Starting phenix.real_space_refine on Mon Jun 9 07:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpa_16147/06_2025/8bpa_16147.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpa_16147/06_2025/8bpa_16147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bpa_16147/06_2025/8bpa_16147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpa_16147/06_2025/8bpa_16147.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpa_16147/06_2025/8bpa_16147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpa_16147/06_2025/8bpa_16147.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 S 71 5.16 5 C 6618 2.51 5 N 1791 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 191} Chain breaks: 3 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8431 SG CYS C 289 39.856 57.677 45.495 1.00125.91 S ATOM 8457 SG CYS C 292 37.187 56.181 43.096 1.00124.81 S ATOM 8640 SG CYS C 315 40.824 55.364 42.492 1.00117.18 S ATOM 8315 SG CYS C 274 39.422 44.839 47.811 1.00110.14 S ATOM 8339 SG CYS C 277 40.602 41.173 47.436 1.00113.17 S ATOM 8523 SG CYS C 300 42.904 43.509 48.758 1.00 86.93 S ATOM 7590 SG CYS C 71 48.790 94.141 75.277 1.00204.68 S ATOM 7614 SG CYS C 74 45.627 93.112 73.314 1.00205.36 S ATOM 7806 SG CYS C 99 47.990 95.411 71.662 1.00187.58 S ATOM 7833 SG CYS C 102 46.167 96.786 74.406 1.00184.08 S ATOM 7508 SG CYS C 59 50.564 85.329 66.806 1.00204.38 S ATOM 7528 SG CYS C 62 51.157 83.018 63.861 1.00188.96 S ATOM 7675 SG CYS C 82 53.191 86.280 64.136 1.00181.00 S Time building chain proxies: 6.34, per 1000 atoms: 0.61 Number of scatterers: 10393 At special positions: 0 Unit cell: (122.094, 124.146, 112.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 71 16.00 O 1906 8.00 N 1791 7.00 C 6618 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: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 99 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 102 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 74 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 71 " pdb=" ZN C1104 " pdb="ZN ZN C1104 " - pdb=" ND1 HIS C 79 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 62 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 59 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 82 " Number of angles added : 15 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 59.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.583A pdb=" N TYR A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.594A pdb=" N LEU A 424 " --> pdb=" O CYS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.760A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 486 No H-bonds generated for 'chain 'A' and resid 485 through 486' Processing helix chain 'A' and resid 487 through 494 removed outlier: 5.005A pdb=" N GLU A 492 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.880A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 561 removed outlier: 3.560A pdb=" N ALA A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.630A pdb=" N ASP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.126A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.909A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.171A pdb=" N VAL A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Proline residue: A 664 - end of helix Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.918A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.548A pdb=" N ARG A 792 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 829 removed outlier: 4.797A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.889A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.671A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 916 removed outlier: 5.379A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.721A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 87 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.734A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.740A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 253 Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.922A pdb=" N SER B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.982A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.903A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.787A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.509A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 removed outlier: 3.583A pdb=" N LYS C 360 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 3.975A pdb=" N VAL D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.914A pdb=" N SER D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 3.995A pdb=" N GLU D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 299 through 313 removed outlier: 3.859A pdb=" N LEU D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.706A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 3.639A pdb=" N LEU A 926 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS A 920 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.576A pdb=" N TYR B 14 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 195 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'C' and resid 287 through 288 532 hydrogen bonds defined for protein. 1548 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: 3.05 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2411 1.33 - 1.45: 2238 1.45 - 1.57: 5872 1.57 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 10627 Sorted by residual: bond pdb=" CB PRO A 521 " pdb=" CG PRO A 521 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CG PRO B 102 " pdb=" CD PRO B 102 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 3.03e+00 bond pdb=" CB PRO B 102 " pdb=" CG PRO B 102 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" CG PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 1.503 1.448 0.055 3.40e-02 8.65e+02 2.61e+00 bond pdb=" CB PRO C 316 " pdb=" CG PRO C 316 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.40e+00 ... (remaining 10622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 14012 2.34 - 4.67: 269 4.67 - 7.01: 51 7.01 - 9.35: 13 9.35 - 11.69: 7 Bond angle restraints: 14352 Sorted by residual: angle pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.68e+01 angle pdb=" CA GLU A 562 " pdb=" CB GLU A 562 " pdb=" CG GLU A 562 " ideal model delta sigma weight residual 114.10 124.56 -10.46 2.00e+00 2.50e-01 2.73e+01 angle pdb=" C LYS C 32 " pdb=" CA LYS C 32 " pdb=" CB LYS C 32 " ideal model delta sigma weight residual 115.79 110.05 5.74 1.19e+00 7.06e-01 2.33e+01 angle pdb=" CA LYS A 885 " pdb=" CB LYS A 885 " pdb=" CG LYS A 885 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU A 879 " pdb=" CB GLU A 879 " pdb=" CG GLU A 879 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 ... (remaining 14347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5369 17.86 - 35.72: 779 35.72 - 53.58: 245 53.58 - 71.44: 40 71.44 - 89.29: 16 Dihedral angle restraints: 6449 sinusoidal: 2681 harmonic: 3768 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ARG A 402 " pdb=" C ARG A 402 " pdb=" N ALA A 403 " pdb=" CA ALA A 