Starting phenix.real_space_refine on Tue Nov 18 05:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eoc_19851/11_2025/9eoc_19851.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eoc_19851/11_2025/9eoc_19851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eoc_19851/11_2025/9eoc_19851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eoc_19851/11_2025/9eoc_19851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eoc_19851/11_2025/9eoc_19851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eoc_19851/11_2025/9eoc_19851.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 83 5.16 5 C 7268 2.51 5 N 1972 2.21 5 O 2113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11437 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3917 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 26, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 8, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3717 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 3802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3802 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 543} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1092 Unresolved non-hydrogen dihedrals: 706 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 9, 'GLU:plan': 26, 'PHE:plan': 13, 'ARG:plan': 22, 'TRP:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 15, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 537 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 0.26 Number of scatterers: 11437 At special positions: 0 Unit cell: (114.8, 125.46, 215.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 83 16.00 Mg 1 11.99 O 2113 8.00 N 1972 7.00 C 7268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 400.2 milliseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 55.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 17 through 22 removed outlier: 4.021A pdb=" N GLU A 22 " --> pdb=" O TYR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 70 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.660A pdb=" N CYS A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 168 through 193 removed outlier: 3.926A pdb=" N ASN A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.843A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 removed outlier: 3.503A pdb=" N VAL A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 414 through 425 Processing helix chain 'A' and resid 443 through 456 removed outlier: 3.546A pdb=" N THR A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 473 removed outlier: 4.106A pdb=" N MET A 471 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA A 473 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.897A pdb=" N VAL A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.518A pdb=" N ALA A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.128A pdb=" N SER B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 160 through 167 removed outlier: 3.780A pdb=" N GLN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.628A pdb=" N LEU B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.810A pdb=" N LEU B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 448 Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.507A pdb=" N LEU B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.848A pdb=" N ALA B 476 " --> pdb=" O HIS B 472 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 18 removed outlier: 3.744A pdb=" N ASP D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.623A pdb=" N GLN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.745A pdb=" N LEU D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 124 through 139 Processing helix chain 'D' and resid 140 through 145 removed outlier: 4.033A pdb=" N VAL D 144 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN D 145 " --> pdb=" O THR D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 191 through 212 Processing helix chain 'D' and resid 254 through 270 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 303 through 329 removed outlier: 4.201A pdb=" N THR D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 426 removed outlier: 3.580A pdb=" N VAL D 409 " --> pdb=" O ASN D 405 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 440 Processing helix chain 'D' and resid 446 through 460 Processing helix chain 'D' and resid 462 through 476 Processing helix chain 'D' and resid 494 through 506 removed outlier: 3.588A pdb=" N LEU D 506 " --> pdb=" O CYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 520 Processing helix chain 'D' and resid 521 through 523 No H-bonds generated for 'chain 'D' and resid 521 through 523' Processing helix chain 'D' and resid 556 through 577 Proline residue: D 562 - end of helix Processing helix chain 'D' and resid 583 through 592 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.648A pdb=" N TYR D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 638 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 684 through 686 No H-bonds generated for 'chain 'D' and resid 684 through 686' Processing helix chain 'D' and resid 689 through 701 Processing helix chain 'D' and resid 703 through 709 removed outlier: 4.429A pdb=" N GLN D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.928A pdb=" N THR A 231 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 234 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 222 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 