Starting phenix.real_space_refine on Wed Aug 5 09:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/08_2026/9c0f_45082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0f_45082/08_2026/9c0f_45082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/08_2026/9c0f_45082.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0f_45082/08_2026/9c0f_45082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/08_2026/9c0f_45082.cif" } 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-2.2rc3-6140/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: 1.68, per 1000 atoms: 0.18 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: 0.64 Conformation dependent library (CDL) restraints added in 187.8 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: 0.86 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: 1.30 Time building geometry restraints manager: 0.81 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: 11518 2.52 - 5.03: 1766 5.03 - 7.55: 256 7.55 - 10.06: 42 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.000 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.400 ------------------------------------------------------------------------------- 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= 1.616 Angle : 1.953 29.708 13597 Z= 1.441 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 1.90116 / 1.44 (13591) hydrogen bonds : bond 0.22469 / 25.22 ( 362) hydrogen bonds : angle 6.83821 / 9.17 ( 915) metal coordination : bond 0.24310 / 23.53 ( 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 : 0.281 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: 0.7409 (ttt) outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.1129 time to fit residues: 19.2363 Evaluate side-chains 60 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 538 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.062520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.049048 restraints weight = 54942.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.050786 restraints weight = 30589.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.051892 restraints weight = 20872.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.052683 restraints weight = 16116.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.053165 restraints weight = 13397.400| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9880 Z= 0.259 Angle : 0.909 12.674 13597 Z= 0.501 Chirality : 0.054 0.503 1455 Planarity : 0.006 0.068 1470 Dihedral : 21.665 163.661 1842 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 2.13 % Allowed : 6.61 % Favored : 91.27 % 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: 0.29 (0.28), residues: 331 sheet: 0.58 (0.56), residues: 74 loop : -0.75 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 434 TYR 0.038 0.003 TYR C 422 PHE 0.028 0.003 PHE C 149 TRP 0.037 0.003 TRP C 138 HIS 0.010 0.002 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 ( 9865) covalent geometry : angle 0.89731 / 0.50 (13591) hydrogen bonds : bond 0.08887 / 9.80 ( 362) hydrogen bonds : angle 5.38289 / 7.51 ( 915) metal coordination : bond 0.01109 / 1.19 ( 15) metal coordination : angle 7.04729 / 13.54 ( 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 86 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.351 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: 0.7945 (OUTLIER) cc_final: 0.7693 (m) REVERT: D 138 TRP cc_start: 0.8183 (p-90) cc_final: 0.7941 (p-90) REVERT: D 231 HIS cc_start: 0.5495 (m170) cc_final: 0.5266 (m170) REVERT: D 382 MET cc_start: 0.9575 (mmm) cc_final: 0.8271 (mmm) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.1072 time to fit residues: 11.2127 Evaluate side-chains 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 94 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.064106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.051122 restraints weight = 57533.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.052831 restraints weight = 31871.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.053906 restraints weight = 21627.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.054675 restraints weight = 16703.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.055147 restraints weight = 13900.436| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9880 Z= 0.189 Angle : 0.720 9.873 13597 Z= 0.397 Chirality : 0.046 0.416 1455 Planarity : 0.004 0.036 1470 Dihedral : 21.939 177.417 1841 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 2.02 % Allowed : 7.61 % Favored : 90.37 % 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: -0.26 (0.26), residues: 956 helix: 0.71 (0.28), residues: 330 sheet: 0.73 (0.60), residues: 73 loop : -0.85 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 434 TYR 0.035 0.002 TYR C 422 PHE 0.017 0.002 PHE D 248 TRP 0.047 0.002 TRP C 138 HIS 0.006 0.002 HIS D 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 ( 9865) covalent geometry : angle 0.71586 / 0.40 (13591) hydrogen bonds : bond 0.06806 / 7.49 ( 362) hydrogen bonds : angle 4.84482 / 6.75 ( 915) metal coordination : bond 0.01058 / 1.36 ( 15) metal coordination : angle 3.56023 / 7.18 ( 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 80 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.268 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: C 264 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7719 (m) REVERT: C 513 MET cc_start: 0.8617 (mmm) cc_final: 0.8398 (mmt) REVERT: D 373 LEU cc_start: 0.9416 (tt) cc_final: 0.8865 (mp) REVERT: D 382 MET cc_start: 0.9345 (mmm) cc_final: 0.8965 (mmm) REVERT: D 496 MET cc_start: 0.7887 (tmm) cc_final: 0.7206 (tmm) REVERT: D 549 MET cc_start: 0.8760 (ttp) cc_final: 0.8065 (tmm) outliers start: 18 outliers final: 12 residues processed: 72 average time/residue: 0.0937 time to fit residues: 9.3376 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 VAL 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 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 431 TRP Chi-restraints excluded: chain D residue 440 ILE 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: 9.9990 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.064308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.051365 restraints weight = 58007.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.053078 restraints weight = 31918.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.054193 restraints weight = 21572.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.054900 restraints weight = 16562.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.055455 restraints weight = 13861.222| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9880 Z= 0.144 Angle : 0.641 8.937 13597 Z= 0.355 Chirality : 0.043 0.309 1455 Planarity : 0.004 0.056 1470 Dihedral : 21.842 165.142 1841 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 1.90 % Allowed : 8.51 % 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: -0.08 (0.27), residues: 956 helix: 1.06 (0.29), residues: 332 sheet: 0.61 (0.58), residues: 73 loop : -0.85 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 434 TYR 0.023 0.002 TYR C 312 PHE 0.013 0.002 PHE D 249 TRP 0.010 0.001 TRP D 195 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9865) covalent geometry : angle 0.63733 / 0.36 (13591) hydrogen bonds : bond 0.05611 / 6.10 ( 362) hydrogen bonds : angle 4.48036 / 6.28 ( 915) metal coordination : bond 0.00521 / 0.53 ( 15) metal coordination : angle 3.38591 / 7.24 ( 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 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.8277 (ptm) cc_final: 0.8060 (ptm) REVERT: C 513 MET cc_start: 0.8643 (mmm) cc_final: 0.8390 (mmt) REVERT: D 183 MET cc_start: 0.8168 (mtt) cc_final: 0.7848 (mtt) REVERT: D 382 MET cc_start: 0.9175 (mmm) cc_final: 0.8663 (mmm) REVERT: D 496 MET cc_start: 0.7738 (tmm) cc_final: 0.7181 (tmm) outliers start: 17 outliers final: 8 residues processed: 72 average time/residue: 0.1105 time to fit residues: 11.1210 Evaluate side-chains 64 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 D residue 315 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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** D 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.063988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050662 restraints weight = 54352.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.052395 restraints weight = 29658.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.053580 restraints weight = 19988.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.054280 restraints weight = 15190.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.054831 restraints weight = 12748.462| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9880 Z= 0.120 Angle : 0.621 9.557 13597 Z= 0.337 Chirality : 0.041 0.140 1455 Planarity : 0.003 0.047 1470 Dihedral : 21.752 142.732 1841 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % 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: -0.02 (0.27), residues: 956 helix: 1.23 (0.30), residues: 330 sheet: 0.44 (0.57), residues: 73 loop : -0.87 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 356 TYR 0.024 0.001 TYR C 312 PHE 0.010 0.001 PHE D 249 TRP 0.006 0.001 TRP D 195 HIS 0.016 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 9865) covalent geometry : angle 0.61992 / 0.34 (13591) hydrogen bonds : bond 0.04968 / 5.45 ( 362) hydrogen bonds : angle 4.20518 / 5.93 ( 915) metal coordination : bond 0.00311 / 0.35 ( 15) metal coordination : angle 1.90260 / 4.05 ( 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 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.8298 (ptm) cc_final: 0.8084 (ptm) REVERT: C 513 MET cc_start: 0.8649 (mmm) cc_final: 0.8389 (mmt) REVERT: D 130 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8669 (ptpp) REVERT: D 156 MET cc_start: 0.8770 (ttm) cc_final: 0.8415 (mmm) REVERT: D 183 MET cc_start: 0.8167 (mtt) cc_final: 0.7861 (mtt) REVERT: D 304 TYR cc_start: 0.8636 (m-80) cc_final: 0.7775 (m-80) REVERT: D 382 MET cc_start: 0.9216 (mmm) cc_final: 0.8796 (mmm) REVERT: D 496 MET cc_start: 0.7556 (tmm) cc_final: 0.7220 (tmm) REVERT: D 549 MET cc_start: 0.8608 (ttp) cc_final: 0.7632 (tmm) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.1074 time to fit residues: 9.7107 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 : 0.347 ------------------------------------------------------------------------------- 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 D residue 130 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 513 MET 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: 3.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 47 optimal weight: 0.2980 chunk 39 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.062885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.049586 restraints weight = 53604.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.051285 restraints weight = 29346.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.052400 restraints weight = 19870.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.053166 restraints weight = 15253.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.053635 restraints weight = 12676.240| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9880 Z= 0.144 Angle : 0.603 9.883 13597 Z= 0.331 Chirality : 0.041 0.152 1455 Planarity : 0.003 0.044 1470 Dihedral : 21.770 133.000 1841 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 1.79 % Allowed : 9.63 % Favored : 88.58 % 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: 0.09 (0.27), residues: 956 helix: 1.33 (0.30), residues: 332 sheet: 0.36 (0.56), residues: 73 loop : -0.79 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 356 TYR 0.021 0.002 TYR C 312 PHE 0.011 0.001 PHE C 149 TRP 0.008 0.001 TRP D 195 HIS 0.014 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9865) covalent geometry : angle 0.60109 / 0.33 (13591) hydrogen bonds : bond 0.05235 / 5.60 ( 362) hydrogen bonds : angle 4.23344 / 6.00 ( 915) metal coordination : bond 0.00677 / 0.75 ( 15) metal coordination : angle 2.53684 / 5.48 ( 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: 16 poor density : 55 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 513 MET cc_start: 0.8647 (mmm) cc_final: 0.8358 (mmt) REVERT: D 130 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8630 (ptpp) REVERT: D 183 MET cc_start: 0.8247 (mtt) cc_final: 0.7941 (mtt) REVERT: D 292 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7987 (pt) REVERT: D 382 MET cc_start: 0.9179 (mmm) cc_final: 0.8419 (mmm) REVERT: D 439 MET cc_start: 0.8807 (mtp) cc_final: 0.8591 (mtt) REVERT: D 496 MET cc_start: 0.7531 (tmm) cc_final: 0.7177 (tmm) outliers start: 16 outliers final: 10 residues processed: 66 average time/residue: 0.0860 time to fit residues: 8.2444 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 : 0.329 ------------------------------------------------------------------------------- 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 130 LYS 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 513 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 37 optimal weight: 0.0070 chunk 52 optimal weight: 7.9990 chunk 99 optimal weight: 0.0570 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.4720 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.063450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.050052 restraints weight = 53956.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.051771 restraints weight = 29574.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.052932 restraints weight = 20033.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.053641 restraints weight = 15277.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.054184 restraints weight = 12810.558| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9880 Z= 0.116 Angle : 0.596 10.781 13597 Z= 0.322 Chirality : 0.041 0.138 1455 Planarity : 0.003 0.043 1470 Dihedral : 21.713 131.993 1841 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 1.68 % Allowed : 9.74 % Favored : 88.58 % 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: 0.12 (0.27), residues: 956 helix: 1.37 (0.30), residues: 333 sheet: 0.29 (0.56), residues: 73 loop : -0.77 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 434 TYR 0.024 0.001 TYR C 422 PHE 0.009 0.001 PHE C 149 TRP 0.005 0.001 TRP D 195 HIS 0.009 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 9865) covalent geometry : angle 0.59562 / 0.32 (13591) hydrogen bonds : bond 0.04727 / 5.14 ( 362) hydrogen bonds : angle 4.05603 / 5.71 ( 915) metal coordination : bond 0.00506 / 0.63 ( 15) metal coordination : angle 1.62448 / 3.33 ( 