403 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA MET A 934 " pdb=" C MET A 934 " pdb=" N THR A 935 " pdb=" CA THR A 935 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1009 0.041 - 0.081: 398 0.081 - 0.122: 108 0.122 - 0.163: 16 0.163 - 0.203: 3 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CB VAL A 923 " pdb=" CA VAL A 923 " pdb=" CG1 VAL A 923 " pdb=" CG2 VAL A 923 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" C PRO A 521 " pdb=" CB PRO A 521 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CG LEU B 212 " pdb=" CB LEU B 212 " pdb=" CD1 LEU B 212 " pdb=" CD2 LEU B 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 1531 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.067 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 521 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 315 " -0.047 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO C 316 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 562 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C GLU A 562 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU A 562 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 563 " -0.015 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 282 2.68 - 3.24: 10701 3.24 - 3.79: 17009 3.79 - 4.35: 21650 4.35 - 4.90: 34359 Nonbonded interactions: 84001 Sorted by model distance: nonbonded pdb=" O HIS B 179 " pdb="CA CA B 502 " model vdw 2.127 2.510 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 2.141 2.230 nonbonded pdb=" OG1 THR C 330 " pdb=" OD1 ASN C 333 " model vdw 2.154 3.040 nonbonded pdb=" OD1 ASP B 175 " pdb="CA CA B 502 " model vdw 2.172 2.510 nonbonded pdb=" N GLN A 835 " pdb=" OE1 GLN A 835 " model vdw 2.194 3.120 ... (remaining 83996 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.640 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.005 0.087 10644 Z= 0.216 Angle : 0.863 12.165 14367 Z= 0.447 Chirality : 0.046 0.203 1534 Planarity : 0.006 0.095 1862 Dihedral : 18.501 89.294 4015 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.97 % Allowed : 33.75 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.00 (0.24), residues: 1260 helix: 0.74 (0.20), residues: 672 sheet: -0.57 (0.60), residues: 77 loop : -0.81 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 434 HIS 0.006 0.001 HIS A 574 PHE 0.027 0.002 PHE B 335 TYR 0.030 0.002 TYR B 16 ARG 0.009 0.001 ARG A 903 Details of bonding type rmsd hydrogen bonds : bond 0.13988 ( 532) hydrogen bonds : angle 5.67936 ( 1548) metal coordination : bond 0.01205 ( 17) metal coordination : angle 4.58591 ( 15) covalent geometry : bond 0.00476 (10627) covalent geometry : angle 0.85040 (14352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 349 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.6464 (t80) cc_final: 0.6263 (t80) REVERT: A 315 ARG cc_start: 0.6055 (mmm160) cc_final: 0.5842 (tpm170) REVERT: A 327 PHE cc_start: 0.7344 (t80) cc_final: 0.7120 (t80) REVERT: A 449 GLU cc_start: 0.7502 (tt0) cc_final: 0.7238 (tp30) REVERT: A 462 LEU cc_start: 0.8402 (tp) cc_final: 0.8027 (mp) REVERT: A 469 ASN cc_start: 0.8342 (t0) cc_final: 0.8026 (t0) REVERT: A 539 LEU cc_start: 0.8167 (mp) cc_final: 0.7900 (tp) REVERT: A 563 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7887 (tp40) REVERT: A 566 LYS cc_start: 0.7793 (mtpm) cc_final: 0.7590 (mtpm) REVERT: A 595 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 636 LEU cc_start: 0.8653 (mm) cc_final: 0.8288 (mm) REVERT: A 772 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7539 (tmmt) REVERT: A 835 GLN cc_start: 0.8066 (pm20) cc_final: 0.7782 (pm20) REVERT: A 859 GLN cc_start: 0.7272 (pt0) cc_final: 0.6918 (mt0) REVERT: A 863 ARG cc_start: 0.7605 (mmp-170) cc_final: 0.7217 (mmp-170) REVERT: A 922 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7881 (ttmm) REVERT: B 41 ASN cc_start: 0.8234 (t0) cc_final: 0.7857 (t0) REVERT: B 56 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7299 (mmm-85) REVERT: B 91 GLN cc_start: 0.8126 (mt0) cc_final: 0.7771 (mm-40) REVERT: B 156 ASP cc_start: 0.7474 (t0) cc_final: 0.7214 (t0) REVERT: B 308 ASN cc_start: 0.8400 (m-40) cc_final: 0.8182 (m110) REVERT: D 312 MET cc_start: 0.6319 (mmm) cc_final: 0.6055 (mmm) REVERT: D 335 LYS cc_start: 0.8830 (pptt) cc_final: 0.8333 (pttt) REVERT: D 336 TYR cc_start: 0.7208 (t80) cc_final: 0.6640 (t80) outliers start: 11 outliers final: 5 residues processed: 352 average time/residue: 0.2689 time to fit residues: 125.5955 Evaluate side-chains 339 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 333 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 332 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 563 GLN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 883 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.138865 restraints weight = 20410.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.143328 restraints weight = 11069.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.146319 restraints weight = 7085.083| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10644 Z= 0.159 Angle : 0.691 11.982 14367 Z= 0.346 Chirality : 0.043 0.188 1534 Planarity : 0.005 0.050 1862 Dihedral : 5.501 52.958 1421 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.15 % Allowed : 26.86 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.27 (0.24), residues: 1260 helix: 1.06 (0.20), residues: 676 sheet: -0.50 (0.58), residues: 74 loop : -0.86 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 428 HIS 0.006 0.001 HIS A 574 PHE 0.020 0.001 PHE A 921 TYR 0.024 0.002 TYR D 329 ARG 0.005 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 532) hydrogen bonds : angle 4.82973 ( 1548) metal coordination : bond 0.01091 ( 17) metal coordination : angle 4.11056 ( 15) covalent geometry : bond 0.00347 (10627) covalent geometry : angle 0.67802 (14352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 344 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.6785 (t80) cc_final: 0.6532 (t80) REVERT: A 325 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 327 PHE cc_start: 0.7353 (t80) cc_final: 0.7027 (t80) REVERT: A 404 LEU cc_start: 0.5244 (mt) cc_final: 0.4743 (mp) REVERT: A 428 TRP cc_start: 0.7965 (m100) cc_final: 0.7684 (m100) REVERT: A 454 ARG cc_start: 0.7282 (tpp80) cc_final: 0.6616 (tpp80) REVERT: A 462 LEU cc_start: 0.8096 (tp) cc_final: 0.7696 (mp) REVERT: A 469 ASN cc_start: 0.8266 (t0) cc_final: 0.8023 (t0) REVERT: A 477 GLU cc_start: 0.7255 (tp30) cc_final: 0.6773 (mm-30) REVERT: A 480 GLN cc_start: 0.8295 (tp-100) cc_final: 0.8064 (tp-100) REVERT: A 505 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 539 LEU cc_start: 0.8401 (mp) cc_final: 0.7824 (tp) REVERT: A 742 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 771 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7932 (tp-100) REVERT: A 772 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7372 (ttmm) REVERT: A 776 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7185 (mt-10) REVERT: A 859 GLN cc_start: 0.7292 (pt0) cc_final: 0.6899 (mt0) REVERT: A 863 ARG cc_start: 0.7640 (mmp-170) cc_final: 0.7256 (mmp-170) REVERT: A 884 GLU cc_start: 0.6786 (tt0) cc_final: 0.6532 (tt0) REVERT: A 903 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7513 (ptp90) REVERT: A 915 MET cc_start: 0.7347 (ppp) cc_final: 0.7114 (ppp) REVERT: A 922 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7598 (ttmm) REVERT: A 934 MET cc_start: 0.7404 (tpt) cc_final: 0.7181 (tpt) REVERT: B 23 TYR cc_start: 0.8318 (m-80) cc_final: 0.7414 (m-80) REVERT: B 41 ASN cc_start: 0.8194 (t0) cc_final: 0.7940 (t0) REVERT: B 56 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7374 (mmm-85) REVERT: B 68 TYR cc_start: 0.7675 (t80) cc_final: 0.7318 (t80) REVERT: B 69 HIS cc_start: 0.7758 (m170) cc_final: 0.7371 (m-70) REVERT: B 114 SER cc_start: 0.7776 (t) cc_final: 0.7456 (p) REVERT: B 156 ASP cc_start: 0.7416 (t0) cc_final: 0.7134 (t0) REVERT: B 166 LYS cc_start: 0.8518 (mmpt) cc_final: 0.8145 (mmpt) REVERT: B 225 VAL cc_start: 0.7612 (p) cc_final: 0.7290 (m) REVERT: B 229 MET cc_start: 0.7831 (mtm) cc_final: 0.7482 (mtm) REVERT: B 248 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7723 (tptm) REVERT: B 253 TYR cc_start: 0.6619 (t80) cc_final: 0.5527 (t80) REVERT: B 290 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7675 (ptmm) REVERT: B 308 ASN cc_start: 0.8302 (m-40) cc_final: 0.8051 (m110) REVERT: D 240 LYS cc_start: 0.4236 (OUTLIER) cc_final: 0.3756 (ttpp) REVERT: D 281 TYR cc_start: 0.6605 (t80) cc_final: 0.6286 (t80) REVERT: D 312 MET cc_start: 0.6196 (mmm) cc_final: 0.5977 (mmm) REVERT: D 335 LYS cc_start: 0.8901 (pptt) cc_final: 0.8392 (pttt) REVERT: D 336 TYR cc_start: 0.7058 (t80) cc_final: 0.6512 (t80) outliers start: 47 outliers final: 25 residues processed: 372 average time/residue: 0.2810 time to fit residues: 141.6557 Evaluate side-chains 370 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 607 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 606 GLN A 607 HIS A 660 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.164533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.137132 restraints weight = 20656.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.141723 restraints weight = 11160.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.144687 restraints weight = 7045.032| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10644 Z= 0.154 Angle : 0.680 12.957 14367 Z= 0.336 Chirality : 0.044 0.453 1534 Planarity : 0.005 0.057 1862 Dihedral : 5.000 46.594 1412 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.80 % Allowed : 27.83 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.33 (0.24), residues: 1260 helix: 1.14 (0.20), residues: 674 sheet: -0.53 (0.57), residues: 75 loop : -0.87 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 909 HIS 0.004 0.001 HIS C 297 PHE 0.010 0.001 PHE A 744 TYR 0.023 0.002 TYR A 513 ARG 0.006 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 532) hydrogen bonds : angle 4.67815 ( 1548) metal coordination : bond 0.00928 ( 17) metal coordination : angle 3.81136 ( 15) covalent geometry : bond 0.00337 (10627) covalent geometry : angle 0.66861 (14352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.6825 (t80) cc_final: 0.6484 (t80) REVERT: A 325 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 327 PHE cc_start: 0.7458 (t80) cc_final: 0.7091 (t80) REVERT: A 404 LEU cc_start: 0.5276 (mt) cc_final: 0.4767 (mp) REVERT: A 449 GLU cc_start: 0.7442 (tt0) cc_final: 0.6914 (tp30) REVERT: A 462 LEU cc_start: 0.8048 (tp) cc_final: 0.7673 (mp) REVERT: A 473 ILE cc_start: 0.8030 (mt) cc_final: 0.7684 (mm) REVERT: A 477 GLU cc_start: 0.7342 (tp30) cc_final: 0.7075 (mm-30) REVERT: A 480 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7995 (tm-30) REVERT: A 483 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7567 (tp) REVERT: A 505 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 510 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.7508 (tpp-160) REVERT: A 539 LEU cc_start: 0.8177 (mp) cc_final: 0.7869 (tp) REVERT: A 545 LYS cc_start: 0.7433 (tptt) cc_final: 0.7157 (mptt) REVERT: A 581 GLN cc_start: 0.7430 (mp-120) cc_final: 0.6952 (mp10) REVERT: A 582 ASN cc_start: 0.7130 (m-40) cc_final: 0.6893 (m-40) REVERT: A 597 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 662 PHE cc_start: 0.6374 (t80) cc_final: 0.6162 (t80) REVERT: A 742 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 748 ASN cc_start: 0.7168 (m-40) cc_final: 0.6501 (m-40) REVERT: A 749 TRP cc_start: 0.5925 (m100) cc_final: 0.5705 (m100) REVERT: A 771 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7999 (tp-100) REVERT: A 772 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7412 (tmmt) REVERT: A 814 GLU cc_start: 0.7640 (tp30) cc_final: 0.7401 (tp30) REVERT: A 864 GLN cc_start: 0.7563 (tp40) cc_final: 0.7260 (mm-40) REVERT: A 871 ASP cc_start: 0.4104 (OUTLIER) cc_final: 0.3793 (t0) REVERT: A 884 GLU cc_start: 0.7011 (tt0) cc_final: 0.6669 (tt0) REVERT: A 903 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7234 (ptp90) REVERT: A 913 ARG cc_start: 0.6173 (ptt90) cc_final: 0.5857 (ptt-90) REVERT: A 915 MET cc_start: 0.7771 (ppp) cc_final: 0.7482 (tmm) REVERT: A 922 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7817 (ttmm) REVERT: A 934 MET cc_start: 0.7546 (tpt) cc_final: 0.7345 (tpp) REVERT: B 41 ASN cc_start: 0.8288 (t0) cc_final: 0.7963 (t0) REVERT: B 56 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7335 (mmm-85) REVERT: B 68 TYR cc_start: 0.7701 (t80) cc_final: 0.7202 (t80) REVERT: B 156 ASP cc_start: 0.7502 (t0) cc_final: 0.7203 (t0) REVERT: B 157 ILE cc_start: 0.8171 (mt) cc_final: 0.7859 (mp) REVERT: B 166 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8145 (mmpt) REVERT: B 229 MET cc_start: 0.7817 (mtm) cc_final: 0.7538 (mtp) REVERT: B 354 GLN cc_start: 0.8288 (mp10) cc_final: 0.7841 (mp10) REVERT: C 23 GLN cc_start: 0.8763 (tt0) cc_final: 0.8285 (tt0) REVERT: C 208 ARG cc_start: 0.4577 (OUTLIER) cc_final: 0.4065 (ptm160) REVERT: C 320 GLU cc_start: 0.6888 (mp0) cc_final: 0.6382 (mp0) REVERT: D 281 TYR cc_start: 0.6545 (t80) cc_final: 0.6148 (t80) REVERT: D 335 LYS cc_start: 0.8893 (pptt) cc_final: 0.8638 (pptt) outliers start: 43 outliers final: 22 residues processed: 372 average time/residue: 0.3320 time to fit residues: 164.4739 Evaluate side-chains 362 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 334 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 607 HIS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 769 GLN A 859 GLN A 908 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 180 HIS B 240 GLN A B 282 HIS B 308 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.163332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.136192 restraints weight = 20500.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140771 restraints weight = 11127.