Starting phenix.real_space_refine on Sat Sep 12 00:19:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.map" model { file = "/net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l49_23158/09_2026/7l49_23158.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Zn 4 6.06 5 P 190 5.49 5 S 37 5.16 5 C 7186 2.51 5 N 2218 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 599 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC%5*END:plan': 1, ' DC%5*END:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2877 Classifications: {'RNAv2': 135} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 14, 'rna3p': 120} Chain breaks: 2 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3858 SG CYS A 478 7.021 61.788 44.308 1.00 37.58 S ATOM 4048 SG CYS A 500 10.720 61.502 41.558 1.00 40.36 S ATOM 364 SG CYS A 50 53.252 98.716 77.958 1.00 42.34 S ATOM 502 SG CYS A 69 57.157 99.263 78.476 1.00 31.65 S ATOM 527 SG CYS A 72 55.385 96.180 79.439 1.00 31.06 S ATOM 8043 SG CYS B 478 59.449 58.052 9.211 1.00 58.65 S ATOM 8229 SG CYS B 500 56.592 59.678 11.519 1.00 65.09 S Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12414 At special positions: 0 Unit cell: (102.9, 121.8, 123.9, 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 4 29.99 S 37 16.00 P 190 15.00 O 2779 8.00 N 2218 7.00 C 7186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 381.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 478 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 500 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 46.0% alpha, 10.5% beta 59 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 Processing helix chain 'A' and resid 52 through 58 removed outlier: 4.153A pdb=" N VAL A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 58' Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.678A pdb=" N ARG A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.931A pdb=" N TYR A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.575A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.644A pdb=" N ASN A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.901A pdb=" N GLU A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 350 through 367 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 382 through 414 removed outlier: 3.707A pdb=" N THR A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 518 removed outlier: 3.597A pdb=" N ALA A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 41 removed outlier: 3.557A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.968A pdb=" N VAL B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.747A pdb=" N ALA B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.626A pdb=" N TYR B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.664A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.958A pdb=" N PHE B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.569A pdb=" N SER B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 4.198A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 3.612A pdb=" N GLU B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.991A pdb=" N LYS B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 414 Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 444 through 459 removed outlier: 3.866A pdb=" N TYR B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.581A pdb=" N LYS B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.632A pdb=" N ALA B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.340A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER A 251 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 16 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP A 302 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR A 287 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.532A pdb=" N VAL A 334 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 416 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 321 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 325 " --> pdb=" O GLN A 420 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 422 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL A 327 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY A 417 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ARG A 464 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 419 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 466 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET A 421 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.713A pdb=" N GLU A 507 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 7.396A pdb=" N SER B 251 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 253 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 255 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TRP B 302 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 6.532A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 499 