Starting phenix.real_space_refine on Tue Jul 29 13:04:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eoc_19851/07_2025/9eoc_19851.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eoc_19851/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eoc_19851/07_2025/9eoc_19851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eoc_19851/07_2025/9eoc_19851.map" model { file = "/net/cci-nas-00/data/ceres_data/9eoc_19851/07_2025/9eoc_19851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eoc_19851/07_2025/9eoc_19851.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3} 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, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 15, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 13, 'GLU:plan': 26, 'ARG:plan': 22} 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: 9.68, per 1000 atoms: 0.85 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: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.19 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: 3.58 Time building geometry restraints manager: 3.14 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: 22.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.430 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), 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 TRP 0.016 0.001 TRP A 318 HIS 0.006 0.001 HIS A 8 PHE 0.015 0.001 PHE D 572 TYR 0.018 0.001 TYR A 62 ARG 0.004 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.14808 ( 664) hydrogen bonds : angle 6.21653 ( 1950) covalent geometry : bond 0.00335 (11653) covalent geometry : angle 0.57301 (15875) *********************** 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 : 1.211 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: 0.2558 time to fit residues: 66.3861 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 : 2.050 ------------------------------------------------------------------------------- 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 130 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 0.0040 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 140 optimal weight: 0.1980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.196877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160983 restraints weight = 14612.930| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.83 r_work: 0.3502 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11653 Z= 0.192 Angle : 0.583 7.517 15875 Z= 0.295 Chirality : 0.041 0.145 1895 Planarity : 0.004 0.038 2044 Dihedral : 6.186 57.372 1681 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 4.55 % Allowed : 25.42 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1525 helix: 1.93 (0.19), residues: 806 sheet: -1.37 (0.41), residues: 164 loop : -1.70 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 318 HIS 0.007 0.001 HIS A 375 PHE 0.015 0.002 PHE A 421 TYR 0.019 0.001 TYR A 62 ARG 0.003 0.000 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 664) hydrogen bonds : angle 4.75313 ( 1950) covalent geometry : bond 0.00455 (11653) covalent geometry : angle 0.58306 (15875) *********************** 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 198 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 3.300 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 450 ASP cc_start: 0.6835 (m-30) cc_final: 0.6613 (m-30) REVERT: A 536 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7980 (mp) REVERT: A 537 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 17 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8079 (m) REVERT: B 144 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6271 (tp) REVERT: B 157 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7091 (ptp) REVERT: B 250 ASP cc_start: 0.8331 (p0) cc_final: 0.8009 (p0) REVERT: B 487 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8216 (pttp) REVERT: D 394 ARG cc_start: 0.6467 (mmm-85) cc_final: 0.4900 (mtm180) REVERT: D 446 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6882 (tt) REVERT: D 574 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6390 (mp) outliers start: 51 outliers final: 27 residues processed: 193 average time/residue: 0.3450 time to fit residues: 103.5747 Evaluate side-chains 174 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS D 614 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.197451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172758 restraints weight = 14917.691| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.35 r_work: 0.3577 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11653 Z= 0.287 Angle : 0.668 8.187 15875 Z= 0.334 Chirality : 0.044 0.179 1895 Planarity : 0.005 0.048 2044 Dihedral : 5.796 56.576 1649 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 6.16 % Allowed : 24.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1525 helix: 1.85 (0.18), residues: 801 sheet: -1.55 (0.40), residues: 164 loop : -1.79 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 318 HIS 0.006 0.001 HIS A 8 PHE 0.020 0.002 PHE B 228 TYR 0.023 0.002 TYR A 62 ARG 0.003 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 664) hydrogen bonds : angle 4.71678 ( 1950) covalent geometry : bond 0.00706 (11653) covalent geometry : angle 0.66770 (15875) *********************** 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 210 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 141 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 450 ASP cc_start: 0.7085 (m-30) cc_final: 0.6857 (m-30) REVERT: A 537 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: B 3 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 17 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8164 (m) REVERT: B 144 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6443 (tp) REVERT: B 157 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7053 (ptp) REVERT: B 250 ASP cc_start: 0.8356 (p0) cc_final: 0.8031 (p0) REVERT: B 487 LYS cc_start: 0.8455 (ptmm) cc_final: 0.8191 (pttp) REVERT: D 394 ARG cc_start: 0.6495 (mmm-85) cc_final: 0.4982 (mtm180) REVERT: D 596 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7565 (mt-10) outliers start: 69 outliers final: 44 residues processed: 200 average time/residue: 0.4051 time to fit residues: 123.1866 Evaluate side-chains 186 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 56 VAL 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 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 386 LEU 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 508 ASN 