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143765 restraints weight = 7042.144| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10644 Z= 0.167 Angle : 0.682 12.871 14367 Z= 0.338 Chirality : 0.043 0.268 1534 Planarity : 0.005 0.067 1862 Dihedral : 4.989 57.565 1412 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.04 % Allowed : 28.53 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.34 (0.24), residues: 1260 helix: 1.16 (0.20), residues: 679 sheet: -0.47 (0.57), residues: 75 loop : -0.91 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 206 HIS 0.008 0.001 HIS A 607 PHE 0.019 0.001 PHE B 338 TYR 0.027 0.002 TYR B 16 ARG 0.006 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 532) hydrogen bonds : angle 4.65987 ( 1548) metal coordination : bond 0.01002 ( 17) metal coordination : angle 4.02741 ( 15) covalent geometry : bond 0.00360 (10627) covalent geometry : angle 0.66943 (14352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 327 PHE cc_start: 0.7437 (t80) cc_final: 0.7074 (t80) REVERT: A 354 LYS cc_start: 0.3683 (OUTLIER) cc_final: 0.2629 (ptpp) REVERT: A 449 GLU cc_start: 0.7423 (tt0) cc_final: 0.6917 (tp30) REVERT: A 458 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7141 (mm-30) REVERT: A 462 LEU cc_start: 0.8056 (tp) cc_final: 0.7593 (mp) REVERT: A 466 LEU cc_start: 0.7815 (mt) cc_final: 0.7589 (mt) REVERT: A 477 GLU cc_start: 0.7346 (tp30) cc_final: 0.7081 (mm-30) REVERT: A 480 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7953 (tm-30) REVERT: A 505 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 510 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7605 (tpp-160) REVERT: A 539 LEU cc_start: 0.8093 (mp) cc_final: 0.7769 (tp) REVERT: A 545 LYS cc_start: 0.7465 (tptt) cc_final: 0.7173 (mptt) REVERT: A 570 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7116 (ttmm) REVERT: A 582 ASN cc_start: 0.7107 (m-40) cc_final: 0.6884 (m-40) REVERT: A 597 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6854 (mt-10) REVERT: A 742 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7876 (tt) REVERT: A 748 ASN cc_start: 0.7196 (m-40) cc_final: 0.6612 (m-40) REVERT: A 771 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7934 (tp-100) REVERT: A 772 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7529 (tmmt) REVERT: A 814 GLU cc_start: 0.7480 (tp30) cc_final: 0.7250 (tp30) REVERT: A 863 ARG cc_start: 0.7467 (mmp-170) cc_final: 0.7150 (mmp80) REVERT: A 864 GLN cc_start: 0.7595 (tp40) cc_final: 0.7315 (mm-40) REVERT: A 884 GLU cc_start: 0.7098 (tt0) cc_final: 0.6870 (tt0) REVERT: A 903 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7157 (ptp90) REVERT: A 909 TRP cc_start: 0.7382 (t60) cc_final: 0.6987 (t60) REVERT: A 915 MET cc_start: 0.7803 (ppp) cc_final: 0.7407 (tmm) REVERT: A 922 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7915 (ttmm) REVERT: B 56 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7318 (mmm-85) REVERT: B 68 TYR cc_start: 0.7741 (t80) cc_final: 0.7321 (t80) REVERT: B 156 ASP cc_start: 0.7518 (t0) cc_final: 0.7212 (t0) REVERT: B 157 ILE cc_start: 0.8156 (mt) cc_final: 0.7831 (mp) REVERT: B 225 VAL cc_start: 0.7617 (p) cc_final: 0.7319 (m) REVERT: B 308 ASN cc_start: 0.8253 (m-40) cc_final: 0.8010 (m-40) REVERT: B 354 GLN cc_start: 0.8333 (mp10) cc_final: 0.7702 (mp10) REVERT: C 23 GLN cc_start: 0.8761 (tt0) cc_final: 0.8233 (tt0) REVERT: C 208 ARG cc_start: 0.4640 (OUTLIER) cc_final: 0.4138 (ptm160) REVERT: C 298 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6572 (tmm) REVERT: C 320 GLU cc_start: 0.6977 (mp0) cc_final: 0.6491 (mp0) REVERT: D 281 TYR cc_start: 0.6520 (t80) cc_final: 0.6088 (t80) REVERT: D 335 LYS cc_start: 0.8907 (pptt) cc_final: 0.8627 (pptt) REVERT: D 344 LEU cc_start: 0.4134 (OUTLIER) cc_final: 0.3909 (tp) outliers start: 57 outliers final: 24 residues processed: 383 average time/residue: 0.3134 time to fit residues: 160.7562 Evaluate side-chains 357 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 327 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 859 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137522 restraints weight = 20385.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.142074 restraints weight = 10985.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.145069 restraints weight = 6927.957| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10644 Z= 0.156 Angle : 0.684 11.600 14367 Z= 0.338 Chirality : 0.043 0.309 1534 Planarity : 0.005 0.063 1862 Dihedral : 4.693 49.935 1409 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.33 % Allowed : 29.77 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.36 (0.24), residues: 1260 helix: 1.18 (0.20), residues: 679 sheet: -0.40 (0.54), residues: 80 loop : -0.93 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 206 HIS 0.005 0.001 HIS B 69 PHE 0.035 0.002 PHE B 108 TYR 0.026 0.002 TYR A 777 ARG 0.007 0.000 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 532) hydrogen bonds : angle 4.60695 ( 1548) metal coordination : bond 0.00992 ( 17) metal coordination : angle 4.38129 ( 15) covalent geometry : bond 0.00346 (10627) covalent geometry : angle 0.66981 (14352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7403 (t80) cc_final: 0.7019 (t80) REVERT: A 346 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6916 (pp30) REVERT: A 347 LEU cc_start: 0.8139 (mp) cc_final: 0.7699 (mp) REVERT: A 354 LYS cc_start: 0.3976 (OUTLIER) cc_final: 0.2940 (ptpp) REVERT: A 428 TRP cc_start: 0.7884 (m100) cc_final: 0.7519 (m100) REVERT: A 449 GLU cc_start: 0.7424 (tt0) cc_final: 0.6933 (tp30) REVERT: A 462 LEU cc_start: 0.8042 (tp) cc_final: 0.7583 (mp) REVERT: A 466 LEU cc_start: 0.7853 (mt) cc_final: 0.7635 (mt) REVERT: A 477 GLU cc_start: 0.7328 (tp30) cc_final: 0.7057 (mm-30) REVERT: A 480 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7919 (tm-30) REVERT: A 495 ARG cc_start: 0.7408 (mmm160) cc_final: 0.7157 (mmm160) REVERT: A 509 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7606 (mtt180) REVERT: A 510 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7514 (tpp-160) REVERT: A 539 LEU cc_start: 0.8102 (mp) cc_final: 0.7784 (tp) REVERT: A 545 LYS cc_start: 0.7494 (tptt) cc_final: 0.7174 (mptt) REVERT: A 570 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7147 (ttmm) REVERT: A 581 GLN cc_start: 0.7456 (mp-120) cc_final: 0.7082 (mp10) REVERT: A 582 ASN cc_start: 0.7082 (m-40) cc_final: 0.6798 (m-40) REVERT: A 597 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 742 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7879 (tt) REVERT: A 748 ASN cc_start: 0.7206 (m-40) cc_final: 0.6629 (m-40) REVERT: A 771 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7941 (tp-100) REVERT: A 772 LYS cc_start: 0.7911 (ttmm) cc_final: 0.7545 (tmmt) REVERT: A 778 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7453 (ptp-110) REVERT: A 814 GLU cc_start: 0.7441 (tp30) cc_final: 0.7180 (tp30) REVERT: A 849 TYR cc_start: 0.7098 (p90) cc_final: 0.6864 (p90) REVERT: A 852 PHE cc_start: 0.7350 (m-80) cc_final: 0.7029 (m-80) REVERT: A 863 ARG cc_start: 0.7509 (mmp-170) cc_final: 0.7103 (mmp80) REVERT: A 864 GLN cc_start: 0.7570 (tp40) cc_final: 0.7291 (mm-40) REVERT: A 879 GLU cc_start: 0.7058 (pp20) cc_final: 0.6745 (pp20) REVERT: A 884 GLU cc_start: 0.7087 (tt0) cc_final: 0.6811 (tt0) REVERT: A 903 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7076 (ptp90) REVERT: A 909 TRP cc_start: 0.7341 (t60) cc_final: 0.7025 (t60) REVERT: A 915 MET cc_start: 0.7780 (ppp) cc_final: 0.7511 (tmm) REVERT: A 922 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7937 (ttmm) REVERT: B 23 TYR cc_start: 0.8321 (m-80) cc_final: 0.7512 (m-80) REVERT: B 42 LEU cc_start: 0.8285 (mt) cc_final: 0.7978 (tt) REVERT: B 56 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7279 (mmm-85) REVERT: B 68 TYR cc_start: 0.7723 (t80) cc_final: 0.7218 (t80) REVERT: B 156 ASP cc_start: 0.7541 (t0) cc_final: 0.7305 (t0) REVERT: B 157 ILE cc_start: 0.8155 (mt) cc_final: 0.7880 (mp) REVERT: B 206 PHE cc_start: 0.7865 (t80) cc_final: 0.7607 (t80) REVERT: B 225 VAL cc_start: 0.7607 (p) cc_final: 0.7312 (m) REVERT: B 229 MET cc_start: 0.7835 (mtm) cc_final: 0.7615 (mtp) REVERT: B 253 TYR cc_start: 0.6323 (t80) cc_final: 0.5922 (t80) REVERT: B 308 ASN cc_start: 0.8259 (m-40) cc_final: 0.8036 (m-40) REVERT: B 354 GLN cc_start: 0.8309 (mp10) cc_final: 0.7617 (mp10) REVERT: C 23 GLN cc_start: 0.8718 (tt0) cc_final: 0.8185 (tt0) REVERT: C 208 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.4120 (ptm160) REVERT: C 298 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6538 (tmm) REVERT: C 320 GLU cc_start: 0.6976 (mp0) cc_final: 0.6497 (mp0) REVERT: D 281 TYR cc_start: 0.6568 (t80) cc_final: 0.6081 (t80) REVERT: D 335 LYS cc_start: 0.8912 (pptt) cc_final: 0.8573 (pptt) REVERT: D 344 LEU cc_start: 0.4165 (OUTLIER) cc_final: 0.3888 (tp) outliers start: 49 outliers final: 31 residues processed: 374 average time/residue: 0.2931 time to fit residues: 145.8553 Evaluate side-chains 376 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 338 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 276 PHE Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 660 HIS A 859 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.164451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.138190 restraints weight = 20393.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.142615 restraints weight = 10982.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.145585 restraints weight = 6973.335| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10644 Z= 0.138 Angle : 0.681 12.054 14367 Z= 0.334 Chirality : 0.042 0.370 1534 Planarity : 0.005 0.061 1862 Dihedral : 4.626 51.068 1409 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.68 % Allowed : 30.48 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.28 (0.20), residues: 673 sheet: -0.37 (0.55), residues: 79 loop : -0.90 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 206 HIS 0.005 0.001 HIS C 297 PHE 0.020 0.001 PHE B 108 TYR 0.030 0.002 TYR A 777 ARG 0.006 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 532) hydrogen bonds : angle 4.49908 ( 1548) metal coordination : bond 0.00932 ( 17) metal coordination : angle 3.93770 ( 15) covalent geometry : bond 0.00309 (10627) covalent geometry : angle 0.66943 (14352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: A 327 PHE cc_start: 0.7387 (t80) cc_final: 0.6984 (t80) REVERT: A 346 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6942 (pp30) REVERT: A 347 LEU cc_start: 0.8171 (mp) cc_final: 0.7698 (mp) REVERT: A 354 LYS cc_start: 0.3995 (OUTLIER) cc_final: 0.2943 (ptpp) REVERT: A 449 GLU cc_start: 0.7390 (tt0) cc_final: 0.6816 (tp30) REVERT: A 462 LEU cc_start: 0.8037 (tp) cc_final: 0.7569 (mp) REVERT: A 466 LEU cc_start: 0.7839 (mt) cc_final: 0.7613 (mt) REVERT: A 477 GLU cc_start: 0.7312 (tp30) cc_final: 0.6809 (mm-30) REVERT: A 480 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7914 (tm-30) REVERT: A 505 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 509 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7812 (ttm110) REVERT: A 510 ARG cc_start: 0.7890 (tpp-160) cc_final: 0.7551 (tpp-160) REVERT: A 539 LEU cc_start: 0.8110 (mp) cc_final: 0.7582 (tp) REVERT: A 545 LYS cc_start: 0.7501 (tptt) cc_final: 0.7197 (mptt) REVERT: A 556 PHE cc_start: 0.7442 (m-10) cc_final: 0.7237 (m-80) REVERT: A 570 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7590 (mtpp) REVERT: A 582 ASN cc_start: 0.7084 (m-40) cc_final: 0.6799 (m-40) REVERT: A 597 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6809 (mt-10) REVERT: A 742 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 748 ASN cc_start: 0.7251 (m-40) cc_final: 0.6678 (m-40) REVERT: A 771 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7897 (tp-100) REVERT: A 772 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7555 (tmmt) REVERT: A 813 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 849 TYR cc_start: 0.7135 (p90) cc_final: 0.6763 (p90) REVERT: A 863 ARG cc_start: 0.7571 (mmp-170) cc_final: 0.7215 (mmp80) REVERT: A 864 GLN cc_start: 0.7532 (tp40) cc_final: 0.7321 (mm-40) REVERT: A 884 GLU cc_start: 0.7259 (tt0) cc_final: 0.7009 (tt0) REVERT: A 903 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7410 (ptp90) REVERT: A 909 TRP cc_start: 0.7313 (t60) cc_final: 0.7049 (t60) REVERT: A 915 MET cc_start: 0.7770 (ppp) cc_final: 0.7493 (tmm) REVERT: A 922 LYS cc_start: 0.8425 (ttmm) cc_final: 0.7960 (ttmm) REVERT: B 42 LEU cc_start: 0.8334 (mt) cc_final: 0.8005 (tt) REVERT: B 56 ARG cc_start: 0.7701 (mtp180) cc_final: 0.7297 (mtp180) REVERT: B 68 TYR cc_start: 0.7717 (t80) cc_final: 0.7395 (t80) REVERT: B 156 ASP cc_start: 0.7522 (t0) cc_final: 0.7284 (t0) REVERT: B 157 ILE cc_start: 0.8159 (mt) cc_final: 0.7887 (mp) REVERT: B 193 ARG cc_start: 0.7201 (mmm160) cc_final: 0.6998 (mmm160) REVERT: B 206 PHE cc_start: 0.7854 (t80) cc_final: 0.7586 (t80) REVERT: B 225 VAL cc_start: 0.7602 (p) cc_final: 0.7296 (m) REVERT: B 229 MET cc_start: 0.7848 (mtm) cc_final: 0.7645 (mtp) REVERT: B 253 TYR cc_start: 0.6348 (t80) cc_final: 0.5960 (t80) REVERT: B 308 ASN cc_start: 0.8226 (m-40) cc_final: 0.7997 (m-40) REVERT: B 354 GLN cc_start: 0.8301 (mp10) cc_final: 0.7567 (mp10) REVERT: C 23 GLN cc_start: 0.8719 (tt0) cc_final: 0.8051 (tt0) REVERT: C 208 ARG cc_start: 0.4636 (OUTLIER) cc_final: 0.4149 (ptm160) REVERT: C 279 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6734 (mtp-110) REVERT: C 298 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6502 (tmm) REVERT: C 320 GLU cc_start: 0.6972 (mp0) cc_final: 0.6512 (mp0) REVERT: D 281 TYR cc_start: 0.6565 (t80) cc_final: 0.6058 (t80) REVERT: D 335 LYS cc_start: 0.8906 (pptt) cc_final: 0.8577 (pptt) outliers start: 53 outliers final: 32 residues processed: 373 average time/residue: 0.3058 time to fit residues: 152.5403 Evaluate side-chains 374 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 859 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.162638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.135476 restraints weight = 20657.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140096 restraints weight = 11386.