5.741A pdb=" N HIS A 208 " --> pdb=" O VAL A 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 286 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 319 removed outlier: 4.491A pdb=" N LEU A 361 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 364 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 373 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER A 374 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 333 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 67 removed outlier: 6.337A pdb=" N MET B 63 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL B 55 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU B 53 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 4 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 114 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 6 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 151 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN B 184 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 152 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 186 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 154 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 17 removed outlier: 4.318A pdb=" N TYR B 25 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 218 removed outlier: 4.283A pdb=" N PHE B 212 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B 269 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 348 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TRP B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER B 338 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N MET B 322 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 323 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 256 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 325 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 252 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY B 329 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ASP B 250 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LEU B 251 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 215 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE B 253 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 217 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY B 255 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 345 through 350 removed outlier: 3.876A pdb=" N ASP D 549 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 552 " --> pdb=" O VAL D 397 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3795 1.34 - 1.46: 2022 1.46 - 1.58: 5711 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 11653 Sorted by residual: bond pdb=" C ASP B 167 " pdb=" O ASP B 167 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.30e-02 5.92e+03 9.60e-01 bond pdb=" C VAL B 9 " pdb=" O VAL B 9 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.82e-01 bond pdb=" CG GLU D 514 " pdb=" CD GLU D 514 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.42e-01 bond pdb=" CA GLU A 233 " pdb=" C GLU A 233 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.20e-02 6.94e+03 8.33e-01 bond pdb=" CG1 ILE A 262 " pdb=" CD1 ILE A 262 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.30e-01 ... (remaining 11648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15636 1.94 - 3.87: 206 3.87 - 5.81: 23 5.81 - 7.75: 7 7.75 - 9.68: 3 Bond angle restraints: 15875 Sorted by residual: angle pdb=" C ARG D 639 " pdb=" N THR D 640 " pdb=" CA THR D 640 " ideal model delta sigma weight residual 122.44 115.11 7.33 1.19e+00 7.06e-01 3.80e+01 angle pdb=" C LEU D 490 " pdb=" CA LEU D 490 " pdb=" CB LEU D 490 " ideal model delta sigma weight residual 116.34 110.58 5.76 1.40e+00 5.10e-01 1.69e+01 angle pdb=" C ASP B 84 " pdb=" N LYS B 85 " pdb=" CA LYS B 85 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA LEU D 426 " pdb=" CB LEU D 426 " pdb=" CG LEU D 426 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 angle pdb=" N PRO A 228 " pdb=" CA PRO A 228 " pdb=" C PRO A 228 " ideal model delta sigma weight residual 114.68 111.83 2.85 1.04e+00 9.25e-01 7.51e+00 ... (remaining 15870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6088 17.79 - 35.58: 716 35.58 - 53.38: 187 53.38 - 71.17: 39 71.17 - 88.96: 16 Dihedral angle restraints: 7046 sinusoidal: 2462 harmonic: 4584 Sorted by residual: dihedral pdb=" CA GLN D 641 " pdb=" C GLN D 641 " pdb=" N GLU D 642 " pdb=" CA GLU D 642 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU D 426 " pdb=" C LEU D 426 " pdb=" N GLU D 427 " pdb=" CA GLU D 427 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU A 142 " pdb=" CG GLU A 142 " pdb=" CD GLU A 142 " pdb=" OE1 GLU A 142 " ideal model delta sinusoidal sigma weight residual 0.00 88.96 -88.96 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1497 0.045 - 0.090: 318 0.090 - 0.136: 79 0.136 - 0.181: 0 0.181 - 0.226: 1 Chirality restraints: 1895 Sorted by residual: chirality pdb=" CB ILE D 207 " pdb=" CA ILE D 207 " pdb=" CG1 ILE D 207 " pdb=" CG2 ILE D 207 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE B 306 " pdb=" N ILE B 306 " pdb=" C ILE B 306 " pdb=" CB ILE B 306 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1892 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 597 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO D 598 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 598 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 