coordination : bond 0.00167 ( 4) covalent geometry : bond 0.00285 (10776) covalent geometry : angle 0.62641 (14643) *********************** 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 231 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6823 (ttm170) REVERT: A 141 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 165 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8356 (tp40) REVERT: A 240 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8390 (pp) REVERT: B 582 MET cc_start: 0.8515 (tpp) cc_final: 0.8179 (tpp) REVERT: B 646 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: B 714 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8090 (mtt-85) outliers start: 53 outliers final: 39 residues processed: 220 average time/residue: 0.2303 time to fit residues: 71.5488 Evaluate side-chains 203 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 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 639 GLN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 VAL 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 199 VAL 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 496 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 648 ILE 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 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 77 optimal weight: 4.9990 chunk 113 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 332 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.130734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110585 restraints weight = 15348.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112668 restraints weight = 10845.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.114128 restraints weight = 8498.844| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10780 Z= 0.143 Angle : 0.634 9.310 14643 Z= 0.311 Chirality : 0.042 0.319 1681 Planarity : 0.004 0.056 1892 Dihedral : 6.416 129.531 1513 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.50 % Favored : 91.42 % Rotamer: Outliers : 5.41 % Allowed : 23.83 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1329 helix: 1.30 (0.21), residues: 686 sheet: -1.16 (0.53), residues: 94 loop : -2.32 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 658 HIS 0.005 0.001 HIS B 402 PHE 0.030 0.001 PHE B 72 TYR 0.008 0.001 TYR B 721 ARG 0.005 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 499) hydrogen bonds : angle 3.68619 ( 1452) metal coordination : bond 0.00248 ( 4) covalent geometry : bond 0.00337 (10776) covalent geometry : angle 0.63418 (14643) *********************** 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 222 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 1.067 Fit side-chains REVERT: A 96 ARG cc_start: 0.7341 (ttm170) cc_final: 0.6837 (ttm170) REVERT: A 124 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: A 141 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 240 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8446 (pp) REVERT: A 287 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8668 (p) REVERT: A 298 PHE cc_start: 0.8828 (t80) cc_final: 0.8561 (t80) REVERT: A 541 PHE cc_start: 0.7043 (t80) cc_final: 0.6762 (t80) REVERT: B 582 MET cc_start: 0.8497 (tpp) cc_final: 0.8145 (tpp) REVERT: B 642 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: B 646 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7555 (mtm-85) REVERT: B 714 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8079 (mtt-85) outliers start: 59 outliers final: 42 residues processed: 207 average time/residue: 0.2214 time to fit residues: 65.7296 Evaluate side-chains 203 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 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 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 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 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 172 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 226 VAL 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 496 VAL 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 642 GLU Chi-restraints excluded: chain B residue 648 ILE 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 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 22 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 0.0270 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115333 restraints weight = 14911.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117481 restraints weight = 10482.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.118806 restraints weight = 8150.557| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10780 Z= 0.111 Angle : 0.617 8.733 14643 Z= 0.300 Chirality : 0.040 0.366 1681 Planarity : 0.004 0.053 1892 Dihedral : 6.127 126.756 1513 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.40 % Allowed : 25.39 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1329 helix: 1.44 (0.21), residues: 691 sheet: -0.93 (0.56), residues: 92 loop : -2.18 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 658 HIS 0.004 0.001 HIS B 402 PHE 0.021 0.001 PHE B 72 TYR 0.010 0.001 TYR B 132 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 499) hydrogen bonds : angle 3.59147 ( 1452) metal coordination : bond 0.00144 ( 4) covalent geometry : bond 0.00241 (10776) covalent geometry : angle 0.61661 (14643) *********************** 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 226 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 1.131 Fit side-chains REVERT: A 96 ARG cc_start: 0.7351 (ttm170) cc_final: 0.6831 (ttm170) REVERT: A 141 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 240 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8326 (pp) REVERT: B 582 MET cc_start: 0.8552 (tpp) cc_final: 0.8203 (tpp) REVERT: B 714 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7922 (mtt-85) REVERT: C 17 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.6690 (pt) outliers start: 48 outliers final: 32 residues processed: 214 average time/residue: 0.2315 time to fit residues: 70.2654 Evaluate side-chains 194 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 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 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 199 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 381 ILE 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 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 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 111 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 117 optimal weight: 0.0670 chunk 61 optimal weight: 0.0870 chunk 78 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.136273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116584 restraints weight = 15174.