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.143140 restraints weight = 7148.177| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10644 Z= 0.179 Angle : 0.710 12.259 14367 Z= 0.351 Chirality : 0.044 0.378 1534 Planarity : 0.005 0.059 1862 Dihedral : 4.756 51.596 1409 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.95 % Allowed : 31.36 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.30 (0.24), residues: 1260 helix: 1.16 (0.20), residues: 672 sheet: -0.43 (0.54), residues: 79 loop : -0.97 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP D 206 HIS 0.005 0.001 HIS C 297 PHE 0.014 0.002 PHE B 108 TYR 0.034 0.002 TYR A 777 ARG 0.008 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 532) hydrogen bonds : angle 4.69551 ( 1548) metal coordination : bond 0.01138 ( 17) metal coordination : angle 4.27130 ( 15) covalent geometry : bond 0.00393 (10627) covalent geometry : angle 0.69642 (14352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: A 327 PHE cc_start: 0.7404 (t80) cc_final: 0.7062 (t80) REVERT: A 346 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7023 (pp30) REVERT: A 347 LEU cc_start: 0.8298 (mp) cc_final: 0.7847 (mp) REVERT: A 354 LYS cc_start: 0.4195 (OUTLIER) cc_final: 0.3058 (ptpp) REVERT: A 449 GLU cc_start: 0.7452 (tt0) cc_final: 0.6868 (tp30) REVERT: A 462 LEU cc_start: 0.8077 (tp) cc_final: 0.7578 (mp) REVERT: A 466 LEU cc_start: 0.7815 (mt) cc_final: 0.7566 (mt) REVERT: A 474 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7498 (ttm110) REVERT: A 477 GLU cc_start: 0.7326 (tp30) cc_final: 0.6816 (mm-30) REVERT: A 480 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7901 (tm-30) REVERT: A 505 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 509 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7769 (ttm110) REVERT: A 510 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7587 (mmm-85) REVERT: A 539 LEU cc_start: 0.8098 (mp) cc_final: 0.7553 (tp) REVERT: A 545 LYS cc_start: 0.7535 (tptt) cc_final: 0.7227 (mptt) REVERT: A 570 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7170 (ttmm) REVERT: A 582 ASN cc_start: 0.7070 (m-40) cc_final: 0.6812 (m-40) REVERT: A 597 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6713 (mt-10) REVERT: A 742 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 748 ASN cc_start: 0.7285 (m-40) cc_final: 0.6705 (m-40) REVERT: A 771 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7965 (tp-100) REVERT: A 778 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7516 (ptp-110) REVERT: A 813 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 849 TYR cc_start: 0.7293 (p90) cc_final: 0.6799 (p90) REVERT: A 863 ARG cc_start: 0.7565 (mmp-170) cc_final: 0.7130 (mmp80) REVERT: A 864 GLN cc_start: 0.7590 (tp40) cc_final: 0.7355 (mm-40) REVERT: A 884 GLU cc_start: 0.7344 (tt0) cc_final: 0.7081 (tt0) REVERT: A 903 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7437 (ptp90) REVERT: A 909 TRP cc_start: 0.7403 (t60) cc_final: 0.7159 (t60) REVERT: A 922 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7991 (ttmm) REVERT: B 42 LEU cc_start: 0.8360 (mt) cc_final: 0.8045 (tt) REVERT: B 56 ARG cc_start: 0.7700 (mtp180) cc_final: 0.7246 (mtp180) REVERT: B 68 TYR cc_start: 0.7682 (t80) cc_final: 0.7388 (t80) REVERT: B 156 ASP cc_start: 0.7574 (t0) cc_final: 0.7358 (t0) REVERT: B 157 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 163 GLU cc_start: 0.7087 (tp30) cc_final: 0.6876 (tp30) REVERT: B 193 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6878 (mmm160) REVERT: B 206 PHE cc_start: 0.7915 (t80) cc_final: 0.7694 (t80) REVERT: B 225 VAL cc_start: 0.7705 (p) cc_final: 0.7394 (m) REVERT: B 229 MET cc_start: 0.7846 (mtm) cc_final: 0.7611 (mtp) REVERT: B 230 ARG cc_start: 0.7681 (mtt90) cc_final: 0.7403 (mtt90) REVERT: B 253 TYR cc_start: 0.6529 (t80) cc_final: 0.6007 (t80) REVERT: B 308 ASN cc_start: 0.8206 (m-40) cc_final: 0.7990 (m-40) REVERT: B 315 TYR cc_start: 0.8136 (t80) cc_final: 0.7324 (t80) REVERT: C 23 GLN cc_start: 0.8625 (tt0) cc_final: 0.8143 (tt0) REVERT: C 208 ARG cc_start: 0.4701 (OUTLIER) cc_final: 0.4185 (ptm160) REVERT: C 279 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6749 (mtp-110) REVERT: C 295 LEU cc_start: 0.7190 (mp) cc_final: 0.6952 (mp) REVERT: C 298 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6533 (tmm) REVERT: C 320 GLU cc_start: 0.7056 (mp0) cc_final: 0.6591 (mp0) REVERT: C 329 MET cc_start: 0.4920 (tpt) cc_final: 0.4624 (tpp) REVERT: D 281 TYR cc_start: 0.6618 (t80) cc_final: 0.6098 (t80) REVERT: D 335 LYS cc_start: 0.8908 (pptt) cc_final: 0.8576 (pptt) outliers start: 56 outliers final: 41 residues processed: 373 average time/residue: 0.2964 time to fit residues: 147.6094 Evaluate side-chains 390 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 0.0000 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 660 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.164797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137816 restraints weight = 20450.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.142452 restraints weight = 11044.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145508 restraints weight = 6983.399| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10644 Z= 0.134 Angle : 0.716 13.399 14367 Z= 0.349 Chirality : 0.042 0.390 1534 Planarity : 0.005 0.059 1862 Dihedral : 4.635 52.882 1409 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.51 % Allowed : 32.16 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.49 (0.24), residues: 1260 helix: 1.37 (0.20), residues: 665 sheet: -0.41 (0.54), residues: 79 loop : -0.90 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 206 HIS 0.005 0.001 HIS C 297 PHE 0.017 0.001 PHE B 76 TYR 0.033 0.002 TYR A 777 ARG 0.012 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 532) hydrogen bonds : angle 4.49282 ( 1548) metal coordination : bond 0.01066 ( 17) metal coordination : angle 4.12890 ( 15) covalent geometry : bond 0.00304 (10627) covalent geometry : angle 0.70372 (14352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: A 327 PHE cc_start: 0.7413 (t80) cc_final: 0.7015 (t80) REVERT: A 346 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7008 (pp30) REVERT: A 347 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 354 LYS cc_start: 0.4024 (OUTLIER) cc_final: 0.2968 (ptpp) REVERT: A 462 LEU cc_start: 0.8027 (tp) cc_final: 0.7543 (mp) REVERT: A 466 LEU cc_start: 0.7824 (mt) cc_final: 0.7569 (mt) REVERT: A 477 GLU cc_start: 0.7313 (tp30) cc_final: 0.6807 (mm-30) REVERT: A 480 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7915 (tm-30) REVERT: A 505 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 509 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7686 (ttm110) REVERT: A 539 LEU cc_start: 0.8084 (mp) cc_final: 0.7550 (tp) REVERT: A 545 LYS cc_start: 0.7527 (tptt) cc_final: 0.7201 (mptt) REVERT: A 570 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7556 (mtpp) REVERT: A 582 ASN cc_start: 0.7086 (m-40) cc_final: 0.6821 (m-40) REVERT: A 597 