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 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 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 194 LEU 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 313 SER 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 596 GLU 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 22 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 7 optimal weight: 0.1980 chunk 115 optimal weight: 0.2980 chunk 106 optimal weight: 8.9990 chunk 129 optimal weight: 0.2980 chunk 71 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 0.2980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN D 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.202160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176472 restraints weight = 14875.028| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.41 r_work: 0.3642 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11653 Z= 0.122 Angle : 0.535 8.308 15875 Z= 0.269 Chirality : 0.039 0.153 1895 Planarity : 0.004 0.034 2044 Dihedral : 5.253 57.243 1646 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 4.91 % Allowed : 24.26 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1525 helix: 2.20 (0.19), residues: 801 sheet: -1.49 (0.40), residues: 164 loop : -1.60 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.008 0.001 HIS D 303 PHE 0.016 0.001 PHE D 323 TYR 0.016 0.001 TYR A 62 ARG 0.004 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 664) hydrogen bonds : angle 4.28703 ( 1950) covalent geometry : bond 0.00279 (11653) covalent geometry : angle 0.53542 (15875) *********************** 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: 55 poor density : 151 time to evaluate : 1.394 Fit side-chains REVERT: A 450 ASP cc_start: 0.6952 (m-30) cc_final: 0.6681 (m-30) REVERT: A 536 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 537 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 3 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8448 (m) REVERT: B 144 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6266 (tp) REVERT: B 157 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6950 (ptp) REVERT: B 250 ASP cc_start: 0.8270 (p0) cc_final: 0.7977 (p0) REVERT: B 459 MET cc_start: 0.7982 (mmm) cc_final: 0.7748 (mtt) REVERT: D 394 ARG cc_start: 0.6389 (mmm-85) cc_final: 0.4607 (mtm180) REVERT: D 574 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6395 (mp) outliers start: 55 outliers final: 27 residues processed: 200 average time/residue: 0.2500 time to fit residues: 74.9606 Evaluate side-chains 172 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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 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 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 192 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain D residue 332 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 151 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS D 588 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.197301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166287 restraints weight = 14782.571| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.47 r_work: 0.3489 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 11653 Z= 0.319 Angle : 0.694 8.512 15875 Z= 0.345 Chirality : 0.045 0.284 1895 Planarity : 0.005 0.052 2044 Dihedral : 5.411 57.823 1642 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.75 % Favored : 93.18 % Rotamer: Outliers : 5.98 % Allowed : 24.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1525 helix: 1.93 (0.18), residues: 801 sheet: -1.55 (0.40), residues: 164 loop : -1.79 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 318 HIS 0.010 0.001 HIS D 286 PHE 0.022 0.002 PHE B 228 TYR 0.023 0.002 TYR A 62 ARG 0.003 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 664) hydrogen bonds : angle 4.58218 ( 1950) covalent geometry : bond 0.00785 (11653) covalent geometry : angle 0.69405 (15875) *********************** 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 206 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 139 time to evaluate : 2.398 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 450 ASP cc_start: 0.7111 (m-30) cc_final: 0.6869 (m-30) REVERT: A 537 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: B 3 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 17 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8172 (m) REVERT: B 144 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6660 (tp) REVERT: B 157 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7439 (ptp) REVERT: B 250 ASP cc_start: 0.8494 (p0) cc_final: 0.8203 (p0) REVERT: B 487 LYS cc_start: 0.8442 (pttp) cc_final: 0.8219 (pttm) REVERT: D 394 ARG cc_start: 0.6405 (mmm-85) cc_final: 0.4638 (mtm180) outliers start: 67 outliers final: 46 residues processed: 197 average time/residue: 0.3481 time to fit residues: 107.8107 Evaluate side-chains 187 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 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 379 SER Chi-restraints excluded: chain A residue 416 THR 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 480 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 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 168 SER 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 439 ARG Chi-restraints excluded: chain D residue 286 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 66 optimal weight: 0.1980 chunk 125 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 153 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 112 optimal weight: 7.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.202297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173638 restraints weight = 15016.130| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.57 r_work: 0.3590 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11653 Z= 0.128 Angle : 0.557 10.829 15875 Z= 0.276 Chirality : 0.040 0.172 1895 Planarity : 0.004 0.038 2044 Dihedral : 5.078 59.797 1642 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 5.00 % Allowed : 24.