376 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3322 1.34 - 1.47: 4068 1.47 - 1.59: 5248 1.59 - 1.71: 365 1.71 - 1.84: 51 Bond restraints: 13054 Sorted by residual: bond pdb=" C3' DC C 51 " pdb=" C2' DC C 51 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.72e+01 bond pdb=" C1' DT C 44 " pdb=" N1 DT C 44 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C3' DG C 52 " pdb=" C2' DG C 52 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" C3' DT D 13 " pdb=" C2' DT D 13 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 13049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 17660 2.53 - 5.06: 735 5.06 - 7.59: 48 7.59 - 10.12: 10 10.12 - 12.65: 2 Bond angle restraints: 18455 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CA PRO B 384 " pdb=" C PRO B 384 " ideal model delta sigma weight residual 113.40 121.56 -8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" C GLU B 65 " pdb=" N ARG B 66 " pdb=" CA ARG B 66 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C CYS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" O4' DG C 38 " pdb=" C4' DG C 38 " pdb=" C3' DG C 38 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" O4' DC F 34 " pdb=" C4' DC F 34 " pdb=" C3' DC F 34 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 ... (remaining 18450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 6615 27.42 - 54.84: 758 54.84 - 82.26: 114 82.26 - 109.68: 2 109.68 - 137.11: 2 Dihedral angle restraints: 7491 sinusoidal: 4424 harmonic: 3067 Sorted by residual: dihedral pdb=" C4' A E 91 " pdb=" C3' A E 91 " pdb=" C2' A E 91 " pdb=" C1' A E 91 " ideal model delta sinusoidal sigma weight residual 36.34 -39.15 75.49 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' U E 70 " pdb=" C3' U E 70 " pdb=" C2' U E 70 " pdb=" C1' U E 70 " ideal model delta sinusoidal sigma weight residual 36.34 -38.85 75.19 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' C E 122 " pdb=" C3' C E 122 " pdb=" C2' C E 122 " pdb=" C1' C E 122 " ideal model delta sinusoidal sigma weight residual 36.34 -37.62 73.97 1 3.10e+00 1.04e-01 7.23e+02 ... (remaining 7488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1810 0.107 - 0.214: 162 0.214 - 0.321: 139 0.321 - 0.429: 2 0.429 - 0.536: 6 Chirality restraints: 2119 Sorted by residual: chirality pdb=" P G E 218 " pdb=" OP1 G E 218 " pdb=" OP2 G E 218 " pdb=" O5' G E 218 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" P G E 194 " pdb=" OP1 G E 194 " pdb=" OP2 G E 194 " pdb=" O5' G E 194 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" P G E 190 " pdb=" OP1 G E 190 " pdb=" OP2 G E 190 " pdb=" O5' G E 190 " both_signs ideal model delta sigma weight residual True 2.17 -2.70 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 2116 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 42 " -0.031 2.00e-02 2.50e+03 2.42e-02 1.61e+01 pdb=" N9 DA C 42 " 0.064 2.00e-02 2.50e+03 pdb=" C8 DA C 42 " -0.033 2.00e-02 2.50e+03 pdb=" N7 DA C 42 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA C 42 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA C 42 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA C 42 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA C 42 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA C 42 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 197 " 0.024 2.00e-02 2.50e+03 2.31e-02 1.20e+01 pdb=" N1 U E 197 " -0.055 2.00e-02 2.50e+03 pdb=" C2 U E 197 " 0.031 2.00e-02 2.50e+03 pdb=" O2 U E 197 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U E 197 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U E 197 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U E 197 " 0.001 2.00e-02 2.50e+03 pdb=" C5 U E 197 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U E 197 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 123 " 0.026 2.00e-02 2.50e+03 2.19e-02 1.08e+01 pdb=" N1 C E 123 " -0.056 2.00e-02 2.50e+03 pdb=" C2 C E 123 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C E 123 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C E 123 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C E 123 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C E 123 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C E 123 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C E 123 " 0.005 2.00e-02 2.50e+03 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1453 2.76 - 3.29: 10809 3.29 - 3.83: 22411 3.83 - 4.36: 27377 4.36 - 4.90: 41752 Nonbonded interactions: 103802 Sorted by model distance: nonbonded pdb=" N3 C E 22 " pdb=" N1 G E 71 " model vdw 2.220 3.200 nonbonded pdb=" OG1 THR A 9 " pdb=" O2' A E 203 " model vdw 2.282 3.040 nonbonded pdb=" N4 C E 22 " pdb=" O6 G E 71 " model vdw 2.283 3.120 nonbonded pdb=" O2 C E 87 " pdb=" O2' A E 129 " model vdw 2.291 3.040 nonbonded pdb=" O PHE B 341 " pdb=" OH TYR B 511 " model vdw 2.296 3.040 ... (remaining 103797 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.006 0.370 13062 Z= 0.355 Angle : 1.054 12.650 18458 Z= 0.605 Chirality : 0.090 0.536 2119 Planarity : 0.007 0.065 1666 Dihedral : 20.014 137.105 5501 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.21), residues: 1037 helix: -2.17 (0.19), residues: 444 sheet: -2.23 (0.37), residues: 167 loop : -3.07 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 16 TYR 0.021 0.002 TYR B 113 PHE 0.026 0.002 PHE B 220 TRP 0.039 0.003 TRP B 223 HIS 0.014 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.35 (13054) covalent geometry : angle 1.04845 / 0.60 (18455) hydrogen bonds : bond 0.13537 / 9.36 ( 525) hydrogen bonds : angle 6.51030 / 4.41 ( 1386) metal coordination : bond 0.13335 / 6.38 ( 8) metal coordination : angle 8.41972 / 4.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 232 TYR cc_start: 0.6934 (m-80) cc_final: 0.6706 (m-10) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1519 time to fit residues: 25.8078 Evaluate side-chains 87 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 chunk 117 optimal weight: 9.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 209 ASN A 380 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 HIS ** B 480 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 = 0.4146 r_free = 0.4146 target = 0.187412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144814 restraints weight = 13696.101| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.45 r_work: 0.3394 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 13062 Z= 0.234 Angle : 1.091 28.171 18458 Z= 0.479 Chirality : 0.094 1.289 2119 Planarity : 0.005 0.053 1666 Dihedral : 19.148 157.580 3349 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.11 % Allowed : 9.58 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.24), residues: 1037 helix: -0.50 (0.23), residues: 454 sheet: -1.28 (0.42), residues: 154 loop : -2.81 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 16 TYR 0.028 0.002 TYR A 82 PHE 0.020 0.002 PHE B 220 TRP 0.013 0.002 TRP B 223 HIS 0.014 0.002 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (13054) covalent geometry : angle 1.08772 / 0.48 (18455) hydrogen bonds : bond 0.05196 / 3.50 ( 525) hydrogen bonds : angle 4.49080 / 3.08 ( 1386) metal coordination : bond 0.03928 / 1.87 ( 8) metal coordination : angle 6.71922 / 4.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.382 Fit side-chains REVERT: A 18 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: B 343 ARG cc_start: 0.8199 (ptp-170) cc_final: 0.7998 (ptp-170) outliers start: 10 outliers final: 8 residues processed: 116 average time/residue: 0.1415 time to fit residues: 22.0708 Evaluate side-chains 104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 512 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 96 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 ASN A 449 GLN ** B 480 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 = 0.4094 r_free = 0.4094 target = 0.182143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139165 restraints weight = 13724.308| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.54 r_work: 0.3323 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 13062 Z= 0.217 Angle : 0.872 16.218 18458 Z= 0.397 Chirality : 0.067 0.669 2119 Planarity : 0.004 0.052 1666 Dihedral : 19.207 164.565 3349 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.00 % Allowed : 12.92 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.25), residues: 1037 helix: 0.19 (0.24), residues: 461 sheet: -1.11 (0.42), residues: 156 loop : -2.64 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 13 TYR 0.023 0.002 TYR B 511 PHE 0.016 0.002 PHE A 205 TRP 0.011 0.002 TRP B 223 HIS 0.011 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (13054) covalent geometry : angle 0.87051 / 0.40 (18455) hydrogen bonds : bond 0.05007 / 3.33 ( 525) hydrogen bonds : angle 4.18554 / 2.89 ( 1386) metal coordination : bond 0.03369 / 1.61 ( 8) metal coordination : angle 4.64863 / 2.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.297 Fit side-chains REVERT: A 438 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7374 (ttm110) REVERT: B 98 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 153 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7342 (p90) REVERT: B 276 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7996 (mmmm) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.1332 time to fit residues: 21.4214 Evaluate side-chains 110 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 119 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 155 ASN A 355 ASN B 211 ASN ** B 480 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 = 0.4120 r_free = 0.4120 target = 0.184559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142122 restraints weight = 