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 75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.257 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 513 MET cc_start: 0.8633 (mmm) cc_final: 0.8216 (mmt) REVERT: D 130 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8621 (ptpp) REVERT: D 183 MET cc_start: 0.8214 (mtt) cc_final: 0.7930 (mtt) REVERT: D 382 MET cc_start: 0.9173 (mmm) cc_final: 0.8739 (mmm) REVERT: D 386 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8045 (tp40) REVERT: D 496 MET cc_start: 0.7432 (tmm) cc_final: 0.7145 (tmm) REVERT: D 513 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8777 (pmm) REVERT: D 549 MET cc_start: 0.8592 (ttp) cc_final: 0.7704 (tmm) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.0973 time to fit residues: 9.5364 Evaluate side-chains 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 312 TYR Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 130 LYS 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 Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.062068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048626 restraints weight = 55219.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.050302 restraints weight = 30601.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.051435 restraints weight = 20867.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.052186 restraints weight = 15993.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.052688 restraints weight = 13356.771| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9880 Z= 0.162 Angle : 0.620 10.911 13597 Z= 0.337 Chirality : 0.041 0.161 1455 Planarity : 0.004 0.063 1470 Dihedral : 21.748 129.318 1841 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.68 % Allowed : 10.41 % Favored : 87.91 % 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: 1.39 (0.30), residues: 337 sheet: 0.38 (0.60), residues: 70 loop : -0.87 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 514 TYR 0.033 0.002 TYR C 422 PHE 0.013 0.001 PHE C 149 TRP 0.009 0.001 TRP D 431 HIS 0.006 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 9865) covalent geometry : angle 0.61793 / 0.34 (13591) hydrogen bonds : bond 0.05265 / 5.61 ( 362) hydrogen bonds : angle 4.24363 / 5.97 ( 915) metal coordination : bond 0.01205 / 1.18 ( 15) metal coordination : angle 2.32870 / 4.74 ( 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 73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 513 MET cc_start: 0.8620 (mmm) cc_final: 0.8366 (mmt) REVERT: D 130 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8615 (ptpp) REVERT: D 183 MET cc_start: 0.8256 (mtt) cc_final: 0.8019 (mtt) REVERT: D 292 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7995 (pt) REVERT: D 382 MET cc_start: 0.9159 (mmm) cc_final: 0.8725 (mmm) REVERT: D 386 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: D 549 MET cc_start: 0.8594 (ttp) cc_final: 0.7752 (tmm) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1088 time to fit residues: 10.4531 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 : 0.342 ------------------------------------------------------------------------------- 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 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 130 LYS 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 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: 0.0050 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 40.0000 overall best weight: 2.4800 ------------------------------------------------------------------------------- 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 = 0.063402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.050392 restraints weight = 57591.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.052064 restraints weight = 32094.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.053186 restraints weight = 21901.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.053931 restraints weight = 16806.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.054394 restraints weight = 14021.652| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9880 Z= 0.137 Angle : 0.624 13.581 13597 Z= 0.332 Chirality : 0.041 0.142 1455 Planarity : 0.003 0.044 1470 Dihedral : 21.720 129.183 1841 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 2.02 % Allowed : 10.30 % Favored : 87.68 % 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: 0.09 (0.27), residues: 956 helix: 1.41 (0.30), residues: 338 sheet: 0.28 (0.61), residues: 70 loop : -0.85 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 497 TYR 0.037 0.002 TYR C 422 PHE 0.012 0.001 PHE C 149 TRP 0.007 0.001 TRP D 431 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 9865) covalent geometry : angle 0.62281 / 0.33 (13591) hydrogen bonds : bond 0.04779 / 5.10 ( 362) hydrogen bonds : angle 4.11467 / 5.78 ( 915) metal coordination : bond 0.00690 / 0.80 ( 