598 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 233 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 227 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 228 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " 0.019 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 58 2.51 - 3.11: 8331 3.11 - 3.71: 17613 3.71 - 4.30: 23919 4.30 - 4.90: 41100 Nonbonded interactions: 91021 Sorted by model distance: nonbonded pdb=" OG SER B 12 " pdb="MG MG B 601 " model vdw 1.914 2.170 nonbonded pdb=" OG1 THR B 86 " pdb="MG MG B 601 " model vdw 1.923 2.170 nonbonded pdb=" O GLU B 49 " pdb=" OH TYR B 70 " model vdw 2.211 3.040 nonbonded pdb=" O ASP A 509 " pdb=" OH TYR A 529 " model vdw 2.225 3.040 nonbonded pdb=" O THR B 404 " pdb=" OG1 THR B 404 " model vdw 2.233 3.040 ... (remaining 91016 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.960 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.003 0.036 11653 Z= 0.146 Angle : 0.573 9.681 15875 Z= 0.294 Chirality : 0.039 0.226 1895 Planarity : 0.004 0.057 2044 Dihedral : 17.344 88.960 4042 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.57 % Allowed : 27.56 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1525 helix: 1.99 (0.19), residues: 774 sheet: -1.49 (0.41), residues: 163 loop : -1.53 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 541 TYR 0.018 0.001 TYR A 62 PHE 0.015 0.001 PHE D 572 TRP 0.016 0.001 TRP A 318 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00335 (11653) covalent geometry : angle 0.57301 (15875) hydrogen bonds : bond 0.14808 ( 664) hydrogen bonds : angle 6.21653 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 450 ASP cc_start: 0.6929 (m-30) cc_final: 0.6719 (m-30) REVERT: A 536 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 250 ASP cc_start: 0.8448 (p0) cc_final: 0.8169 (p0) REVERT: D 394 ARG cc_start: 0.6461 (mmm-85) cc_final: 0.4986 (mtm180) outliers start: 40 outliers final: 35 residues processed: 174 average time/residue: 0.0947 time to fit residues: 24.9229 Evaluate side-chains 173 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 629 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS D 614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.195975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160114 restraints weight = 14721.262| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.77 r_work: 0.3518 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11653 Z= 0.221 Angle : 0.607 7.633 15875 Z= 0.306 Chirality : 0.042 0.146 1895 Planarity : 0.004 0.039 2044 Dihedral : 6.290 57.747 1681 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.03 % Favored : 93.90 % Rotamer: Outliers : 4.73 % Allowed : 25.42 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1525 helix: 1.87 (0.19), residues: 806 sheet: -1.39 (0.41), residues: 164 loop : -1.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 397 TYR 0.021 0.002 TYR A 62 PHE 0.015 0.002 PHE A 421 TRP 0.019 0.002 TRP A 318 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00534 (11653) covalent geometry : angle 0.60676 (15875) hydrogen bonds : bond 0.04300 ( 664) hydrogen bonds : angle 4.78351 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: A 450 ASP cc_start: 0.6860 (m-30) cc_final: 0.6626 (m-30) REVERT: A 536 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 537 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: B 17 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8077 (m) REVERT: B 144 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6373 (tp) REVERT: B 157 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7146 (ptp) REVERT: B 250 ASP cc_start: 0.8302 (p0) cc_final: 0.7962 (p0) REVERT: B 487 LYS cc_start: 0.8454 (ptmm) cc_final: 0.8176 (pttp) REVERT: D 394 ARG cc_start: 0.6475 (mmm-85) cc_final: 0.4421 (mtm180) REVERT: D 446 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6879 (tt) REVERT: D 574 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6433 (mp) outliers start: 53 outliers final: 28 residues processed: 195 average time/residue: 0.0962 time to fit residues: 28.2083 Evaluate side-chains 177 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 0.0970 chunk 72 optimal weight: 0.0980 chunk 109 optimal weight: 30.0000 chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 106 optimal weight: 10.0000 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175998 restraints weight = 14990.212| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.41 r_work: 0.3675 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11653 Z= 0.134 Angle : 0.538 7.906 15875 Z= 0.270 Chirality : 0.040 0.177 1895 Planarity : 0.004 0.042 2044 Dihedral : 5.281 54.767 1649 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.62 % Rotamer: Outliers : 5.35 % Allowed : 24.09 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1525 helix: 2.18 (0.19), residues: 802 sheet: -1.34 (0.41), residues: 155 loop : -1.58 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 541 TYR 0.017 0.001 TYR A 62 PHE 0.015 0.001 PHE A 421 TRP 0.015 0.001 TRP A 318 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00311 (11653) covalent geometry : angle 0.53800 (15875) hydrogen bonds : bond 0.03552 ( 664) hydrogen bonds : angle 4.40441 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 450 ASP cc_start: 0.6907 (m-30) cc_final: 0.6681 (m-30) REVERT: A 536 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 