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.118765 restraints weight = 10584.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120227 restraints weight = 8219.437| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3273 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= 0.114 Angle : 0.630 10.304 14643 Z= 0.305 Chirality : 0.041 0.348 1681 Planarity : 0.004 0.058 1892 Dihedral : 5.916 125.239 1512 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.57 % Allowed : 26.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1329 helix: 1.64 (0.20), residues: 681 sheet: -0.90 (0.56), residues: 93 loop : -2.08 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.020 0.001 PHE A 298 TYR 0.009 0.001 TYR B 132 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 499) hydrogen bonds : angle 3.55189 ( 1452) metal coordination : bond 0.00105 ( 4) covalent geometry : bond 0.00254 (10776) covalent geometry : angle 0.62978 (14643) *********************** 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 209 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 1.066 Fit side-chains REVERT: A 96 ARG cc_start: 0.7307 (ttm170) cc_final: 0.6907 (ttm170) REVERT: A 141 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7817 (mp) REVERT: B 582 MET cc_start: 0.8515 (tpp) cc_final: 0.8190 (tpp) REVERT: B 714 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7909 (mtt-85) outliers start: 39 outliers final: 31 residues processed: 199 average time/residue: 0.2230 time to fit residues: 64.0177 Evaluate side-chains 189 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 235 VAL 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 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 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 199 VAL Chi-restraints excluded: chain B residue 381 ILE 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 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 103 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.0020 chunk 88 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 0.0370 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 540 HIS B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.136320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.116696 restraints weight = 14999.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.118844 restraints weight = 10528.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120382 restraints weight = 8157.721| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10780 Z= 0.118 Angle : 0.653 9.245 14643 Z= 0.318 Chirality : 0.041 0.347 1681 Planarity : 0.004 0.059 1892 Dihedral : 5.857 124.340 1511 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.02 % Allowed : 27.77 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1329 helix: 1.68 (0.20), residues: 687 sheet: -0.59 (0.59), residues: 86 loop : -2.04 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 658 HIS 0.006 0.001 HIS B 535 PHE 0.021 0.001 PHE A 298 TYR 0.011 0.001 TYR A 620 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.02965 ( 499) hydrogen bonds : angle 3.52867 ( 1452) metal coordination : bond 0.00196 ( 4) covalent geometry : bond 0.00267 (10776) covalent geometry : angle 0.65315 (14643) ********************** 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 202 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.069 Fit side-chains REVERT: A 96 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6787 (ttm170) REVERT: A 240 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8220 (pp) REVERT: B 582 MET cc_start: 0.8517 (tpp) cc_final: 0.8211 (tpp) REVERT: B 714 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7896 (mtt-85) outliers start: 33 outliers final: 29 residues processed: 195 average time/residue: 0.2149 time to fit residues: 60.4302 Evaluate side-chains 191 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 601 HIS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 667 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 172 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 496 VAL 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 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 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 540 HIS B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.115916 restraints weight = 15009.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118011 restraints weight = 10588.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.119303 restraints weight = 8273.211| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10780 Z= 0.128 Angle : 0.644 8.595 14643 Z= 0.314 Chirality : 0.041 0.332 1681 Planarity : 0.004 0.060 1892 Dihedral : 5.780 125.193 1509 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.98 % Favored : 91.95 % Rotamer: Outliers : 3.21 % Allowed : 27.77 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1329 helix: 1.62 (0.20), residues: 694 sheet: -0.93 (0.56), residues: 93 loop : -1.97 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 658 HIS 0.005 0.001 HIS B 535 PHE 0.026 0.001 PHE B 72 TYR 0.027 0.001 TYR B 721 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 499) hydrogen bonds : angle 3.52355 ( 1452) metal coordination : bond 0.00162 ( 4) covalent geometry : bond 0.00299 (10776) covalent geometry : angle 0.64419 (14643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.67 seconds wall clock time: 59 minutes 12.10 seconds (3552.10 seconds total)