15) metal coordination : angle 2.03755 / 4.15 ( 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 75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 437 MET cc_start: 0.7733 (ttp) cc_final: 0.7476 (tpt) REVERT: C 459 MET cc_start: 0.8463 (ptp) cc_final: 0.7631 (pmm) REVERT: C 513 MET cc_start: 0.8902 (mmm) cc_final: 0.8599 (mmt) REVERT: D 130 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8606 (ptpp) REVERT: D 183 MET cc_start: 0.8251 (mtt) cc_final: 0.8018 (mtt) REVERT: D 382 MET cc_start: 0.9143 (mmm) cc_final: 0.8855 (mmm) REVERT: D 386 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8161 (tp40) REVERT: D 409 MET cc_start: 0.8021 (tpp) cc_final: 0.7772 (mmp) REVERT: D 549 MET cc_start: 0.8637 (ttp) cc_final: 0.7709 (tmm) outliers start: 18 outliers final: 12 residues processed: 69 average time/residue: 0.1052 time to fit residues: 10.1860 Evaluate side-chains 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 530 ILE Chi-restraints excluded: chain D residue 130 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 21.9990 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 3 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.061421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.048061 restraints weight = 55353.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049704 restraints weight = 31086.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.050796 restraints weight = 21355.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.051527 restraints weight = 16445.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.051990 restraints weight = 13784.582| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9880 Z= 0.189 Angle : 0.672 12.025 13597 Z= 0.359 Chirality : 0.042 0.173 1455 Planarity : 0.004 0.064 1470 Dihedral : 21.779 127.850 1841 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 1.57 % Allowed : 11.09 % Favored : 87.35 % 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: -0.10 (0.27), residues: 956 helix: 1.21 (0.30), residues: 344 sheet: 0.17 (0.61), residues: 70 loop : -0.97 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 514 TYR 0.035 0.002 TYR C 422 PHE 0.015 0.002 PHE C 149 TRP 0.012 0.001 TRP D 431 HIS 0.005 0.001 HIS D 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 ( 9865) covalent geometry : angle 0.66999 / 0.36 (13591) hydrogen bonds : bond 0.05469 / 5.88 ( 362) hydrogen bonds : angle 4.40432 / 6.15 ( 915) metal coordination : bond 0.01227 / 1.33 ( 15) metal coordination : angle 2.52894 / 5.01 ( 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 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 437 MET cc_start: 0.7767 (ttp) cc_final: 0.7492 (tpt) REVERT: C 459 MET cc_start: 0.8544 (ptp) cc_final: 0.7782 (pmm) REVERT: D 130 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8585 (ptpp) REVERT: D 183 MET cc_start: 0.8323 (mtt) cc_final: 0.8090 (mtt) REVERT: D 292 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8050 (pt) REVERT: D 382 MET cc_start: 0.9135 (mmm) cc_final: 0.8682 (mmm) REVERT: D 549 MET cc_start: 0.8614 (ttp) cc_final: 0.7746 (tmm) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.1026 time to fit residues: 10.0190 Evaluate side-chains 68 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 130 LYS 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 459 MET 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: 8.9990 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.063437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050414 restraints weight = 57569.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.052101 restraints weight = 32122.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.053247 restraints weight = 21902.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.053981 restraints weight = 16718.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.054437 restraints weight = 13966.304| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9880 Z= 0.123 Angle : 0.630 11.939 13597 Z= 0.336 Chirality : 0.041 0.170 1455 Planarity : 0.003 0.044 1470 Dihedral : 21.664 129.209 1841 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.34 % Allowed : 10.75 % Favored : 87.91 % 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: 0.03 (0.28), residues: 956 helix: 1.38 (0.31), residues: 338 sheet: 0.17 (0.62), residues: 70 loop : -0.90 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.032 0.002 TYR C 422 PHE 0.012 0.001 PHE C 149 TRP 0.008 0.001 TRP C 138 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9865) covalent geometry : angle 0.62851 / 0.34 (13591) hydrogen bonds : bond 0.04586 / 4.95 ( 362) hydrogen bonds : angle 4.13451 / 5.79 ( 915) metal coordination : bond 0.00484 / 0.54 ( 15) metal coordination : angle 1.92969 / 3.95 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.96 seconds wall clock time: 29 minutes 16.85 seconds (1756.85 seconds total)