537 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 3 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8452 (m) REVERT: B 144 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6283 (tp) REVERT: B 157 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6893 (ptp) REVERT: B 250 ASP cc_start: 0.8330 (p0) cc_final: 0.8031 (p0) REVERT: D 394 ARG cc_start: 0.6422 (mmm-85) cc_final: 0.4643 (mtm180) REVERT: D 574 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6303 (mp) outliers start: 60 outliers final: 30 residues processed: 205 average time/residue: 0.0919 time to fit residues: 28.6624 Evaluate side-chains 177 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 148 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.197442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167456 restraints weight = 14967.603| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.50 r_work: 0.3606 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11653 Z= 0.264 Angle : 0.642 8.248 15875 Z= 0.321 Chirality : 0.043 0.149 1895 Planarity : 0.004 0.046 2044 Dihedral : 5.402 56.497 1645 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 5.71 % Allowed : 24.17 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1525 helix: 2.02 (0.19), residues: 802 sheet: -1.49 (0.40), residues: 164 loop : -1.77 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.022 0.002 TYR A 62 PHE 0.019 0.002 PHE B 228 TRP 0.021 0.002 TRP A 318 HIS 0.007 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00648 (11653) covalent geometry : angle 0.64227 (15875) hydrogen bonds : bond 0.04039 ( 664) hydrogen bonds : angle 4.52627 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 0.457 Fit side-chains REVERT: A 100 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 450 ASP cc_start: 0.6806 (m-30) cc_final: 0.6534 (m-30) REVERT: A 537 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: B 3 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8674 (m) REVERT: B 144 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6458 (tp) REVERT: B 157 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6999 (ptp) REVERT: B 250 ASP cc_start: 0.8420 (p0) cc_final: 0.8143 (p0) REVERT: D 394 ARG cc_start: 0.6473 (mmm-85) cc_final: 0.4954 (mtm180) outliers start: 64 outliers final: 45 residues processed: 197 average time/residue: 0.0959 time to fit residues: 28.3044 Evaluate side-chains 189 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 50.0000 chunk 34 optimal weight: 0.1980 chunk 87 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.0370 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 110 optimal weight: 50.0000 chunk 31 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177899 restraints weight = 14962.770| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.36 r_work: 0.3657 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11653 Z= 0.128 Angle : 0.548 9.575 15875 Z= 0.271 Chirality : 0.039 0.156 1895 Planarity : 0.004 0.047 2044 Dihedral : 4.986 58.109 1642 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 4.82 % Allowed : 25.07 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1525 helix: 2.22 (0.19), residues: 803 sheet: -1.43 (0.41), residues: 155 loop : -1.57 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.017 0.001 TYR A 62 PHE 0.016 0.001 PHE A 421 TRP 0.015 0.001 TRP A 318 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00296 (11653) covalent geometry : angle 0.54764 (15875) hydrogen bonds : bond 0.03356 ( 664) hydrogen bonds : angle 4.23326 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: A 450 ASP cc_start: 0.6929 (m-30) cc_final: 0.6653 (m-30) REVERT: A 536 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 537 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: B 3 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8447 (m) REVERT: B 144 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6207 (tp) REVERT: B 157 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7007 (ptp) REVERT: B 250 ASP cc_start: 0.8244 (p0) cc_final: 0.7927 (p0) REVERT: B 487 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8071 (pttp) REVERT: D 325 TYR cc_start: 0.7801 (t80) cc_final: 0.7431 (t80) REVERT: D 394 ARG cc_start: 0.6446 (mmm-85) cc_final: 0.4824 (mtm180) REVERT: D 574 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6382 (mp) outliers start: 54 outliers final: 37 residues processed: 195 average time/residue: 0.0976 time to fit residues: 28.4100 Evaluate side-chains 187 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 50.0000 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 84 optimal weight: 0.0970 chunk 5 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 132 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.201607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173129 restraints weight = 15014.250| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.52 r_work: 0.3581 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11653 Z= 0.179 Angle : 0.573 9.249 15875 Z= 0.284 Chirality : 0.041 0.189 1895 Planarity : 0.004 0.039 2044 Dihedral : 5.047 59.794 1642 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 4.82 % Allowed : 24.98 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1525 helix: 2.24 (0.19), residues: 801 sheet: -1.41 (0.40), residues: 164 loop : -1.61 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.019 0.001 TYR A 62 PHE 0.017 