Starting phenix.real_space_refine on Wed Sep 17 15:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0f_45082/09_2025/9c0f_45082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0f_45082/09_2025/9c0f_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_45082/09_2025/9c0f_45082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0f_45082/09_2025/9c0f_45082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c0f_45082/09_2025/9c0f_45082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0f_45082/09_2025/9c0f_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 2.35, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 296.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.08 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: 1.61 Time building geometry restraints manager: 1.20 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=" 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=" CB HIS C 231 " pdb=" CG HIS C 231 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.20e+01 bond pdb=" CB PHE D 464 " pdb=" CG PHE D 464 " ideal model delta sigma weight residual 1.502 1.304 0.198 2.30e-02 1.89e+03 7.43e+01 bond pdb=" CB HIS D 558 " pdb=" CG HIS D 558 " ideal model delta sigma weight residual 1.497 1.383 0.114 1.40e-02 5.10e+03 6.58e+01 bond pdb=" CB PHE C 464 " pdb=" CG PHE C 464 " ideal model delta sigma weight residual 1.502 1.323 0.179 2.30e-02 1.89e+03 6.05e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11558 2.52 - 5.03: 1730 5.03 - 7.55: 255 7.55 - 10.06: 39 10.06 - 12.58: 9 Bond angle restraints: 13591 Sorted by residual: 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 angle pdb=" C THR D 176 " pdb=" N PRO D 177 " pdb=" CA PRO D 177 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 angle pdb=" N ILE C 240 " pdb=" CA ILE C 240 " pdb=" C ILE C 240 " ideal model delta sigma weight residual 108.11 119.48 -11.37 1.40e+00 5.10e-01 6.59e+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: 1036 0.114 - 0.228: 350 0.228 - 0.341: 58 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: 1.280 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.050 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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= 1.463 Angle : 1.942 29.708 13597 Z= 1.280 Chirality : 0.114 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 aren 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 covalent geometry : bond 0.02627 ( 9865) covalent geometry : angle 1.88991 (13591) hydrogen bonds : bond 0.22469 ( 362) hydrogen bonds : angle 6.83821 ( 915) metal coordination : bond 0.24310 ( 15) metal coordination : angle 21.34610 ( 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 : 0.347 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: 0 residues processed: 129 average time/residue: 0.1311 time to fit residues: 22.2804 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 : 0.444 ------------------------------------------------------------------------------- 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: 0.7980 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: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.064497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051616 restraints weight = 57686.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.053327 restraints weight = 31944.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.054421 restraints weight = 21666.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.055183 restraints weight = 16699.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.055653 restraints weight = 13894.957| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2833 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= 0.224 Angle : 0.795 10.897 13597 Z= 0.439 Chirality : 0.046 0.388 1455 Planarity : 0.005 0.039 1470 Dihedral : 21.625 158.761 1841 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 1.57 % Allowed : 6.83 % Favored : 91.60 % 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 aren not related in a simple way. whole: -0.28 (0.25), residues: 956 helix: 0.40 (0.28), residues: 333 sheet: 0.70 (0.52), residues: 83 loop : -0.67 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 434 TYR 0.040 0.003 TYR C 422 PHE 0.019 0.002 PHE D 563 TRP 0.028 0.002 TRP C 138 HIS 0.008 0.002 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9865) covalent geometry : angle 0.78579 (13591) hydrogen bonds : bond 0.07220 ( 362) hydrogen bonds : angle 5.03841 ( 915) metal coordination : bond 0.01035 ( 15) metal coordination : angle 5.64547 ( 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 79 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.432 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 262 ILE cc_start: 0.8139 (mp) cc_final: 0.7683 (mm) REVERT: D 373 LEU cc_start: 0.9412 (tt) cc_final: 0.8859 (mp) REVERT: D 382 MET cc_start: 0.9615 (mmm) cc_final: 0.9123 (tpp) outliers start: 14 outliers final: 8 residues processed: 71 average time/residue: 0.1169 time to fit residues: 11.3735 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 : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 440 ILE 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: 10.0000 chunk 60 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047524 restraints weight = 54884.