Starting phenix.real_space_refine on Thu Jul 2 16:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/07_2026/9c0f_45082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/07_2026/9c0f_45082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c0f_45082/07_2026/9c0f_45082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/07_2026/9c0f_45082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c0f_45082/07_2026/9c0f_45082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/07_2026/9c0f_45082.map" } resolution = 3.6 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= 0.001 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 70 5.49 5 S 60 5.16 5 C 5845 2.51 5 N 1682 2.21 5 O 1846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 725 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 710 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3883 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 450} Chain breaks: 3 Chain: "D" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4185 Classifications: {'peptide': 504} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 484} Chain breaks: 2 Chain: "C" 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: "D" 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 5131 SG CYS C 550 61.208 48.152 33.030 1.00 65.65 S ATOM 5157 SG CYS C 553 59.580 50.916 32.456 1.00 69.88 S ATOM 4997 SG CYS C 534 52.649 39.523 29.596 1.00 66.98 S ATOM 5021 SG CYS C 537 50.886 37.901 27.221 1.00 71.35 S ATOM 5222 SG CYS C 562 54.572 38.672 26.797 1.00 70.35 S ATOM 9316 SG CYS D 550 72.168 38.504 21.727 1.00104.21 S ATOM 9342 SG CYS D 553 75.805 38.342 20.784 1.00108.94 S ATOM 9206 SG CYS D 537 77.529 32.093 35.072 1.00114.33 S ATOM 9407 SG CYS D 562 74.973 36.015 34.245 1.00105.23 S Time building chain proxies: 1.39, per 1000 atoms: 0.15 Number of scatterers: 9507 At special positions: 0 Unit cell: (108.36, 134.16, 98.9, 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 60 16.00 P 70 15.00 O 1846 8.00 N 1682 7.00 C 5845 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: 0.69 Conformation dependent library (CDL) restraints added in 265.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" NE2 HIS C 567 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 516 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 550 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 553 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" ND1 HIS C 558 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 537 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 534 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 516 " pdb="ZN ZN D 601 " - pdb=" NE2 HIS D 567 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 550 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 553 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 558 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 537 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 562 " Number of angles added : 6 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 39.4% alpha, 11.0% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 107 through 125 Processing helix chain 'C' and resid 142 through 156 Processing helix chain 'C' and resid 163 through 169 removed outlier: 4.063A pdb=" N TYR C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 181 removed outlier: 4.358A pdb=" N GLY C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.571A pdb=" N ALA C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 227 Proline residue: C 222 - end of helix removed outlier: 3.526A pdb=" N ILE C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.796A pdb=" N LYS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.759A pdb=" N LYS C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 430 through 455 Processing helix chain 'C' and resid 460 through 473 Processing helix chain 'C' and resid 505 through 510 removed outlier: 4.345A pdb=" N LEU C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.747A pdb=" N VAL C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 removed outlier: 4.007A pdb=" N LYS C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C 567 " --> pdb=" O PHE C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 Processing helix chain 'D' and resid 107 through 125 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.850A pdb=" N LYS D 130 " --> pdb=" O ASN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 156 removed outlier: 3.814A pdb=" N LYS D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.935A pdb=" N GLU D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.641A pdb=" N TYR D 219 " --> pdb=" O PRO D 215 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 222 - end of helix removed outlier: 4.395A pdb=" N TYR D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 296 through 300 Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.134A