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6776 (mt-10) REVERT: A 742 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 748 ASN cc_start: 0.7257 (m-40) cc_final: 0.6584 (m-40) REVERT: A 771 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7912 (tp-100) REVERT: A 772 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7633 (tmmt) REVERT: A 849 TYR cc_start: 0.7248 (p90) cc_final: 0.6798 (p90) REVERT: A 863 ARG cc_start: 0.7605 (mmp-170) cc_final: 0.7207 (mmp80) REVERT: A 864 GLN cc_start: 0.7567 (tp40) cc_final: 0.7331 (mm-40) REVERT: A 867 HIS cc_start: 0.6988 (t70) cc_final: 0.6625 (t70) REVERT: A 884 GLU cc_start: 0.7342 (tt0) cc_final: 0.7049 (tt0) REVERT: A 903 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7397 (ptp90) REVERT: A 909 TRP cc_start: 0.7363 (t60) cc_final: 0.7057 (t60) REVERT: A 915 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7643 (tmm) REVERT: A 922 LYS cc_start: 0.8464 (ttmm) cc_final: 0.7989 (ttmm) REVERT: B 22 ASN cc_start: 0.7644 (t0) cc_final: 0.7404 (t0) REVERT: B 42 LEU cc_start: 0.8355 (mt) cc_final: 0.8029 (tt) REVERT: B 68 TYR cc_start: 0.7680 (t80) cc_final: 0.7440 (t80) REVERT: B 156 ASP cc_start: 0.7513 (t0) cc_final: 0.7259 (t0) REVERT: B 157 ILE cc_start: 0.8148 (mt) cc_final: 0.7882 (mp) REVERT: B 163 GLU cc_start: 0.7074 (tp30) cc_final: 0.6828 (tp30) REVERT: B 193 ARG cc_start: 0.7072 (mmm160) cc_final: 0.6557 (mtp85) REVERT: B 206 PHE cc_start: 0.7863 (t80) cc_final: 0.7616 (t80) REVERT: B 225 VAL cc_start: 0.7639 (p) cc_final: 0.7352 (m) REVERT: B 236 GLU cc_start: 0.7665 (pm20) cc_final: 0.7423 (pm20) REVERT: B 253 TYR cc_start: 0.6470 (t80) cc_final: 0.6009 (t80) REVERT: B 335 PHE cc_start: 0.8166 (t80) cc_final: 0.7928 (t80) REVERT: B 337 TYR cc_start: 0.7600 (m-80) cc_final: 0.6928 (m-80) REVERT: C 208 ARG cc_start: 0.4710 (OUTLIER) cc_final: 0.4220 (ptm160) REVERT: C 279 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6765 (mtm-85) REVERT: C 295 LEU cc_start: 0.7185 (mp) cc_final: 0.6953 (mp) REVERT: C 298 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6596 (tmm) REVERT: C 313 TRP cc_start: 0.7408 (t60) cc_final: 0.7115 (t60) REVERT: C 320 GLU cc_start: 0.7062 (mp0) cc_final: 0.6614 (mp0) REVERT: D 281 TYR cc_start: 0.6603 (t80) cc_final: 0.6062 (t80) REVERT: D 335 LYS cc_start: 0.8905 (pptt) cc_final: 0.8552 (pptt) outliers start: 51 outliers final: 36 residues processed: 360 average time/residue: 0.2683 time to fit residues: 129.8526 Evaluate side-chains 383 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 469 ASN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 63 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 660 HIS A 859 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.164647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137837 restraints weight = 20752.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.142220 restraints weight = 11263.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.145286 restraints weight = 7230.802| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10644 Z= 0.135 Angle : 0.729 13.749 14367 Z= 0.355 Chirality : 0.043 0.395 1534 Planarity : 0.005 0.060 1862 Dihedral : 4.496 39.474 1409 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.24 % Allowed : 32.16 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.33 (0.20), residues: 665 sheet: -0.56 (0.54), residues: 79 loop : -0.92 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 206 HIS 0.004 0.001 HIS C 297 PHE 0.021 0.001 PHE B 342 TYR 0.034 0.002 TYR A 777 ARG 0.008 0.001 ARG A 778 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 532) hydrogen bonds : angle 4.48073 ( 1548) metal coordination : bond 0.01080 ( 17) metal coordination : angle 3.92307 ( 15) covalent geometry : bond 0.00309 (10627) covalent geometry : angle 0.71779 (14352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7387 (t80) cc_final: 0.7017 (t80) REVERT: A 346 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7023 (pp30) REVERT: A 347 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 354 LYS cc_start: 0.3898 (OUTLIER) cc_final: 0.2782 (ptpp) REVERT: A 462 LEU cc_start: 0.8034 (tp) cc_final: 0.7555 (mp) REVERT: A 466 LEU cc_start: 0.7819 (mt) cc_final: 0.7561 (mt) REVERT: A 474 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7471 (ttm110) REVERT: A 477 GLU cc_start: 0.7293 (tp30) cc_final: 0.6838 (mm-30) REVERT: A 480 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7919 (tm-30) REVERT: A 505 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 509 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7585 (ttm110) REVERT: A 510 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7407 (tpp-160) REVERT: A 539 LEU cc_start: 0.8111 (mp) cc_final: 0.7513 (tp) REVERT: A 545 LYS cc_start: 0.7549 (tptt) cc_final: 0.7238 (mptt) REVERT: A 570 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7570 (mtpp) REVERT: A 582 ASN cc_start: 0.7081 (m-40) cc_final: 0.6804 (m110) REVERT: A 597 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6797 (mt-10) REVERT: A 742 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7828 (tt) REVERT: A 748 ASN cc_start: 0.7291 (m-40) cc_final: 0.6633 (m-40) REVERT: A 771 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7894 (tp-100) REVERT: A 772 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7650 (tmmt) REVERT: A 778 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7403 (ptp-110) REVERT: A 849 TYR cc_start: 0.7139 (p90) cc_final: 0.6700 (p90) REVERT: A 859 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: A 863 ARG cc_start: 0.7605 (mmp-170) cc_final: 0.7179 (mmp80) REVERT: A 864 GLN cc_start: 0.7571 (tp40) cc_final: 0.7358 (mm-40) REVERT: A 867 HIS cc_start: 0.7002 (t70) cc_final: 0.6607 (t70) REVERT: A 903 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7422 (ptp90) REVERT: A 909 TRP cc_start: 0.7335 (t60) cc_final: 0.7041 (t60) REVERT: A 915 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7574 (tmm) REVERT: A 922 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8066 (ttmm) REVERT: B 41 ASN cc_start: 0.8298 (t0) cc_final: 0.7901 (t0) REVERT: B 42 LEU cc_start: 0.8343 (mt) cc_final: 0.8023 (tt) REVERT: B 65 MET cc_start: 0.6930 (mtt) cc_final: 0.6533 (mtp) REVERT: B 85 MET cc_start: 0.5883 (mtp) cc_final: 0.5682 (mtp) REVERT: B 156 ASP cc_start: 0.7495 (t0) cc_final: 0.7256 (t0) REVERT: B 157 ILE cc_start: 0.8159 (mt) cc_final: 0.7918 (mp) REVERT: B 163 GLU cc_start: 0.7036 (tp30) cc_final: 0.6822 (tp30) REVERT: B 206 PHE cc_start: 0.7820 (t80) cc_final: 0.7552 (t80) REVERT: B 225 VAL cc_start: 0.7664 (p) cc_final: 0.7366 (m) REVERT: B 236 GLU cc_start: 0.7598 (pm20) cc_final: 0.7385 (pm20) REVERT: B 253 TYR cc_start: 0.6459 (t80) cc_final: 0.5967 (t80) REVERT: C 208 ARG cc_start: 0.4784 (OUTLIER) cc_final: 0.4283 (ptm160) REVERT: C 279 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6810 (mtm-85) REVERT: C 295 LEU cc_start: 0.7167 (mp) cc_final: 0.6945 (mp) REVERT: C 298 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6634 (tmm) REVERT: C 302 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6580 (tm-30) REVERT: C 305 LEU cc_start: 0.7254 (mt) cc_final: 0.6697 (mt) REVERT: C 320 GLU cc_start: 0.7064 (mp0) cc_final: 0.6624 (mp0) REVERT: D 335 LYS cc_start: 0.8873 (pptt) cc_final: 0.8519 (pptt) outliers start: 48 outliers final: 33 residues processed: 362 average time/residue: 0.2743 time to fit residues: 132.8917 Evaluate side-chains 375 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 332 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 121 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 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 = 0.4285 r_free = 0.4285 target = 0.165006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.138008 restraints weight = 20508.