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049130 restraints weight = 31116.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050171 restraints weight = 21500.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.050913 restraints weight = 16729.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.051423 restraints weight = 14010.813| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9880 Z= 0.262 Angle : 0.742 10.988 13597 Z= 0.405 Chirality : 0.044 0.195 1455 Planarity : 0.004 0.037 1470 Dihedral : 21.821 162.849 1841 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.68 % Allowed : 7.17 % Favored : 91.15 % 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 aren not related in a simple way. whole: -0.26 (0.26), residues: 956 helix: 0.71 (0.28), residues: 337 sheet: 0.80 (0.61), residues: 71 loop : -0.87 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 434 TYR 0.026 0.002 TYR C 422 PHE 0.023 0.002 PHE C 149 TRP 0.017 0.002 TRP D 195 HIS 0.007 0.002 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 9865) covalent geometry : angle 0.73348 (13591) hydrogen bonds : bond 0.06751 ( 362) hydrogen bonds : angle 4.96310 ( 915) metal coordination : bond 0.01471 ( 15) metal coordination : angle 5.25905 ( 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 76 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.8183 (ptm) cc_final: 0.7972 (ptm) REVERT: D 382 MET cc_start: 0.9616 (mmm) cc_final: 0.9174 (mmm) REVERT: D 496 MET cc_start: 0.7776 (tmm) cc_final: 0.7077 (tmm) outliers start: 15 outliers final: 13 residues processed: 69 average time/residue: 0.1215 time to fit residues: 11.5550 Evaluate side-chains 67 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 276 CYS 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 362 LEU Chi-restraints excluded: chain C residue 536 VAL 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 431 TRP Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3760 r_free = 0.3760 target = 0.061557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.048021 restraints weight = 55276.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.049668 restraints weight = 31140.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.050753 restraints weight = 21431.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.051536 restraints weight = 16553.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.052009 restraints weight = 13842.491| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9880 Z= 0.164 Angle : 0.635 8.737 13597 Z= 0.348 Chirality : 0.041 0.147 1455 Planarity : 0.004 0.044 1470 Dihedral : 21.616 164.085 1841 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.46 % Allowed : 9.18 % Favored : 89.36 % 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 aren not related in a simple way. whole: -0.08 (0.27), residues: 956 helix: 1.19 (0.29), residues: 330 sheet: 0.38 (0.60), residues: 78 loop : -0.91 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 287 TYR 0.022 0.002 TYR C 422 PHE 0.013 0.001 PHE D 249 TRP 0.010 0.001 TRP C 138 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9865) covalent geometry : angle 0.63062 (13591) hydrogen bonds : bond 0.05228 ( 362) hydrogen bonds : angle 4.51794 ( 915) metal coordination : bond 0.00719 ( 15) metal coordination : angle 3.49926 ( 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 71 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 382 MET cc_start: 0.9650 (mmm) cc_final: 0.9004 (mmm) REVERT: D 496 MET cc_start: 0.7724 (tmm) cc_final: 0.7244 (tmm) REVERT: D 549 MET cc_start: 0.8579 (ttp) cc_final: 0.7705 (tmm) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 0.1067 time to fit residues: 9.8361 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 241 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 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 431 TRP Chi-restraints excluded: chain D residue 459 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 231 HIS D 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.063374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.049944 restraints weight = 54108.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.051673 restraints weight = 29842.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.052843 restraints weight = 20269.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.053593 restraints weight = 15468.