pdb=" N ALA D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 400 through 408 Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.500A pdb=" N GLN D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 413 through 418' Processing helix chain 'D' and resid 419 through 426 removed outlier: 3.801A pdb=" N SER D 423 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE D 424 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 455 Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.815A pdb=" N HIS D 540 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 569 Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AA2, first strand: chain 'C' and resid 275 through 280 removed outlier: 6.610A pdb=" N LEU C 267 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET C 278 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG C 265 " --> pdb=" O MET C 278 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE C 280 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 263 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 382 through 386 Processing sheet with id=AA4, first strand: chain 'C' and resid 518 through 520 removed outlier: 4.151A pdb=" N TYR C 548 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE C 555 " --> pdb=" O CYS C 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 532 through 533 Processing sheet with id=AA6, first strand: chain 'D' and resid 275 through 280 removed outlier: 6.707A pdb=" N LEU D 267 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET D 278 " --> pdb=" O ARG D 265 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG D 265 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU D 234 " --> pdb=" O TYR D 307 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR D 331 " --> pdb=" O MET D 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AA8, first strand: chain 'D' and resid 518 through 520 Processing sheet with id=AA9, first strand: chain 'D' and resid 532 through 533 278 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1514 1.30 - 1.44: 3413 1.44 - 1.58: 4693 1.58 - 1.72: 158 1.72 - 1.86: 87 Bond restraints: 9865 Sorted by residual: bond pdb=" N1 DC A 1 " pdb=" C6 DC A 1 " ideal model delta sigma weight residual 1.367 1.436 -0.069 6.00e-03 2.78e+04 1.33e+02 bond pdb=" N1 DC B -35 " pdb=" C6 DC B -35 " ideal model delta sigma weight residual 1.367 1.435 -0.068 6.00e-03 2.78e+04 1.27e+02 bond pdb=" CB HIS D 471 " pdb=" CG HIS D 471 " ideal model delta sigma weight residual 1.497 1.345 0.152 1.40e-02 5.10e+03 1.18e+02 bond pdb=" N3 DG B -1 " pdb=" C4 DG B -1 " ideal model delta sigma weight residual 1.350 1.421 -0.071 7.00e-03 2.04e+04 1.04e+02 bond pdb=" N3 DG A 35 " pdb=" C4 DG A 35 " ideal model delta sigma weight residual 1.350 1.417 -0.067 7.00e-03 2.04e+04 9.11e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11530 2.52 - 5.03: 1761 5.03 - 7.55: 251 7.55 - 10.06: 40 10.06 - 12.58: 9 Bond angle restraints: 13591 Sorted by residual: angle pdb=" O4' DT B -2 " pdb=" C1' DT B -2 " pdb=" N1 DT B -2 " ideal model delta sigma weight residual 108.00 115.22 -7.22 7.00e-01 2.04e+00 1.06e+02 angle pdb=" O5' DA A 26 " pdb=" C5' DA A 26 " pdb=" C4' DA A 26 " ideal model delta sigma weight residual 109.40 116.95 -7.55 8.00e-01 1.56e+00 8.91e+01 angle pdb=" N VAL D 241 " pdb=" CA VAL D 241 " pdb=" C VAL D 241 " ideal model delta sigma weight residual 109.02 117.60 -8.58 9.30e-01 1.16e+00 8.52e+01 angle pdb=" C LYS D 229 " pdb=" N PRO D 230 " pdb=" CA PRO D 230 " ideal model delta sigma weight residual 120.52 129.30 -8.78 9.90e-01 1.02e+00 7.86e+01 angle pdb=" C THR C 176 " pdb=" N PRO C 177 " pdb=" CA PRO C 177 " ideal model delta sigma weight residual 119.56 128.60 -9.04 1.02e+00 9.61e-01 7.86e+01 ... (remaining 13586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 5400 31.31 - 62.62: 355 62.62 - 93.93: 8 93.93 - 125.24: 0 125.24 - 156.55: 1 Dihedral angle restraints: 5764 sinusoidal: 2892 harmonic: 2872 Sorted by residual: dihedral pdb=" C PHE C 248 " pdb=" N PHE C 248 " pdb=" CA PHE C 248 " pdb=" CB PHE C 248 " ideal model delta harmonic sigma weight residual -122.60 -110.79 -11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" C ARG C 547 " pdb=" N ARG C 547 " pdb=" CA ARG C 547 " pdb=" CB ARG C 547 " ideal model delta harmonic sigma weight residual -122.60 -133.87 11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS C 541 " pdb=" N LYS C 541 " pdb=" CA LYS C 541 " pdb=" CB LYS C 541 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 5761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1039 0.114 - 0.228: 346 0.228 - 0.341: 59 0.341 - 0.455: 7 0.455 - 0.569: 4 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CA TYR D 260 " pdb=" N TYR D 260 " pdb=" C TYR D 260 " pdb=" CB TYR D 260 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CG LEU C 288 " pdb=" CB