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1525 helix: 2.20 (0.19), residues: 800 sheet: -1.45 (0.40), residues: 164 loop : -1.61 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 318 HIS 0.010 0.001 HIS D 286 PHE 0.017 0.001 PHE A 421 TYR 0.017 0.001 TYR A 62 ARG 0.004 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 664) hydrogen bonds : angle 4.26647 ( 1950) covalent geometry : bond 0.00298 (11653) covalent geometry : angle 0.55729 (15875) *********************** 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 200 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 450 ASP cc_start: 0.7043 (m-30) cc_final: 0.6805 (m-30) REVERT: A 536 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 537 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: B 3 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8503 (m) REVERT: B 17 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 46 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8932 (t80) REVERT: B 144 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6252 (tp) REVERT: B 157 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6999 (ptp) REVERT: B 250 ASP cc_start: 0.8398 (p0) cc_final: 0.8103 (p0) REVERT: D 325 TYR cc_start: 0.7831 (t80) cc_final: 0.7571 (t80) REVERT: D 394 ARG cc_start: 0.6417 (mmm-85) cc_final: 0.4813 (mtm180) outliers start: 56 outliers final: 39 residues processed: 194 average time/residue: 0.2090 time to fit residues: 60.0819 Evaluate side-chains 186 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 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 216 SER 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 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 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 17 VAL 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 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 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 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 58 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.198279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170172 restraints weight = 14978.489| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.50 r_work: 0.3543 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11653 Z= 0.222 Angle : 0.615 10.088 15875 Z= 0.305 Chirality : 0.042 0.185 1895 Planarity : 0.004 0.039 2044 Dihedral : 5.218 59.641 1642 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 5.17 % Allowed : 24.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1525 helix: 2.11 (0.19), residues: 801 sheet: -1.45 (0.40), residues: 164 loop : -1.67 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 318 HIS 0.009 0.001 HIS D 303 PHE 0.019 0.002 PHE A 421 TYR 0.021 0.002 TYR A 62 ARG 0.003 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 664) hydrogen bonds : angle 4.37007 ( 1950) covalent geometry : bond 0.00544 (11653) covalent geometry : angle 0.61521 (15875) *********************** 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 195 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 1.422 Fit side-chains REVERT: A 100 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 450 ASP cc_start: 0.7080 (m-30) cc_final: 0.6843 (m-30) REVERT: A 537 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: B 3 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8616 (m) REVERT: B 17 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 46 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.9008 (t80) REVERT: B 144 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6386 (tp) REVERT: B 157 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7117 (ptp) REVERT: B 250 ASP cc_start: 0.8449 (p0) cc_final: 0.8131 (p0) REVERT: D 394 ARG cc_start: 0.6446 (mmm-85) cc_final: 0.4772 (mtm180) REVERT: D 574 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6523 (mp) outliers start: 58 outliers final: 45 residues processed: 187 average time/residue: 0.2328 time to fit residues: 65.5480 Evaluate side-chains 189 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 216 SER 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 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 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 553 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 17 VAL 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 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 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 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 117 optimal weight: 0.9980 chunk 138 optimal weight: 0.0980 chunk 143 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN ** A 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168941 restraints weight = 14847.072| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.55 r_work: 0.3578 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11653 Z= 0.190 Angle : 0.590 9.875 15875 Z= 0.292 Chirality : 0.041 0.192 1895 Planarity : 0.004 0.035 2044 Dihedral : 5.169 58.648 1642 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.80 % Allowed : 24.62 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1525 helix: 2.16 (0.19), residues: 800 sheet: -1.44 (0.40), residues: 164 loop : -1.63 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 318 HIS 0.007 0.001 HIS A 8 PHE 0.019 0.002 PHE A 421 TYR 0.019 0.001 TYR A 62 ARG 0.003 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 664) hydrogen bonds : angle 4.29553 ( 1950) covalent geometry : bond 0.00464 (11653) covalent geometry : angle 0.58961 (15875) *********************** 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 205 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 140 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 450 ASP cc_start: 0.6996 (m-30) cc_final: 0.6761 (m-30) REVERT: A 537 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: B 3 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8583 (m) REVERT: B 46 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8964 (t80) REVERT: B 144 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6228 (tp) REVERT: B 157 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6992 (ptp) REVERT: B 250 ASP cc_start: 0.8491 (p0) cc_final: 0.8200 (p0) REVERT: B 487 LYS cc_start: 0.8482 (ptmm) cc_final: 0.8080 (pttp) REVERT: D 325 TYR cc_start: 0.7879 (t80) cc_final: 0.7641 (t80) REVERT: D 394 ARG cc_start: 0.6439 (mmm-85) cc_final: 0.4796 (mtm180) REVERT: D 574 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6557 (mp) outliers start: 65 outliers final: 49 residues processed: 197 average time/residue: 0.2074 time to fit residues: 60.9044 Evaluate side-chains 190 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 216 SER 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 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 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 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR 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 