Starting phenix.real_space_refine on Wed Sep 17 19:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h1z_51786/09_2025/9h1z_51786_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h1z_51786/09_2025/9h1z_51786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h1z_51786/09_2025/9h1z_51786_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h1z_51786/09_2025/9h1z_51786_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h1z_51786/09_2025/9h1z_51786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h1z_51786/09_2025/9h1z_51786.map" } resolution = 3.3 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= 0.005 sd= 0.165 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 7037 2.51 5 N 1833 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 10892 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5454 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 630} Chain breaks: 3 Chain: "B" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5437 Classifications: {'peptide': 669} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 627} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10617 SG CYS B 652 54.847 58.539 56.662 1.00139.49 S Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10892 At special positions: 0 Unit cell: (115.431, 115.431, 91.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1983 8.00 N 1833 7.00 C 7037 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: 0.86 Conformation dependent library (CDL) restraints added in 374.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS B 652 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 654 " 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 7 sheets defined 55.0% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 27 through 45 removed outlier: 4.313A pdb=" N GLU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 86 through 93 removed outlier: 4.648A pdb=" N SER A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 removed outlier: 4.134A pdb=" N LEU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.671A pdb=" N LYS A 115 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 156 through 170 removed outlier: 4.033A pdb=" N TYR A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 4.301A pdb=" N VAL A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.616A pdb=" N PHE A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 214 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.313A pdb=" N LEU A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.637A pdb=" N ARG A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.715A pdb=" N ILE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.876A pdb=" N TRP A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 359 through 381 Processing helix chain 'A' and resid 424 through 447 removed outlier: 3.806A pdb=" N GLU A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.192A pdb=" N TYR A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 523 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.027A pdb=" N LYS A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 565 through 581 removed outlier: 3.995A pdb=" N LEU A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 601 Processing helix chain 'A' and resid 617 through 628 removed outlier: 3.685A pdb=" N LYS A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.833A pdb=" N LEU A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 5.978A pdb=" N CYS A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 27 through 46 removed outlier: 4.187A pdb=" N LEU B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 92 through 93 No H-bonds generated for 'chain 'B' and resid 92 through 93' Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.801A pdb=" N CYS B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.487A pdb=" N LYS B 115 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 156 through 170 removed outlier: 3.713A pdb=" N TYR B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 removed outlier: 4.350A pdb=" N VAL B 179 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 removed outlier: 3.666A pdb=" N PHE B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 214 Processing helix chain 'B' and resid 221 through 236 removed outlier: 4.333A pdb=" N LEU B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.779A pdb=" N ILE B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 320 removed outlier: 3.901A pdb=" N TRP B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.507A pdb=" N LYS B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 381 Processing helix chain 'B' and resid 424 through 447 removed outlier: 3.847A pdb=" N GLU B 447 " --> pdb=" O TRP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 4.211A pdb=" N TYR B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 