LEU C 288 " pdb=" CD1 LEU C 288 " pdb=" CD2 LEU C 288 " both_signs ideal model delta sigma weight residual False -2.59 -3.09 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CA ARG C 547 " pdb=" N ARG C 547 " pdb=" C ARG C 547 " pdb=" CB ARG C 547 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 1452 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA A 18 " 0.170 2.00e-02 2.50e+03 7.04e-02 1.36e+02 pdb=" N9 DA A 18 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DA A 18 " -0.075 2.00e-02 2.50e+03 pdb=" N7 DA A 18 " -0.036 2.00e-02 2.50e+03 pdb=" C5 DA A 18 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DA A 18 " 0.024 2.00e-02 2.50e+03 pdb=" N6 DA A 18 " 0.102 2.00e-02 2.50e+03 pdb=" N1 DA A 18 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA A 18 " -0.035 2.00e-02 2.50e+03 pdb=" N3 DA A 18 " -0.052 2.00e-02 2.50e+03 pdb=" C4 DA A 18 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA A 17 " 0.123 2.00e-02 2.50e+03 5.23e-02 7.51e+01 pdb=" N9 DA A 17 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA A 17 " -0.049 2.00e-02 2.50e+03 pdb=" N7 DA A 17 " -0.037 2.00e-02 2.50e+03 pdb=" C5 DA A 17 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DA A 17 " 0.025 2.00e-02 2.50e+03 pdb=" N6 DA A 17 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DA A 17 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DA A 17 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DA A 17 " -0.053 2.00e-02 2.50e+03 pdb=" C4 DA A 17 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B -24 " 0.100 2.00e-02 2.50e+03 4.83e-02 6.42e+01 pdb=" N9 DA B -24 " 0.004 2.00e-02 2.50e+03 pdb=" C8 DA B -24 " -0.061 2.00e-02 2.50e+03 pdb=" N7 DA B -24 " -0.044 2.00e-02 2.50e+03 pdb=" C5 DA B -24 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DA B -24 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA B -24 " 0.083 2.00e-02 2.50e+03 pdb=" N1 DA B -24 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DA B -24 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DA B -24 " -0.029 2.00e-02 2.50e+03 pdb=" C4 DA B -24 " -0.011 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2943 2.83 - 3.35: 8450 3.35 - 3.87: 15941 3.87 - 4.38: 19590 4.38 - 4.90: 29074 Nonbonded interactions: 75998 Sorted by model distance: nonbonded pdb=" OG1 THR C 428 " pdb=" N VAL C 429 " model vdw 2.314 3.120 nonbonded pdb=" OG SER C 423 " pdb=" N ILE C 424 " model vdw 2.321 3.120 nonbonded pdb=" OG SER C 367 " pdb=" N LYS C 368 " model vdw 2.322 3.120 nonbonded pdb=" N LEU D 289 " pdb=" O LEU D 289 " model vdw 2.387 2.496 nonbonded pdb=" O5' DG B -34 " pdb=" O4' DG B -34 " model vdw 2.411 2.432 ... (remaining 75993 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 'C' selection = (chain 'D' and (resid 78 through 284 or resid 288 through 332 or resid 341 throu \ gh 476 or resid 495 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.450 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.028 0.454 9880 Z= 1.615 Angle : 1.948 29.708 13597 Z= 1.430 Chirality : 0.115 0.569 1455 Planarity : 0.011 0.085 1470 Dihedral : 16.991 156.551 3908 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.70 % Rotamer: Outliers : 0.34 % Allowed : 0.90 % Favored : 98.77 % Cbeta Deviations : 0.54 % 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: -0.53 (0.25), residues: 956 helix: -0.91 (0.26), residues: 324 sheet: 0.73 (0.49), residues: 95 loop : -0.05 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 533 TYR 0.085 0.012 TYR D 312 PHE 0.033 0.008 PHE D 563 TRP 0.057 0.009 TRP C 243 HIS 0.015 0.003 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.02622 / 1.59 ( 9865) covalent geometry : angle 1.89614 / 1.43 (13591) hydrogen bonds : bond 0.22469 / 25.13 ( 362) hydrogen bonds : angle 6.83821 / 9.16 ( 915) metal coordination : bond 0.24310 / 23.18 ( 15) metal coordination : angle 21.34610 / 34.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.262 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: symmetry clash REVERT: C 382 MET cc_start: 0.7622 (ttt) cc_final: 0.7408 (ttt) outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 0.0967 time to fit residues: 16.4437 Evaluate side-chains 59 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 73 HIS D 317 ASN D 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.062974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.049408 restraints weight = 54013.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.051176 restraints weight = 29400.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.052341 restraints weight = 19773.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.053130 restraints weight = 15061.