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.054118 restraints weight = 12885.397| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9880 Z= 0.121 Angle : 0.596 10.446 13597 Z= 0.322 Chirality : 0.039 0.148 1455 Planarity : 0.003 0.041 1470 Dihedral : 21.438 165.223 1841 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.34 % Allowed : 9.18 % Favored : 89.47 % 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 aren not related in a simple way. whole: 0.17 (0.27), residues: 956 helix: 1.51 (0.30), residues: 326 sheet: 0.28 (0.55), residues: 78 loop : -0.79 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 514 TYR 0.022 0.001 TYR C 422 PHE 0.009 0.001 PHE D 249 TRP 0.007 0.001 TRP C 138 HIS 0.009 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9865) covalent geometry : angle 0.59461 (13591) hydrogen bonds : bond 0.04289 ( 362) hydrogen bonds : angle 4.09694 ( 915) metal coordination : bond 0.00496 ( 15) metal coordination : angle 2.08052 ( 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 74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 ILE cc_start: 0.7969 (mp) cc_final: 0.7682 (mm) REVERT: C 289 LEU cc_start: 0.8934 (tt) cc_final: 0.8577 (tp) REVERT: C 513 MET cc_start: 0.8452 (mtt) cc_final: 0.8024 (mtt) REVERT: D 130 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (ptpp) REVERT: D 292 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7982 (pt) REVERT: D 382 MET cc_start: 0.9662 (mmm) cc_final: 0.9056 (mmm) REVERT: D 386 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: D 409 MET cc_start: 0.8057 (tpp) cc_final: 0.7734 (mmp) REVERT: D 513 MET cc_start: 0.9473 (mpp) cc_final: 0.9169 (mpp) REVERT: D 549 MET cc_start: 0.8564 (ttp) cc_final: 0.7660 (tmm) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.1200 time to fit residues: 11.7263 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 373 LEU 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 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: 20.0000 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 overall best weight: 4.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3740 r_free = 0.3740 target = 0.060491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047176 restraints weight = 55288.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.048787 restraints weight = 31084.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.049865 restraints weight = 21351.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.050527 restraints weight = 16489.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.051059 restraints weight = 13936.085| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9880 Z= 0.221 Angle : 0.653 11.796 13597 Z= 0.353 Chirality : 0.042 0.163 1455 Planarity : 0.004 0.055 1470 Dihedral : 21.517 159.892 1841 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 2.02 % Allowed : 9.07 % Favored : 88.91 % 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 aren not related in a simple way. whole: -0.06 (0.27), residues: 956 helix: 1.32 (0.30), residues: 342 sheet: 0.32 (0.56), residues: 80 loop : -1.04 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 514 TYR 0.036 0.002 TYR C 422 PHE 0.019 0.002 PHE C 149 TRP 0.051 0.002 TRP D 138 HIS 0.006 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9865) covalent geometry : angle 0.64839 (13591) hydrogen bonds : bond 0.05658 ( 362) hydrogen bonds : angle 4.47418 ( 915) metal coordination : bond 0.01509 ( 15) metal coordination : angle 3.71990 ( 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 75 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 459 MET cc_start: 0.8277 (ptp) cc_final: 0.7969 (pmm) REVERT: C 513 MET cc_start: 0.8513 (mtt) cc_final: 0.7780 (mtt) REVERT: D 130 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8796 (ptpp) REVERT: D 183 MET cc_start: 0.8386 (mtt) cc_final: 0.8106 (mtt) REVERT: D 308 MET cc_start: 0.8334 (ptm) cc_final: 0.8034 (ptp) REVERT: D 382 MET cc_start: 0.9631 (mmm) cc_final: 0.9036 (mmm) REVERT: D 511 MET cc_start: 0.8393 (mmm) cc_final: 0.7893 (mmm) REVERT: D 513 MET cc_start: 0.9468 (mpp) cc_final: 0.9076 (mpp) outliers start: 18 outliers final: 11 residues processed: 70 average time/residue: 0.1162 time to fit residues: 11.5231 Evaluate side-chains 65 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 373 LEU 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 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: 10.0000 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3743 r_free = 0.3743 target = 0.060547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047147 restraints weight = 55768.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.048745 restraints weight = 31664.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.049838 restraints weight = 21826.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050558 restraints weight = 16842.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051043 restraints weight = 14140.449| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9880 Z= 0.181 Angle : 0.634 11.163 13597 Z= 0.341 Chirality : 0.041 0.173 1455 Planarity : 0.004 0.062 1470 Dihedral : 21.551 158.280 1841 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.98 % Rotamer: Outliers : 1.79 % Allowed : 9.52 % Favored : 88.69 % 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 aren not related in a simple way. whole: -0.10 (0.27), residues: 956 helix: 1.32 (0.30), residues: 341 sheet: 0.25 (0.58), residues: 80 loop : -1.08 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 514 TYR 0.029 0.002 TYR C 422 PHE 0.013 0.001 PHE C 149 TRP 0.028 0.001 TRP D 138 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9865) covalent geometry : angle 0.62997 (13591) hydrogen bonds : bond 0.05030 ( 362) hydrogen bonds : angle 4.39308 ( 915) metal coordination : bond 0.01070 ( 15) metal coordination : angle 3.35470 ( 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 77 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9224 (mttt) cc_final: 0.8935 (mtpt) REVERT: C 278 MET cc_start: 0.8445 (ttp) cc_final: 0.7589 (tpp) REVERT: C 459 MET cc_start: 0.8277 (ptp) cc_final: 0.8041 (pmm) REVERT: C 513 MET cc_start: 0.8578 (mtt) cc_final: 0.7865 (mtt) REVERT: D 130 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8726 (ptpp) REVERT: D 183 MET cc_start: 0.8355 (mtt) cc_final: 0.8095 (mtt) REVERT: D 308 MET cc_start: 0.8351 (ptm) cc_final: 0.8124 (ptp) REVERT: D 382 MET cc_start: 0.9653 (mmm) cc_final: 0.9061 (mmm) REVERT: D 511 MET cc_start: 0.8383 (mmm) cc_final: 0.7840 (mmm) REVERT: D 513 MET cc_start: 0.9472 (mpp) cc_final: 0.9164 (mpp) REVERT: D 549 MET cc_start: 0.8593 (ttp) cc_final: 0.7633 (tmm) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.1247 time to fit residues: 12.8376 Evaluate side-chains 73 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 217 LEU Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 373 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3775 r_free = 0.3775 target = 0.061629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048263 restraints weight = 54631.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.049919 restraints weight = 30558.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050978 restraints weight = 20877.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.051747 restraints weight = 16137.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.052205 restraints weight = 13487.447| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9880 Z= 0.130 Angle : 0.600 11.425 13597 Z= 0.322 Chirality : 0.039 0.148 1455 Planarity : 0.004 0.063 1470 Dihedral : 21.428 156.980 1841 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 1.46 % Allowed : 9.74 % Favored : 88.80 % 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 aren not related in a simple way. whole: 0.00 (0.28), residues: 956 helix: 1.39 (0.30), residues: 342 sheet: 0.54 (0.64), residues: 70 loop : -1.02 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 514 TYR 0.027 0.001 TYR C 422 PHE 0.016 0.001 PHE C 342 TRP 0.021 0.001 TRP D 138 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9865) covalent geometry : angle 0.59836 (13591) hydrogen bonds : bond 0.04208 ( 362) hydrogen bonds : angle 4.16947 ( 915) metal coordination : bond 0.00526 ( 15) metal coordination : angle 2.41968 ( 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 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 181 LYS cc_start: 0.9212 (mttt) cc_final: 0.8911 (mtpt) REVERT: C 278 MET cc_start: 0.8326 (ttp) cc_final: 0.7548 (tpp) REVERT: C 308 MET cc_start: 0.7788 (mtp) cc_final: 0.6799 (ttm) REVERT: C 513 MET cc_start: 0.8611 (mtt) cc_final: 0.8360 (mtt) REVERT: C 514 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8539 (tpp80) REVERT: D 130 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8721 (ptpp) REVERT: D 183 MET cc_start: 0.8330 (mtt) cc_final: 0.8074 (mtt) REVERT: D 292 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8147 (pt) REVERT: D 382 MET cc_start: 0.9660 (mmm) cc_final: 0.9069 (mmm) REVERT: D 409 MET cc_start: 0.7927 (tpp) cc_final: 0.7706 (mmp) REVERT: D 549 MET cc_start: 0.8559 (ttp) cc_final: 0.7568 (tmm) outliers start: 13 outliers final: 7 residues processed: 69 average time/residue: 0.1242 time to fit residues: 11.7711 Evaluate side-chains 66 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 217 LEU 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 354 PHE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3743 r_free = 0.3743 target = 0.060491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.047133 restraints weight = 55685.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.048740 restraints weight = 31520.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049814 restraints weight = 21723.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.050510 restraints weight = 16805.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051010 restraints weight = 14186.497| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9880 Z= 0.171 Angle : 0.629 12.517 13597 Z= 0.336 Chirality : 0.040 0.153 1455 Planarity : 0.004 0.055 1470 Dihedral : 21.426 154.739 1841 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 1.34 % Allowed : 9.52 % Favored : 89.14 % 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 aren not related in a simple way. whole: -0.03 (0.28), residues: 956 helix: 1.35 (0.30), residues: 342 sheet: 0.48 (0.64), residues: 70 loop : -1.02 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 514 TYR 0.030 0.002 TYR C 422 PHE 0.015 0.001 PHE C 342 TRP 0.020 0.001 TRP D 138 HIS 0.004 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9865) covalent geometry : angle 0.62620 (13591) hydrogen bonds : bond 0.04841 ( 362) hydrogen bonds : angle 4.30676 ( 915) metal coordination : bond 0.01115 ( 15) metal coordination : angle 2.96320 ( 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 70 