509 " --> pdb=" O GLY B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 523 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.961A pdb=" N LYS B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 581 removed outlier: 4.200A pdb=" N LEU B 569 " --> pdb=" O PRO B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 601 Processing helix chain 'B' and resid 619 through 629 removed outlier: 3.668A pdb=" N SER B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 3.908A pdb=" N LEU B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 5.999A pdb=" N CYS B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 4.064A pdb=" N GLY A 56 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 75 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 394 removed outlier: 4.529A pdb=" N SER A 407 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 479 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 465 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA5, first strand: chain 'B' and resid 54 through 60 removed outlier: 3.975A pdb=" N GLY B 56 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA7, first strand: chain 'B' and resid 390 through 394 removed outlier: 4.500A pdb=" N SER B 407 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 479 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 465 " --> pdb=" O VAL B 482 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.55: 11108 1.55 - 1.88: 58 1.88 - 2.21: 0 2.21 - 2.53: 0 2.53 - 2.86: 1 Bond restraints: 11167 Sorted by residual: bond pdb=" C ASN B 152 " pdb=" N ASN B 154 " ideal model delta sigma weight residual 1.329 2.864 -1.535 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C THR B 631 " pdb=" N ARG B 632 " ideal model delta sigma weight residual 1.332 1.382 -0.050 1.38e-02 5.25e+03 1.30e+01 bond pdb=" N GLU A 47 " pdb=" CA GLU A 47 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.10e+01 bond pdb=" N VAL B 634 " pdb=" CA VAL B 634 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.18e+00 bond pdb=" N ASP A 617 " pdb=" CA ASP A 617 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.05e+00 ... (remaining 11162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.09: 15121 8.09 - 16.18: 3 16.18 - 24.26: 3 24.26 - 32.35: 0 32.35 - 40.44: 2 Bond angle restraints: 15129 Sorted by residual: angle pdb=" O ASN B 152 " pdb=" C ASN B 152 " pdb=" N ASN B 154 " ideal model delta sigma weight residual 122.59 85.64 36.95 1.33e+00 5.65e-01 7.72e+02 angle pdb=" CA ASN B 152 " pdb=" C ASN B 152 " pdb=" N ASN B 154 " ideal model delta sigma weight residual 116.84 157.28 -40.44 1.71e+00 3.42e-01 5.59e+02 angle pdb=" N PHE B 51 " pdb=" CA PHE B 51 " pdb=" CB PHE B 51 " ideal model delta sigma weight residual 110.50 131.71 -21.21 1.70e+00 3.46e-01 1.56e+02 angle pdb=" N GLN A 50 " pdb=" CA GLN A 50 " pdb=" CB GLN A 50 " ideal model delta sigma weight residual 110.50 129.01 -18.51 1.70e+00 3.46e-01 1.19e+02 angle pdb=" N PHE B 51 " pdb=" CA PHE B 51 " pdb=" C PHE B 51 " ideal model delta sigma weight residual 111.00 93.54 17.46 2.80e+00 1.28e-01 3.89e+01 ... (remaining 15124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6161 17.08 - 34.15: 410 34.15 - 51.23: 99 51.23 - 68.30: 47 68.30 - 85.38: 12 Dihedral angle restraints: 6729 sinusoidal: 2817 harmonic: 3912 Sorted by residual: dihedral pdb=" CA ARG A 288 " pdb=" C ARG A 288 " pdb=" N PRO A 289 " pdb=" CA PRO A 289 " ideal model delta harmonic sigma weight residual 0.00 43.96 -43.96 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" N GLN A 50 " pdb=" C GLN A 50 " pdb=" CA GLN A 50 " pdb=" CB GLN A 50 " ideal model delta harmonic sigma weight residual 122.80 143.71 -20.91 0 2.50e+00 1.60e-01 7.00e+01 dihedral pdb=" CA ARG B 288 " pdb=" C ARG B 288 " pdb=" N PRO B 289 " pdb=" CA PRO B 289 " ideal model delta harmonic sigma weight residual 0.00 36.55 -36.55 0 5.00e+00 4.00e-02 5.34e+01 ... (remaining 6726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1635 0.139 - 0.278: 15 0.278 - 0.417: 1 0.417 - 0.556: 0 0.556 - 0.695: 1 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CA GLN A 50 " pdb=" N GLN A 50 " pdb=" C GLN A 50 " pdb=" CB GLN A 50 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA PHE B 51 " pdb=" N PHE B 51 " pdb=" C PHE B 51 " pdb=" CB PHE B 51 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA ILE B 635 " pdb=" N ILE B 635 " pdb=" C ILE B 635 " pdb=" CB ILE B 635 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1649 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 288 " -0.385 9.50e-02 1.11e+02 1.73e-01 1.83e+01 pdb=" NE ARG A 288 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 288 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 288 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 288 