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.053603 restraints weight = 12498.413| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9880 Z= 0.254 Angle : 0.908 12.797 13597 Z= 0.500 Chirality : 0.053 0.466 1455 Planarity : 0.006 0.069 1470 Dihedral : 21.639 163.668 1841 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 2.02 % Allowed : 6.27 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.44 (0.25), residues: 956 helix: 0.27 (0.28), residues: 331 sheet: 0.59 (0.56), residues: 74 loop : -0.74 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 434 TYR 0.037 0.003 TYR C 422 PHE 0.028 0.003 PHE C 149 TRP 0.034 0.003 TRP C 138 HIS 0.011 0.002 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 ( 9865) covalent geometry : angle 0.89647 / 0.50 (13591) hydrogen bonds : bond 0.08904 / 9.82 ( 362) hydrogen bonds : angle 5.36894 / 7.47 ( 915) metal coordination : bond 0.01217 / 1.23 ( 15) metal coordination : angle 7.00427 / 13.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 264 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7699 (m) REVERT: D 138 TRP cc_start: 0.8204 (p-90) cc_final: 0.7962 (p-90) REVERT: D 231 HIS cc_start: 0.5465 (m170) cc_final: 0.5239 (m170) REVERT: D 382 MET cc_start: 0.9581 (mmm) cc_final: 0.8302 (mmm) REVERT: D 496 MET cc_start: 0.7763 (tmm) cc_final: 0.6808 (tmm) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.0975 time to fit residues: 9.9918 Evaluate side-chains 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 94 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 GLN C 196 HIS ** C 519 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.064674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.051675 restraints weight = 57410.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.053404 restraints weight = 31632.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.054521 restraints weight = 21410.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.055273 restraints weight = 16436.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.055743 restraints weight = 13708.971| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9880 Z= 0.174 Angle : 0.712 8.460 13597 Z= 0.394 Chirality : 0.045 0.405 1455 Planarity : 0.004 0.035 1470 Dihedral : 21.959 176.199 1841 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 1.79 % Allowed : 7.95 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.20 (0.26), residues: 956 helix: 0.76 (0.28), residues: 331 sheet: 0.75 (0.59), residues: 73 loop : -0.81 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 434 TYR 0.037 0.002 TYR C 422 PHE 0.017 0.002 PHE D 248 TRP 0.048 0.002 TRP C 138 HIS 0.007 0.002 HIS D 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9865) covalent geometry : angle 0.70885 / 0.39 (13591) hydrogen bonds : bond 0.06732 / 7.42 ( 362) hydrogen bonds : angle 4.80814 / 6.69 ( 915) metal coordination : bond 0.00764 / 0.92 ( 15) metal coordination : angle 3.47518 / 7.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 264 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7685 (m) REVERT: D 373 LEU cc_start: 0.9406 (tt) cc_final: 0.8862 (mp) REVERT: D 382 MET cc_start: 0.9299 (mmm) cc_final: 0.8842 (mmm) REVERT: D 496 MET cc_start: 0.7900 (tmm) cc_final: 0.6993 (tmm) REVERT: D 549 MET cc_start: 0.8762 (ttp) cc_final: 0.8022 (tmm) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.0862 time to fit residues: 8.7732 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 431 TRP Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** 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 = 0.3794 r_free = 0.3794 target = 0.063648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.050684 restraints weight = 58276.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.052372 restraints weight = 31996.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.053473 restraints weight = 21777.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.054159 restraints weight = 16736.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.054706 restraints weight = 14067.713| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9880 Z= 0.174 Angle : 0.664 9.166 13597 Z= 0.367 Chirality : 0.044 0.320 1455 Planarity : 0.004 0.060 1470 Dihedral : 21.950 169.449 1841 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 2.13 % Allowed : 8.29 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.14 (0.26), residues: 956 helix: 0.94 (0.29), residues: 334 sheet: 0.87 (0.64), residues: 63 loop : -0.86 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 434 TYR 0.026 0.002 TYR C 422 PHE 0.015 0.002 PHE C 149 TRP 0.023 0.001 TRP C 138 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 9865) covalent geometry : angle 0.65978 / 0.37 (13591) hydrogen bonds : bond 0.06116 / 6.62 ( 362) hydrogen bonds : angle 4.65047 / 6.49 ( 915) metal coordination : bond 0.00931 / 1.18 ( 15) metal coordination : angle 3.57632 / 7.