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.8369 (ttp) cc_final: 0.7547 (tpp) REVERT: C 308 MET cc_start: 0.7714 (mtp) cc_final: 0.6693 (ttm) REVERT: C 437 MET cc_start: 0.7882 (ttp) cc_final: 0.7436 (tpt) REVERT: C 514 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8527 (tpp80) REVERT: D 130 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8550 (ptpp) REVERT: D 183 MET cc_start: 0.8398 (mtt) cc_final: 0.8109 (mtt) REVERT: D 292 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8222 (pt) REVERT: D 382 MET cc_start: 0.9643 (mmm) cc_final: 0.9032 (mmm) REVERT: D 409 MET cc_start: 0.8015 (tpp) cc_final: 0.7796 (mmp) REVERT: D 549 MET cc_start: 0.8576 (ttp) cc_final: 0.7643 (tmm) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.1264 time to fit residues: 11.7176 Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 217 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 496 MET 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 328 ILE Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3737 r_free = 0.3737 target = 0.060057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.046735 restraints weight = 55420.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.048293 restraints weight = 31633.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.049303 restraints weight = 21867.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050036 restraints weight = 17028.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050474 restraints weight = 14280.752| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9880 Z= 0.199 Angle : 0.657 12.001 13597 Z= 0.350 Chirality : 0.041 0.157 1455 Planarity : 0.005 0.128 1470 Dihedral : 21.451 153.973 1841 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 1.57 % Allowed : 9.63 % Favored : 88.80 % 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 aren not related in a simple way. whole: -0.14 (0.28), residues: 956 helix: 1.26 (0.30), residues: 342 sheet: 0.56 (0.65), residues: 70 loop : -1.11 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 514 TYR 0.030 0.002 TYR C 422 PHE 0.016 0.002 PHE C 342 TRP 0.021 0.002 TRP D 138 HIS 0.005 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9865) covalent geometry : angle 0.65350 (13591) hydrogen bonds : bond 0.05202 ( 362) hydrogen bonds : angle 4.44481 ( 915) metal coordination : bond 0.01371 ( 15) metal coordination : angle 3.27244 ( 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 72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 278 MET cc_start: 0.8367 (ttp) cc_final: 0.7622 (tpp) REVERT: C 308 MET cc_start: 0.7663 (mtp) cc_final: 0.6581 (ttm) REVERT: C 356 ARG cc_start: 0.7376 (mtm180) cc_final: 0.6976 (mtt90) REVERT: C 437 MET cc_start: 0.7874 (ttp) cc_final: 0.7568 (tpt) REVERT: C 514 ARG cc_start: 0.8881 (mmm160) cc_final: 0.8544 (tpp80) REVERT: D 183 MET cc_start: 0.8422 (mtt) cc_final: 0.8172 (mtt) REVERT: D 292 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8258 (pt) REVERT: D 382 MET cc_start: 0.9645 (mmm) cc_final: 0.9008 (mmm) REVERT: D 409 MET cc_start: 0.8076 (tpp) cc_final: 0.7871 (mmp) REVERT: D 549 MET cc_start: 0.8594 (ttp) cc_final: 0.7667 (tmm) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1164 time to fit residues: 11.3202 Evaluate side-chains 69 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 217 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 D residue 292 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 328 ILE 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: 8.9990 chunk 36 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 68 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3718 r_free = 0.3718 target = 0.059296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046451 restraints weight = 58582.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.047931 restraints weight = 34679.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.048895 restraints weight = 24441.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.049540 restraints weight = 19340.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.049973 restraints weight = 16450.860| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9880 Z= 0.222 Angle : 0.682 14.609 13597 Z= 0.361 Chirality : 0.042 0.161 1455 Planarity : 0.005 0.101 1470 Dihedral : 21.502 153.883 1841 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.14 % Rotamer: Outliers : 1.68 % Allowed : 10.08 % Favored : 88.24 % 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 aren not related in a simple way. whole: -0.49 (0.27), residues: 956 helix: 0.97 (0.30), residues: 348 sheet: -0.12 (0.64), residues: 77 loop : -1.28 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 514 TYR 0.032 0.002 TYR C 422 PHE 0.016 0.002 PHE C 342 TRP 0.022 0.002 TRP D 138 HIS 0.005 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9865) covalent geometry : angle 0.67764 (13591) hydrogen bonds : bond 0.05499 ( 362) hydrogen bonds : angle 4.56133 ( 915) metal coordination : bond 0.01668 ( 15) metal coordination : angle 3.52417 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.13 seconds wall clock time: 34 minutes 48.41 seconds (2088.41 seconds total)