0.002 PHE A 421 TRP 0.018 0.002 TRP A 318 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00434 (11653) covalent geometry : angle 0.57285 (15875) hydrogen bonds : bond 0.03488 ( 664) hydrogen bonds : angle 4.25206 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: A 450 ASP cc_start: 0.7032 (m-30) cc_final: 0.6804 (m-30) REVERT: A 536 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 537 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: B 144 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6324 (tp) REVERT: B 157 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7049 (ptp) REVERT: B 250 ASP cc_start: 0.8447 (p0) cc_final: 0.8141 (p0) REVERT: B 487 LYS cc_start: 0.8494 (ptmm) cc_final: 0.8153 (pttp) REVERT: D 325 TYR cc_start: 0.7835 (t80) cc_final: 0.7493 (t80) REVERT: D 394 ARG cc_start: 0.6462 (mmm-85) cc_final: 0.4831 (mtm180) REVERT: D 574 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6369 (mp) outliers start: 54 outliers final: 39 residues processed: 190 average time/residue: 0.0941 time to fit residues: 26.8628 Evaluate side-chains 184 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159016 restraints weight = 14682.015| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.65 r_work: 0.3454 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11653 Z= 0.189 Angle : 0.580 9.573 15875 Z= 0.289 Chirality : 0.041 0.189 1895 Planarity : 0.004 0.035 2044 Dihedral : 5.086 59.121 1642 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.35 % Allowed : 24.44 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1525 helix: 2.22 (0.19), residues: 800 sheet: -1.38 (0.40), residues: 164 loop : -1.62 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.019 0.001 TYR A 62 PHE 0.018 0.002 PHE A 421 TRP 0.018 0.002 TRP A 318 HIS 0.007 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00460 (11653) covalent geometry : angle 0.58016 (15875) hydrogen bonds : bond 0.03515 ( 664) hydrogen bonds : angle 4.27932 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: A 536 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 537 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: B 3 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8580 (m) REVERT: B 46 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8972 (t80) REVERT: B 144 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6271 (tp) REVERT: B 157 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7404 (ptp) REVERT: B 250 ASP cc_start: 0.8293 (p0) cc_final: 0.7977 (p0) REVERT: B 417 GLN cc_start: 0.7496 (mm110) cc_final: 0.6304 (mt0) REVERT: B 487 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8293 (pttp) REVERT: D 325 TYR cc_start: 0.7984 (t80) cc_final: 0.7584 (t80) REVERT: D 394 ARG cc_start: 0.6429 (mmm-85) cc_final: 0.4832 (mtm180) REVERT: D 574 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6533 (mp) outliers start: 60 outliers final: 44 residues processed: 192 average time/residue: 0.1025 time to fit residues: 29.1284 Evaluate side-chains 190 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 0.0970 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 50.0000 chunk 127 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 73 optimal weight: 0.0980 chunk 113 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170316 restraints weight = 14715.153| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.35 r_work: 0.3556 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11653 Z= 0.140 Angle : 0.546 10.814 15875 Z= 0.271 Chirality : 0.040 0.189 1895 Planarity : 0.004 0.035 2044 Dihedral : 4.902 57.836 1641 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.00 % Allowed : 25.07 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1525 helix: 2.30 (0.19), residues: 802 sheet: -1.33 (0.41), residues: 155 loop : -1.52 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.017 0.001 TYR A 62 PHE 0.016 0.001 PHE A 421 TRP 0.016 0.001 TRP A 318 HIS 0.007 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00334 (11653) covalent geometry : angle 0.54552 (15875) hydrogen bonds : bond 0.03275 ( 664) hydrogen bonds : angle 4.14839 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: A 450 ASP cc_start: 0.7108 (m-30) cc_final: 0.6873 (m-30) REVERT: A 536 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 537 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: B 3 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (m) REVERT: B 46 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8952 (t80) REVERT: B 144 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6378 (tp) REVERT: B 157 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7425 (ptp) REVERT: B 250 ASP cc_start: 0.8472 (p0) cc_final: 0.8182 (p0) REVERT: B 417 GLN cc_start: 0.7641 (mm110) cc_final: 0.6393 (mt0) REVERT: B 487 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8343 (pttp) REVERT: D 325 TYR cc_start: 0.8030 (t80) cc_final: 0.7503 (t80) REVERT: D 394 ARG cc_start: 0.6370 (mmm-85) cc_final: 0.4679 (mtm180) REVERT: D 574 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6580 (mp) outliers start: 56 outliers final: 44 residues processed: 190 average time/residue: 0.1002 time to fit residues: 28.1334 Evaluate side-chains 190 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 43 optimal weight: 0.0050 chunk 68 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.194661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170160 