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.330 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: C 459 MET cc_start: 0.8289 (ptm) cc_final: 0.8068 (ptm) REVERT: D 496 MET cc_start: 0.8029 (tmm) cc_final: 0.7208 (tmm) outliers start: 19 outliers final: 11 residues processed: 70 average time/residue: 0.0942 time to fit residues: 9.3258 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 431 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** 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 = 0.3802 r_free = 0.3802 target = 0.063859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.050854 restraints weight = 57989.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.052535 restraints weight = 31958.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.053630 restraints weight = 21754.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.054337 restraints weight = 16741.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.054875 restraints weight = 14039.385| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9880 Z= 0.147 Angle : 0.632 9.667 13597 Z= 0.346 Chirality : 0.042 0.193 1455 Planarity : 0.003 0.047 1470 Dihedral : 21.888 152.147 1841 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 1.12 % Allowed : 9.85 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.08 (0.27), residues: 956 helix: 1.11 (0.29), residues: 333 sheet: 0.70 (0.64), residues: 63 loop : -0.88 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 434 TYR 0.024 0.002 TYR C 422 PHE 0.013 0.001 PHE C 149 TRP 0.007 0.001 TRP D 195 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 9865) covalent geometry : angle 0.62978 / 0.35 (13591) hydrogen bonds : bond 0.05537 / 6.05 ( 362) hydrogen bonds : angle 4.46394 / 6.29 ( 915) metal coordination : bond 0.00817 / 0.98 ( 15) metal coordination : angle 2.61378 / 5.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.8294 (ptm) cc_final: 0.8054 (ptm) REVERT: D 382 MET cc_start: 0.9160 (tpp) cc_final: 0.8679 (tpp) REVERT: D 439 MET cc_start: 0.8768 (mtp) cc_final: 0.8548 (mtt) REVERT: D 496 MET cc_start: 0.8051 (tmm) cc_final: 0.7399 (tmm) REVERT: D 549 MET cc_start: 0.8644 (ttp) cc_final: 0.7711 (tmm) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0783 time to fit residues: 7.0032 Evaluate side-chains 61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 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 = 0.3799 r_free = 0.3799 target = 0.063553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.050532 restraints weight = 57634.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.052214 restraints weight = 31872.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.053332 restraints weight = 21698.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.054067 restraints weight = 16647.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.054522 restraints weight = 13921.535| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9880 Z= 0.142 Angle : 0.610 9.540 13597 Z= 0.336 Chirality : 0.041 0.150 1455 Planarity : 0.003 0.044 1470 Dihedral : 21.846 135.432 1841 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.68 % Allowed : 10.19 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.06 (0.27), residues: 956 helix: 1.30 (0.30), residues: 333 sheet: 0.01 (0.56), residues: 79 loop : -0.92 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 356 TYR 0.023 0.002 TYR C 422 PHE 0.012 0.001 PHE C 149 TRP 0.006 0.001 TRP C 138 HIS 0.014 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 9865) covalent geometry : angle 0.60753 / 0.34 (13591) hydrogen bonds : bond 0.05235 / 5.65 ( 362) hydrogen bonds : angle 4.36933 / 6.19 ( 915) metal coordination : bond 0.00676 / 0.76 ( 15) metal coordination : angle 2.65159 / 5.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 156 MET cc_start: 0.8829 (ttm) cc_final: 0.8418 (mmm) REVERT: D 183 MET cc_start: 0.8238 (mtt) cc_final: 0.7916 (mtt) REVERT: D 292 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7981 (pt) REVERT: D 382 MET cc_start: 0.9092 (tpp) cc_final: 0.8642 (mmm) REVERT: D 434 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7440 (ttm-80) REVERT: D 439 MET cc_start: 0.8789 (mtp) cc_final: 0.8582 (mtt) REVERT: D 496 MET cc_start: 0.7930 (tmm) cc_final: 0.7499 (tmm) REVERT: D 513 MET cc_start: 0.9294 (mpp) cc_final: 0.8795 (mpp) REVERT: D 549 MET cc_start: 0.8558 (ttp) cc_final: 0.7462 (tmm) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.0946 time to fit residues: 8.6669 Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 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 = 0.3769 r_free = 0.3769 target = 0.062304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.049275 restraints weight = 58382.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.050921 restraints weight = 32529.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.052030 restraints weight = 22257.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.052766 restraints weight = 17079.