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.142637 restraints weight = 11250.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.145679 restraints weight = 7066.871| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10644 Z= 0.140 Angle : 0.724 13.748 14367 Z= 0.354 Chirality : 0.043 0.400 1534 Planarity : 0.005 0.059 1862 Dihedral : 4.474 36.440 1409 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.98 % Allowed : 32.51 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1260 helix: 1.34 (0.20), residues: 664 sheet: -0.45 (0.55), residues: 79 loop : -0.91 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP D 206 HIS 0.005 0.001 HIS C 297 PHE 0.019 0.002 PHE B 76 TYR 0.034 0.002 TYR A 513 ARG 0.007 0.001 ARG A 778 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 532) hydrogen bonds : angle 4.50090 ( 1548) metal coordination : bond 0.01004 ( 17) metal coordination : angle 3.94583 ( 15) covalent geometry : bond 0.00321 (10627) covalent geometry : angle 0.71345 (14352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 337 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7425 (t80) cc_final: 0.7025 (t80) REVERT: A 346 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7040 (pp30) REVERT: A 347 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 354 LYS cc_start: 0.3920 (OUTLIER) cc_final: 0.2823 (ptpp) REVERT: A 462 LEU cc_start: 0.8014 (tp) cc_final: 0.7555 (mp) REVERT: A 466 LEU cc_start: 0.7831 (mt) cc_final: 0.7580 (mt) REVERT: A 477 GLU cc_start: 0.7302 (tp30) cc_final: 0.6865 (mm-30) REVERT: A 480 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7913 (tm-30) REVERT: A 505 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 509 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7621 (ttm110) REVERT: A 510 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: A 539 LEU cc_start: 0.8130 (mp) cc_final: 0.7571 (tp) REVERT: A 541 ARG cc_start: 0.6840 (mtp85) cc_final: 0.6597 (mtp85) REVERT: A 545 LYS cc_start: 0.7543 (tptt) cc_final: 0.7224 (mptt) REVERT: A 570 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7568 (mtpp) REVERT: A 582 ASN cc_start: 0.7087 (m-40) cc_final: 0.6808 (m110) REVERT: A 597 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6810 (mt-10) REVERT: A 742 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 748 ASN cc_start: 0.7304 (m-40) cc_final: 0.6639 (m-40) REVERT: A 771 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7922 (tp-100) REVERT: A 772 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7646 (tmmt) REVERT: A 778 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7396 (ptp-110) REVERT: A 849 TYR cc_start: 0.7167 (p90) cc_final: 0.6689 (p90) REVERT: A 859 GLN cc_start: 0.7491 (mt0) cc_final: 0.7038 (pm20) REVERT: A 863 ARG cc_start: 0.7628 (mmp-170) cc_final: 0.7226 (mmp80) REVERT: A 864 GLN cc_start: 0.7601 (tp40) cc_final: 0.7396 (mm-40) REVERT: A 867 HIS cc_start: 0.6992 (t70) cc_final: 0.6596 (t70) REVERT: A 903 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7403 (ptp90) REVERT: A 909 TRP cc_start: 0.7358 (t60) cc_final: 0.7065 (t60) REVERT: A 915 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7532 (tmm) REVERT: A 922 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8048 (ttmm) REVERT: B 42 LEU cc_start: 0.8355 (mt) cc_final: 0.8010 (tt) REVERT: B 65 MET cc_start: 0.6929 (mtt) cc_final: 0.6537 (mtp) REVERT: B 85 MET cc_start: 0.5934 (mtp) cc_final: 0.5713 (mtp) REVERT: B 156 ASP cc_start: 0.7506 (t0) cc_final: 0.7262 (t0) REVERT: B 157 ILE cc_start: 0.8155 (mt) cc_final: 0.7909 (mp) REVERT: B 163 GLU cc_start: 0.7070 (tp30) cc_final: 0.6825 (tp30) REVERT: B 225 VAL cc_start: 0.7674 (p) cc_final: 0.7389 (m) REVERT: B 253 TYR cc_start: 0.6479 (t80) cc_final: 0.6024 (t80) REVERT: B 337 TYR cc_start: 0.7612 (m-80) cc_final: 0.6981 (m-80) REVERT: C 208 ARG cc_start: 0.4505 (OUTLIER) cc_final: 0.4064 (ptm160) REVERT: C 279 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6710 (mtm-85) REVERT: C 295 LEU cc_start: 0.7158 (mp) cc_final: 0.6929 (mp) REVERT: C 298 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6617 (tmm) REVERT: C 305 LEU cc_start: 0.7250 (mt) cc_final: 0.6677 (mt) REVERT: C 320 GLU cc_start: 0.7078 (mp0) cc_final: 0.6637 (mp0) REVERT: D 335 LYS cc_start: 0.8869 (pptt) cc_final: 0.8511 (pptt) outliers start: 45 outliers final: 30 residues processed: 356 average time/residue: 0.2938 time to fit residues: 142.0046 Evaluate side-chains 375 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 336 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 866 HIS Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 359 HIS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 276 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 115 optimal weight: 0.0010 chunk 36 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 118 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 660 HIS A 859 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.165680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.139152 restraints weight = 20466.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143621 restraints weight = 11031.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.146659 restraints weight = 7038.214| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10644 Z= 0.131 Angle : 0.724 13.709 14367 Z= 0.352 Chirality : 0.043 0.386 1534 Planarity : 0.005 0.059 1862 Dihedral : 4.398 31.270 1409 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.80 % Allowed : 32.95 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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 (0.24), residues: 1260 helix: 1.31 (0.20), residues: 669 sheet: -0.49 (0.56), residues: 79 loop : -0.92 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 206 HIS 0.004 0.001 HIS C 297 PHE 0.016 0.001 PHE B 335 TYR 0.034 0.002 TYR A 777 ARG 0.006 0.001 ARG A 778 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 532) hydrogen bonds : angle 4.45331 ( 1548) metal coordination : bond 0.01032 ( 17) metal coordination : angle 3.78313 ( 15) covalent geometry : bond 0.00301 (10627) covalent geometry : angle 0.71434 (14352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4669.34 seconds wall clock time: 83 minutes 28.40 seconds (5008.40 seconds total)