13677.649| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.50 r_work: 0.3353 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13062 Z= 0.161 Angle : 0.774 12.915 18458 Z= 0.358 Chirality : 0.060 0.534 2119 Planarity : 0.004 0.043 1666 Dihedral : 19.084 163.308 3349 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.67 % Allowed : 14.70 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.26), residues: 1037 helix: 0.63 (0.24), residues: 460 sheet: -0.99 (0.44), residues: 152 loop : -2.53 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 343 TYR 0.031 0.001 TYR B 511 PHE 0.015 0.001 PHE A 205 TRP 0.008 0.001 TRP B 223 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (13054) covalent geometry : angle 0.77299 / 0.36 (18455) hydrogen bonds : bond 0.04518 / 2.99 ( 525) hydrogen bonds : angle 3.97349 / 2.74 ( 1386) metal coordination : bond 0.01699 / 0.81 ( 8) metal coordination : angle 3.35253 / 2.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.396 Fit side-chains REVERT: A 425 GLU cc_start: 0.7124 (tp30) cc_final: 0.6206 (pp20) REVERT: A 438 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7361 (ttm110) REVERT: B 98 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7930 (tt) REVERT: B 138 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7671 (tp30) REVERT: B 153 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7344 (p90) REVERT: B 276 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8055 (mmmm) REVERT: B 438 ARG cc_start: 0.6703 (mpt-90) cc_final: 0.6002 (mmm160) REVERT: B 459 TYR cc_start: 0.8500 (m-10) cc_final: 0.8168 (m-10) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 0.1334 time to fit residues: 20.5432 Evaluate side-chains 107 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 449 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.185849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142420 restraints weight = 13715.342| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.45 r_work: 0.3351 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13062 Z= 0.161 Angle : 0.738 10.363 18458 Z= 0.344 Chirality : 0.058 0.456 2119 Planarity : 0.003 0.041 1666 Dihedral : 19.102 170.336 3349 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.67 % Allowed : 15.48 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.26), residues: 1037 helix: 0.91 (0.25), residues: 459 sheet: -0.73 (0.45), residues: 142 loop : -2.44 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.016 0.001 TYR B 113 PHE 0.015 0.001 PHE A 205 TRP 0.008 0.001 TRP B 443 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (13054) covalent geometry : angle 0.73741 / 0.34 (18455) hydrogen bonds : bond 0.04475 / 2.93 ( 525) hydrogen bonds : angle 3.88122 / 2.68 ( 1386) metal coordination : bond 0.01467 / 0.70 ( 8) metal coordination : angle 2.89017 / 1.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8600 (tptp) cc_final: 0.8398 (tptp) REVERT: A 425 GLU cc_start: 0.7221 (tp30) cc_final: 0.6471 (pt0) REVERT: A 438 ARG cc_start: 0.7686 (tpp-160) cc_final: 0.7394 (ttm110) REVERT: B 98 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8028 (tt) REVERT: B 138 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7758 (tp30) REVERT: B 153 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7515 (p90) REVERT: B 438 ARG cc_start: 0.6992 (mpt-90) cc_final: 0.6241 (mmm160) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.1385 time to fit residues: 20.6744 Evaluate side-chains 103 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 96 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 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 = 0.4117 r_free = 0.4117 target = 0.184146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140665 restraints weight = 13455.089| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.37 r_work: 0.3353 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13062 Z= 0.162 Angle : 0.737 13.046 18458 Z= 0.344 Chirality : 0.058 0.493 2119 Planarity : 0.004 0.042 1666 Dihedral : 19.103 171.064 3349 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.78 % Allowed : 15.92 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.26), residues: 1037 helix: 1.00 (0.25), residues: 460 sheet: -0.75 (0.45), residues: 142 loop : -2.39 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 86 TYR 0.017 0.001 TYR B 113 PHE 0.015 0.001 PHE A 205 TRP 0.007 0.001 TRP B 443 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (13054) covalent geometry : angle 0.73616 / 0.34 (18455) hydrogen bonds : bond 0.04416 / 2.90 ( 525) hydrogen bonds : angle 3.84907 / 2.66 ( 1386) metal coordination : bond 0.01161 / 0.55 ( 8) metal coordination : angle 2.74835 / 1.