restraints weight = 14537.051| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.32 r_work: 0.3560 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11653 Z= 0.146 Angle : 0.550 10.267 15875 Z= 0.273 Chirality : 0.040 0.194 1895 Planarity : 0.004 0.035 2044 Dihedral : 4.858 55.143 1641 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.08 % Allowed : 24.98 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1525 helix: 2.31 (0.19), residues: 802 sheet: -1.29 (0.41), residues: 155 loop : -1.51 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.018 0.001 TYR A 62 PHE 0.016 0.001 PHE A 421 TRP 0.016 0.001 TRP A 318 HIS 0.006 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00351 (11653) covalent geometry : angle 0.54977 (15875) hydrogen bonds : bond 0.03270 ( 664) hydrogen bonds : angle 4.11237 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 450 ASP cc_start: 0.7177 (m-30) cc_final: 0.6932 (m-30) REVERT: A 536 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 537 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: B 3 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8646 (m) REVERT: B 46 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (t80) REVERT: B 144 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6348 (tp) REVERT: B 157 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7468 (ptp) REVERT: B 250 ASP cc_start: 0.8490 (p0) cc_final: 0.8201 (p0) REVERT: B 417 GLN cc_start: 0.7630 (mm110) cc_final: 0.6389 (mt0) REVERT: B 487 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8318 (pttp) REVERT: D 325 TYR cc_start: 0.8006 (t80) cc_final: 0.7474 (t80) REVERT: D 394 ARG cc_start: 0.6362 (mmm-85) cc_final: 0.4691 (mtm180) REVERT: D 574 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6609 (mp) outliers start: 57 outliers final: 44 residues processed: 193 average time/residue: 0.0995 time to fit residues: 28.3796 Evaluate side-chains 194 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 0.0010 chunk 36 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 100 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164459 restraints weight = 14781.568| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.48 r_work: 0.3515 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11653 Z= 0.184 Angle : 0.586 10.006 15875 Z= 0.289 Chirality : 0.041 0.196 1895 Planarity : 0.004 0.060 2044 Dihedral : 4.876 57.034 1639 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.91 % Allowed : 25.25 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.23), residues: 1525 helix: 2.31 (0.19), residues: 797 sheet: -1.34 (0.40), residues: 164 loop : -1.51 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.020 0.001 TYR A 62 PHE 0.017 0.002 PHE A 421 TRP 0.018 0.002 TRP A 318 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00450 (11653) covalent geometry : angle 0.58557 (15875) hydrogen bonds : bond 0.03455 ( 664) hydrogen bonds : angle 4.21102 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: A 450 ASP cc_start: 0.7258 (m-30) cc_final: 0.7031 (m-30) REVERT: A 536 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 537 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: B 3 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8664 (m) REVERT: B 46 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8954 (t80) REVERT: B 157 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7604 (ptp) REVERT: B 250 ASP cc_start: 0.8580 (p0) cc_final: 0.8311 (p0) REVERT: B 417 GLN cc_start: 0.7688 (mm110) cc_final: 0.6456 (mt0) REVERT: B 487 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8307 (pttp) REVERT: D 325 TYR cc_start: 0.8038 (t80) cc_final: 0.7580 (t80) REVERT: D 394 ARG cc_start: 0.6397 (mmm-85) cc_final: 0.4710 (mtm180) REVERT: D 523 MET cc_start: 0.6021 (ttt) cc_final: 0.5738 (ttt) REVERT: D 574 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6730 (mp) outliers start: 55 outliers final: 44 residues processed: 188 average time/residue: 0.0980 time to fit residues: 27.2994 Evaluate side-chains 190 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 684 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 chunk 71 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 82 optimal weight: 0.0870 chunk 51 optimal weight: 0.2980 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN D 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.196975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172886 restraints weight = 14762.996| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.37 r_work: 0.3582 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11653 Z= 0.104 Angle : 0.523 9.886 15875 Z= 0.262 Chirality : 0.039 0.194 1895 Planarity : 0.004 0.055 2044 Dihedral : 4.605 52.078 1639 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.03 % Allowed : 27.21 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.23), residues: 1525 helix: 2.45 (0.19), residues: 796 sheet: -1.30 (0.41), residues: 156 loop : -1.34 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.015 0.001 TYR A 62 PHE 0.016 0.001 PHE A 421 TRP 0.012 0.001 TRP A 318 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00237 (11653) covalent geometry : angle 0.52309 (15875) hydrogen bonds : bond 0.02963 ( 664) hydrogen bonds : angle 3.99581 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.61 seconds wall clock time: 62 minutes 18.42 seconds (3738.42 seconds total)