154 ILE 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 432 GLU Chi-restraints excluded: chain D residue 461 GLN Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 520 MET 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 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 71 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 61 optimal weight: 0.2980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN D 707 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168314 restraints weight = 14816.707| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.37 r_work: 0.3549 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11653 Z= 0.123 Angle : 0.537 10.193 15875 Z= 0.269 Chirality : 0.039 0.202 1895 Planarity : 0.004 0.059 2044 Dihedral : 4.903 54.727 1642 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.37 % Allowed : 25.96 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1525 helix: 2.29 (0.19), residues: 802 sheet: -1.38 (0.40), residues: 164 loop : -1.50 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.007 0.001 HIS A 8 PHE 0.017 0.001 PHE A 421 TYR 0.016 0.001 TYR A 62 ARG 0.004 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 664) hydrogen bonds : angle 4.11601 ( 1950) covalent geometry : bond 0.00288 (11653) covalent geometry : angle 0.53747 (15875) *********************** 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 194 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: A 450 ASP cc_start: 0.7199 (m-30) cc_final: 0.6940 (m-30) REVERT: A 536 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7932 (mp) REVERT: A 537 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: B 3 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8570 (m) REVERT: B 46 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8902 (t80) REVERT: B 157 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7409 (ptp) REVERT: B 250 ASP cc_start: 0.8452 (p0) cc_final: 0.8179 (p0) REVERT: B 417 GLN cc_start: 0.7591 (mm110) cc_final: 0.6353 (mt0) REVERT: B 487 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8293 (pttp) REVERT: D 325 TYR cc_start: 0.7989 (t80) cc_final: 0.7523 (t80) REVERT: D 394 ARG cc_start: 0.6328 (mmm-85) cc_final: 0.4323 (mtm180) outliers start: 49 outliers final: 36 residues processed: 187 average time/residue: 0.2706 time to fit residues: 75.6275 Evaluate side-chains 180 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 216 SER 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 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 6 VAL Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 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 185 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 262 ILE 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 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 40 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 44 optimal weight: 0.0370 chunk 77 optimal weight: 0.5980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164576 restraints weight = 14629.613| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.43 r_work: 0.3514 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11653 Z= 0.136 Angle : 0.551 10.392 15875 Z= 0.274 Chirality : 0.040 0.207 1895 Planarity : 0.004 0.054 2044 Dihedral : 4.746 52.612 1638 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.66 % Allowed : 26.32 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1525 helix: 2.37 (0.19), residues: 796 sheet: -1.35 (0.40), residues: 164 loop : -1.42 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.006 0.001 HIS A 8 PHE 0.017 0.001 PHE A 421 TYR 0.016 0.001 TYR A 62 ARG 0.004 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 664) hydrogen bonds : angle 4.10323 ( 1950) covalent geometry : bond 0.00322 (11653) covalent geometry : angle 0.55135 (15875) ********************** 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 186 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 450 ASP cc_start: 0.7087 (m-30) cc_final: 0.6836 (m-30) REVERT: A 536 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 537 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 46 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8905 (t80) REVERT: B 157 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7429 (ptp) REVERT: B 250 ASP cc_start: 0.8456 (p0) cc_final: 0.8160 (p0) REVERT: B 417 GLN cc_start: 0.7587 (mm110) cc_final: 0.6328 (mt0) REVERT: B 487 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8283 (pttp) REVERT: D 325 TYR cc_start: 0.8061 (t80) cc_final: 0.7602 (t80) REVERT: D 394 ARG cc_start: 0.6372 (mmm-85) cc_final: 0.4341 (mtm180) REVERT: D 574 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6626 (mp) outliers start: 41 outliers final: 32 residues processed: 183 average time/residue: 0.2681 time to fit residues: 72.6133 Evaluate side-chains 178 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 216 SER 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 474 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 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 185 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 262 ILE 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 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 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 87 optimal weight: 0.0030 chunk 40 optimal weight: 0.0470 chunk 101 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4888 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.194001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166022 restraints weight = 14697.341| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.41 r_work: 0.3504 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11653 Z= 0.172 Angle : 0.577 10.196 15875 Z= 0.286 Chirality : 0.041 0.203 1895 Planarity : 0.004 0.053 2044 Dihedral : 4.824 53.695 1638 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.84 % Allowed : 26.14 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1525 helix: 2.32 (0.19), residues: 797 sheet: -1.38 (0.40), residues: 164 loop : -1.46 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 318 HIS 0.006 0.001 HIS A 8 PHE 0.018 0.002 PHE A 421 TYR 0.019 0.001 TYR A 62 ARG 0.004 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 664) hydrogen bonds : angle 4.19578 ( 1950) covalent geometry : bond 0.00418 (11653) covalent geometry : angle 0.57658 (15875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9849.50 seconds wall clock time: 182 minutes 36.04 seconds (10956.04 seconds total)