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.053266 restraints weight = 14271.099| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9880 Z= 0.178 Angle : 0.642 11.586 13597 Z= 0.347 Chirality : 0.042 0.167 1455 Planarity : 0.004 0.045 1470 Dihedral : 21.870 132.806 1841 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.68 % Allowed : 10.53 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.07 (0.27), residues: 956 helix: 1.33 (0.30), residues: 337 sheet: 0.67 (0.65), residues: 60 loop : -1.04 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 514 TYR 0.022 0.002 TYR C 422 PHE 0.017 0.002 PHE C 149 TRP 0.010 0.001 TRP D 431 HIS 0.013 0.002 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 9865) covalent geometry : angle 0.63877 / 0.35 (13591) hydrogen bonds : bond 0.05604 / 5.98 ( 362) hydrogen bonds : angle 4.37312 / 6.14 ( 915) metal coordination : bond 0.01413 / 1.46 ( 15) metal coordination : angle 3.01397 / 6.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 511 MET cc_start: 0.9198 (mmm) cc_final: 0.8713 (mmm) REVERT: D 183 MET cc_start: 0.8344 (mtt) cc_final: 0.8071 (mtt) REVERT: D 382 MET cc_start: 0.9086 (tpp) cc_final: 0.8751 (mmm) REVERT: D 386 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: D 439 MET cc_start: 0.8792 (mtp) cc_final: 0.8569 (mtt) REVERT: D 496 MET cc_start: 0.7744 (tmm) cc_final: 0.7479 (tmm) REVERT: D 513 MET cc_start: 0.9240 (mpp) cc_final: 0.8705 (mpp) REVERT: D 549 MET cc_start: 0.8617 (ttp) cc_final: 0.7558 (tmm) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.0885 time to fit residues: 8.3839 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 413 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D 231 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 = 0.3792 r_free = 0.3792 target = 0.062650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.049248 restraints weight = 55027.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.050954 restraints weight = 30506.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.052081 restraints weight = 20736.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.052847 restraints weight = 15943.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.053360 restraints weight = 13270.246| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9880 Z= 0.122 Angle : 0.608 10.438 13597 Z= 0.328 Chirality : 0.041 0.151 1455 Planarity : 0.004 0.048 1470 Dihedral : 21.784 131.364 1841 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.46 % Allowed : 11.09 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.04 (0.27), residues: 956 helix: 1.43 (0.30), residues: 338 sheet: 0.32 (0.61), residues: 70 loop : -0.94 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 497 TYR 0.022 0.002 TYR C 422 PHE 0.011 0.001 PHE D 249 TRP 0.008 0.001 TRP C 138 HIS 0.009 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 9865) covalent geometry : angle 0.60598 / 0.33 (13591) hydrogen bonds : bond 0.04720 / 5.11 ( 362) hydrogen bonds : angle 4.10505 / 5.78 ( 915) metal coordination : bond 0.00480 / 0.51 ( 15) metal coordination : angle 2.17749 / 4.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9198 (mttt) cc_final: 0.8909 (mtpt) REVERT: C 437 MET cc_start: 0.7803 (ttp) cc_final: 0.7575 (ttp) REVERT: C 511 MET cc_start: 0.9204 (mmm) cc_final: 0.8915 (mmm) REVERT: D 183 MET cc_start: 0.8279 (mtt) cc_final: 0.7979 (mtt) REVERT: D 386 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8043 (tp40) REVERT: D 409 MET cc_start: 0.8031 (tpp) cc_final: 0.7761 (mmp) REVERT: D 496 MET cc_start: 0.7676 (tmm) cc_final: 0.7468 (tmm) REVERT: D 513 MET cc_start: 0.9250 (mpp) cc_final: 0.8682 (mpp) REVERT: D 549 MET cc_start: 0.8555 (ttp) cc_final: 0.7459 (tmm) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 0.0834 time to fit residues: 7.9234 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 40.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 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 = 0.3809 r_free = 0.3809 target = 0.063693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.050664 restraints weight = 57331.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.052347 restraints weight = 31863.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.053476 restraints weight = 21709.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.054229 restraints weight = 16629.