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 245 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C ALA B 245 " -0.057 2.00e-02 2.50e+03 pdb=" O ALA B 245 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B 246 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 443 " 0.020 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP B 443 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 443 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 443 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 443 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 443 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 443 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 443 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 443 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 443 " -0.002 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 5 2.26 - 2.92: 4364 2.92 - 3.58: 15210 3.58 - 4.24: 23966 4.24 - 4.90: 41958 Nonbonded interactions: 85503 Sorted by model distance: nonbonded pdb=" SG CYS A 262 " pdb=" NH2 ARG A 288 " model vdw 1.599 3.480 nonbonded pdb=" SG CYS A 262 " pdb=" CZ ARG A 288 " model vdw 1.637 3.630 nonbonded pdb=" NH2 ARG B 238 " pdb=" NH1 ARG B 555 " model vdw 2.044 3.200 nonbonded pdb=" SG CYS A 262 " pdb=" NH1 ARG A 288 " model vdw 2.064 3.480 nonbonded pdb=" NH1 ARG A 288 " pdb=" CB VAL A 290 " model vdw 2.187 3.550 ... (remaining 85498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 48 or resid 51 through 152 or resid 154 through \ 686)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.190 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 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 : 0.015 1.535 11169 Z= 1.084 Angle : 0.995 40.439 15129 Z= 0.622 Chirality : 0.054 0.695 1652 Planarity : 0.010 0.173 1926 Dihedral : 13.834 85.381 4181 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.91 % Allowed : 6.59 % Favored : 92.50 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.10 (0.21), residues: 1322 helix: -1.07 (0.18), residues: 606 sheet: -0.23 (0.46), residues: 134 loop : -0.22 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG B 535 TYR 0.019 0.004 TYR B 27 PHE 0.018 0.002 PHE A 271 TRP 0.052 0.002 TRP B 443 HIS 0.007 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.01536 (11167) covalent geometry : angle 0.99491 (15129) hydrogen bonds : bond 0.15847 ( 543) hydrogen bonds : angle 7.10535 ( 1503) metal coordination : bond 0.13144 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.390 Fit side-chains REVERT: A 325 ASP cc_start: 0.7842 (t0) cc_final: 0.7585 (t0) REVERT: A 455 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7193 (tt0) REVERT: A 470 LYS cc_start: 0.6551 (mtmm) cc_final: 0.6188 (mtpp) REVERT: A 681 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8031 (pptt) REVERT: B 86 GLN cc_start: 0.6467 (mp10) cc_final: 0.5997 (mp10) REVERT: B 109 LEU cc_start: 0.8537 (mm) cc_final: 0.8313 (mm) REVERT: B 176 GLU cc_start: 0.8602 (tp30) cc_final: 0.8284 (tp30) REVERT: B 273 ASP cc_start: 0.6036 (t70) cc_final: 0.5743 (t0) REVERT: B 325 ASP cc_start: 0.7770 (t0) cc_final: 0.7567 (t0) REVERT: B 601 GLN cc_start: 0.6304 (mm-40) cc_final: 0.6040 (mt0) REVERT: B 681 LYS cc_start: 0.8544 (ttpp) cc_final: 0.7846 (pptt) outliers start: 11 outliers final: 4 residues processed: 146 average time/residue: 0.1116 time to fit residues: 23.3611 Evaluate side-chains 114 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 136 GLN A 191 ASN B 604 GLN B 629 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111318 restraints weight = 13112.132| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.84 r_work: 0.3098 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11169 Z= 0.131 Angle : 0.622 17.375 15129 Z= 0.333 Chirality : 0.042 0.273 1652 Planarity : 0.005 0.045 1926 Dihedral : 5.196 47.382 1425 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.99 % Allowed : 7.50 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.08 % 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: 0.67 (0.23), residues: 1324 helix: 1.04 (0.21), residues: 621 sheet: 0.04 (0.44), residues: 139 loop : 0.02 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 288 TYR 0.014 0.001 TYR B 27 PHE 0.013 0.001 PHE A 382 TRP 0.016 0.001 TRP B 443 HIS 0.006 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00274 (11167) covalent geometry : angle 0.62242 (15129) hydrogen bonds : bond 0.04559 ( 543) hydrogen bonds : angle 4.70396 ( 1503) metal coordination : bond 0.00235 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.478 Fit side-chains REVERT: A 162 GLU cc_start: 0.7999 (tp30) cc_final: 0.7681 (tp30) REVERT: A 176 GLU cc_start: 0.8578 (tp30) cc_final: 0.8299 (tt0) REVERT: A 241 ASN cc_start: 0.9086 (t0) cc_final: 0.8834 (t0) REVERT: A 325 