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 425 GLU cc_start: 0.7322 (tp30) cc_final: 0.6300 (pt0) REVERT: A 438 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7500 (ttm110) REVERT: B 98 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8147 (tt) REVERT: B 138 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7951 (tp30) REVERT: B 222 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7648 (mtp85) REVERT: B 383 LYS cc_start: 0.7058 (tptp) cc_final: 0.6399 (mmtt) REVERT: B 481 LEU cc_start: 0.7890 (tp) cc_final: 0.6888 (mt) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.1233 time to fit residues: 18.6261 Evaluate side-chains 104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139201 restraints weight = 13589.456| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.55 r_work: 0.3275 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13062 Z= 0.199 Angle : 0.766 12.754 18458 Z= 0.356 Chirality : 0.059 0.531 2119 Planarity : 0.004 0.046 1666 Dihedral : 19.163 172.001 3349 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.12 % Allowed : 17.26 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.26), residues: 1037 helix: 1.03 (0.25), residues: 461 sheet: -0.99 (0.42), residues: 155 loop : -2.35 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 86 TYR 0.017 0.001 TYR A 82 PHE 0.014 0.002 PHE A 214 TRP 0.009 0.001 TRP A 265 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (13054) covalent geometry : angle 0.76458 / 0.36 (18455) hydrogen bonds : bond 0.04608 / 3.03 ( 525) hydrogen bonds : angle 3.88823 / 2.68 ( 1386) metal coordination : bond 0.01393 / 0.67 ( 8) metal coordination : angle 3.52479 / 2.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 425 GLU cc_start: 0.7374 (tp30) cc_final: 0.6525 (pt0) REVERT: A 438 ARG cc_start: 0.7802 (tpp-160) cc_final: 0.7507 (ttm110) REVERT: B 98 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 138 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7876 (tp30) REVERT: B 153 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7630 (p90) REVERT: B 222 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7561 (mtp85) REVERT: B 383 LYS cc_start: 0.7079 (tptp) cc_final: 0.6320 (mmtt) REVERT: B 481 LEU cc_start: 0.7998 (tp) cc_final: 0.7028 (mt) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.1254 time to fit residues: 18.8788 Evaluate side-chains 103 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 497 HIS Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139458 restraints weight = 13461.983| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.38 r_work: 0.3345 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13062 Z= 0.153 Angle : 0.725 12.092 18458 Z= 0.338 Chirality : 0.057 0.476 2119 Planarity : 0.003 0.040 1666 Dihedral : 19.138 172.491 3349 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.34 % Allowed : 18.15 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1037 helix: 1.16 (0.25), residues: 460 sheet: -0.84 (0.43), residues: 150 loop : -2.32 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 86 TYR 0.016 0.001 TYR B 113 PHE 0.014 0.001 PHE A 205 TRP 0.007 0.001 TRP B 443 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (13054) covalent geometry : angle 0.72427 / 0.34 (18455) hydrogen bonds : bond 0.04337 / 2.84 ( 525) hydrogen bonds : angle 3.83020 / 2.64 ( 1386) metal coordination : bond 0.00932 / 0.44 ( 8) metal coordination : angle 2.59855 / 1.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.258 Fit side-chains REVERT: A 425 GLU cc_start: 0.7328 (tp30) cc_final: 0.6253 (pt0) REVERT: A 438 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7505 (ttm110) REVERT: B 98 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8156 (tt) REVERT: B 138 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7975 (tp30) REVERT: B 153 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7595 (p90) REVERT: B 222 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7662 (mtp85) REVERT: B 383 LYS cc_start: 0.7055 (tptp) cc_final: 0.6304 (mmtt) REVERT: B 438 ARG cc_start: 0.7375 (mpt-90) cc_final: 0.6560 (mmm160) REVERT: B 454 PHE cc_start: 0.8896 (t80) cc_final: 0.8650 (t80) REVERT: B 481 LEU cc_start: 0.7929 (tp) cc_final: 0.6967 (mt) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.1204 time to fit residues: 17.4122 Evaluate side-chains 100 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 30.0000 chunk 64 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 20 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 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 = 0.4153 r_free = 0.4153 target = 0.187924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144723 restraints weight = 13573.196| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.56 r_work: 0.3368 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13062 Z= 0.129 Angle : 0.703 11.724 18458 Z= 0.329 Chirality : 0.055 0.421 2119 Planarity : 0.003 0.036 1666 Dihedral : 19.051 173.375 3349 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.34 % Allowed : 18.71 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.26), residues: 1037 helix: 1.24 (0.25), residues: 462 sheet: -0.78 (0.45), residues: 142 loop : -2.17 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 440 TYR 0.016 0.001 TYR B 113 PHE 0.015 0.001 PHE B 454 TRP 0.008 0.001 TRP A 403 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (13054) covalent geometry : angle 0.70223 / 0.33 (18455) hydrogen bonds : bond 0.04216 / 2.75 ( 525) hydrogen bonds : angle 3.77063 / 2.61 ( 1386) metal coordination : bond 0.00647 / 0.31 ( 8) metal coordination : angle 1.84818 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.298 Fit side-chains REVERT: A 171 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7637 (mtm110) REVERT: A 425 GLU cc_start: 0.7229 (tp30) cc_final: 0.6005 (pp20) REVERT: A 438 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7435 (ttm110) REVERT: B 138 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7817 (tp30) REVERT: B 153 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7374 (p90) REVERT: B 222 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7536 (mtp85) REVERT: B 383 LYS cc_start: 0.7053 (tptp) cc_final: 0.6327 (mmtt) REVERT: B 438 ARG cc_start: 0.7323 (mpt-90) cc_final: 0.6555 (mmm160) REVERT: B 454 PHE cc_start: 0.8763 (t80) cc_final: 0.8535 (t80) REVERT: B 481 LEU cc_start: 0.7923 (tp) cc_final: 0.7036 (mt) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.1283 time to fit residues: 18.7368 Evaluate side-chains 98 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 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 = 0.4102 r_free = 0.4102 target = 0.183229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137305 restraints weight = 13603.242| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.53 r_work: 0.3311 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13062 Z= 0.173 Angle : 0.727 11.656 18458 Z= 0.339 Chirality : 0.056 0.476 2119 Planarity : 0.003 0.035 1666 Dihedral : 19.055 173.020 3349 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.45 % Allowed : 18.60 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1037 helix: 1.25 (0.25), residues: 461 sheet: -0.74 (0.45), residues: 142 loop : -2.14 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.016 0.001 TYR B 113 PHE 0.015 0.001 PHE A 205 TRP 0.008 0.001 TRP B 443 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (13054) covalent geometry : angle 0.72622 / 0.34 (18455) hydrogen bonds : bond 0.04400 / 2.88 ( 525) hydrogen bonds : angle 3.77382 / 2.61 ( 1386) metal coordination : bond 0.01049 / 0.50 ( 8) metal coordination : angle 2.78861 / 1.68 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.300 Fit side-chains REVERT: A 425 GLU cc_start: 0.7227 (tp30) cc_final: 0.5827 (pp20) REVERT: A 438 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7532 (ttm110) REVERT: B 98 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8151 (tt) REVERT: B 138 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8012 (tp30) REVERT: B 153 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7519 (p90) REVERT: B 222 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7661 (mtp85) REVERT: B 383 LYS cc_start: 0.7246 (tptp) cc_final: 0.6368 (mmtt) REVERT: B 438 ARG cc_start: 0.7601 (mpt-90) cc_final: 0.6733 (mmm160) REVERT: B 454 PHE cc_start: 0.8939 (t80) cc_final: 0.8701 (t80) REVERT: B 481 LEU cc_start: 0.8095 (tp) cc_final: 0.7194 (mt) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.1255 time to fit residues: 17.4883 Evaluate side-chains 97 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 517 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 449 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.183835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137933 restraints weight = 13642.787| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.60 r_work: 0.3309 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13062 Z= 0.156 Angle : 0.719 11.489 18458 Z= 0.337 Chirality : 0.056 0.457 2119 Planarity : 0.003 0.033 1666 Dihedral : 19.053 173.186 3349 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.67 % Allowed : 18.60 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 1037 helix: 1.28 (0.25), residues: 461 sheet: -0.73 (0.45), residues: 142 loop : -2.11 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.017 0.001 TYR B 113 PHE 0.013 0.001 PHE B 454 TRP 0.007 0.001 TRP B 443 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (13054) covalent geometry : angle 0.71845 / 0.34 (18455) hydrogen bonds : bond 0.04295 / 2.81 ( 525) hydrogen bonds : angle 3.77129 / 2.61 ( 1386) metal coordination : bond 0.00903 / 0.43 ( 8) metal coordination : angle 2.46804 / 1.53 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2791.57 seconds wall clock time: 48 minutes 42.82 seconds (2922.82 seconds total)