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.054675 restraints weight = 13854.139| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9880 Z= 0.118 Angle : 0.611 12.576 13597 Z= 0.323 Chirality : 0.040 0.140 1455 Planarity : 0.003 0.046 1470 Dihedral : 21.765 129.502 1841 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 1.34 % Allowed : 10.86 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.00 (0.27), residues: 956 helix: 1.39 (0.30), residues: 339 sheet: 0.28 (0.62), residues: 70 loop : -0.97 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.022 0.001 TYR C 422 PHE 0.008 0.001 PHE D 249 TRP 0.009 0.001 TRP C 138 HIS 0.011 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 9865) covalent geometry : angle 0.60927 / 0.32 (13591) hydrogen bonds : bond 0.04534 / 4.81 ( 362) hydrogen bonds : angle 4.08198 / 5.74 ( 915) metal coordination : bond 0.00360 / 0.35 ( 15) metal coordination : angle 1.94331 / 4.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9170 (mttt) cc_final: 0.8856 (mtpt) REVERT: C 308 MET cc_start: 0.7785 (mtp) cc_final: 0.7190 (ttp) REVERT: C 459 MET cc_start: 0.8458 (ptp) cc_final: 0.7816 (pmm) REVERT: D 183 MET cc_start: 0.8214 (mtt) cc_final: 0.7905 (mtt) REVERT: D 382 MET cc_start: 0.9135 (tpp) cc_final: 0.8572 (tpp) REVERT: D 386 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8132 (tp40) REVERT: D 409 MET cc_start: 0.7827 (tpp) cc_final: 0.7582 (mmp) REVERT: D 513 MET cc_start: 0.9117 (mpp) cc_final: 0.8658 (mpp) REVERT: D 549 MET cc_start: 0.8550 (ttp) cc_final: 0.7462 (tmm) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.0764 time to fit residues: 7.7586 Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 386 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 3 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.060651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.047339 restraints weight = 56010.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.048950 restraints weight = 31591.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.050013 restraints weight = 21803.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050726 restraints weight = 16888.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051158 restraints weight = 14214.259| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9880 Z= 0.233 Angle : 0.697 13.648 13597 Z= 0.373 Chirality : 0.043 0.191 1455 Planarity : 0.005 0.078 1470 Dihedral : 21.868 128.622 1841 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.56 % Rotamer: Outliers : 1.23 % Allowed : 11.87 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.17 (0.27), residues: 956 helix: 1.24 (0.30), residues: 343 sheet: 0.68 (0.68), residues: 60 loop : -1.13 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 514 TYR 0.023 0.002 TYR C 422 PHE 0.019 0.002 PHE C 220 TRP 0.016 0.002 TRP D 431 HIS 0.015 0.002 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 ( 9865) covalent geometry : angle 0.69406 / 0.37 (13591) hydrogen bonds : bond 0.05896 / 6.27 ( 362) hydrogen bonds : angle 4.57349 / 6.34 ( 915) metal coordination : bond 0.01632 / 1.79 ( 15) metal coordination : angle 2.92941 / 5.88 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 308 MET cc_start: 0.7944 (mtp) cc_final: 0.7174 (ttp) REVERT: C 437 MET cc_start: 0.7802 (ttp) cc_final: 0.7390 (tpt) REVERT: D 183 MET cc_start: 0.8406 (mtt) cc_final: 0.8151 (mtt) REVERT: D 382 MET cc_start: 0.8992 (tpp) cc_final: 0.8633 (mmm) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.0766 time to fit residues: 7.0642 Evaluate side-chains 63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 413 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 20.0000 chunk 36 optimal weight: 0.0040 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 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 = 0.3772 r_free = 0.3772 target = 0.061621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048217 restraints weight = 54855.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049875 restraints weight = 30614.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.050963 restraints weight = 20957.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.051689 restraints weight = 16183.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.052206 restraints weight = 13546.521| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9880 Z= 0.147 Angle : 0.643 12.342 13597 Z= 0.346 Chirality : 0.041 0.163 1455 Planarity : 0.004 0.103 1470 Dihedral : 21.772 128.873 1841 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 1.23 % Allowed : 11.42 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.10 (0.28), residues: 956 helix: 1.34 (0.30), residues: 343 sheet: 0.72 (0.69), residues: 60 loop : -1.11 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.000 ARG D 287 TYR 0.023 0.002 TYR C 422 PHE 0.017 0.002 PHE D 129 TRP 0.010 0.001 TRP C 138 HIS 0.012 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 9865) covalent geometry : angle 0.64134 / 0.35 (13591) hydrogen bonds : bond 0.04960 / 5.30 ( 362) hydrogen bonds : angle 4.29204 / 6.01 ( 915) metal coordination : bond 0.00987 / 1.16 ( 15) metal coordination : angle 2.17096 / 4.28 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1529.06 seconds wall clock time: 26 minutes 59.68 seconds (1619.68 seconds total)