ASP cc_start: 0.8126 (t0) cc_final: 0.7839 (t0) REVERT: A 455 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7048 (tm-30) REVERT: A 470 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7145 (mtpp) REVERT: A 681 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8131 (pptt) REVERT: B 86 GLN cc_start: 0.7245 (mp10) cc_final: 0.6563 (mp10) REVERT: B 109 LEU cc_start: 0.8698 (mm) cc_final: 0.8457 (mm) REVERT: B 176 GLU cc_start: 0.8726 (tp30) cc_final: 0.8414 (tp30) REVERT: B 325 ASP cc_start: 0.8085 (t0) cc_final: 0.7883 (t0) REVERT: B 455 GLU cc_start: 0.7821 (tt0) cc_final: 0.6652 (tm-30) REVERT: B 470 LYS cc_start: 0.7427 (mtmm) cc_final: 0.7040 (mtpp) REVERT: B 681 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8164 (pptt) outliers start: 12 outliers final: 5 residues processed: 136 average time/residue: 0.1117 time to fit residues: 21.7073 Evaluate side-chains 118 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106984 restraints weight = 13149.100| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.85 r_work: 0.3042 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 11169 Z= 0.156 Angle : 0.587 10.257 15129 Z= 0.308 Chirality : 0.042 0.226 1652 Planarity : 0.004 0.045 1926 Dihedral : 4.780 48.251 1418 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.40 % Allowed : 7.50 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.94 (0.24), residues: 1324 helix: 1.41 (0.21), residues: 619 sheet: 0.18 (0.44), residues: 147 loop : -0.04 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.011 0.001 TYR B 27 PHE 0.020 0.002 PHE B 118 TRP 0.013 0.001 TRP B 443 HIS 0.008 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00374 (11167) covalent geometry : angle 0.58747 (15129) hydrogen bonds : bond 0.04605 ( 543) hydrogen bonds : angle 4.44291 ( 1503) metal coordination : bond 0.00224 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.427 Fit side-chains REVERT: A 55 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8132 (mp10) REVERT: A 162 GLU cc_start: 0.8053 (tp30) cc_final: 0.7677 (tp30) REVERT: A 241 ASN cc_start: 0.9102 (t0) cc_final: 0.8760 (t0) REVERT: A 272 GLU cc_start: 0.8060 (tp30) cc_final: 0.7574 (mt-10) REVERT: A 325 ASP cc_start: 0.8080 (t0) cc_final: 0.7814 (t0) REVERT: A 449 GLU cc_start: 0.8268 (tp30) cc_final: 0.8058 (tp30) REVERT: A 455 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7081 (tm-30) REVERT: A 470 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7242 (mtpp) REVERT: A 681 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8138 (pptt) REVERT: B 86 GLN cc_start: 0.7241 (mp10) cc_final: 0.6499 (mp10) REVERT: B 109 LEU cc_start: 0.8726 (mm) cc_final: 0.8462 (mm) REVERT: B 138 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 176 GLU cc_start: 0.8702 (tp30) cc_final: 0.8319 (tp30) REVERT: B 272 GLU cc_start: 0.8016 (tp30) cc_final: 0.7547 (mt-10) REVERT: B 455 GLU cc_start: 0.7939 (tt0) cc_final: 0.6755 (tm-30) REVERT: B 470 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7158 (mtpp) REVERT: B 510 TYR cc_start: 0.7971 (m-80) cc_final: 0.7647 (m-80) REVERT: B 681 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8175 (pptt) outliers start: 17 outliers final: 9 residues processed: 127 average time/residue: 0.0892 time to fit residues: 17.1917 Evaluate side-chains 118 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 604 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 68 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 191 ASN B 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106902 restraints weight = 13146.384| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.84 r_work: 0.3052 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11169 Z= 0.126 Angle : 0.548 8.745 15129 Z= 0.287 Chirality : 0.041 0.209 1652 Planarity : 0.004 0.052 1926 Dihedral : 4.587 52.099 1418 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.15 % Allowed : 9.64 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.08 (0.24), residues: 1324 helix: 1.62 (0.21), residues: 621 sheet: 0.20 (0.44), residues: 150 loop : -0.08 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 70 TYR 0.009 0.001 TYR B 160 PHE 0.013 0.001 PHE B 118 TRP 0.011 0.001 TRP B 443 HIS 0.005 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00292 (11167) covalent geometry : angle 0.54811 (15129) hydrogen bonds : bond 0.04080 ( 543) hydrogen bonds : angle 4.23122 ( 1503) metal coordination : bond 0.00123 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.297 Fit side-chains REVERT: A 55 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8198 (mp10) REVERT: A 59 ILE cc_start: 0.8147 (mt) cc_final: 0.7899 (mt) REVERT: A 162 GLU cc_start: 0.8036 (tp30) cc_final: 0.7683 (tp30) REVERT: A 176 GLU cc_start: 0.8574 (tp30) cc_final: 0.8222 (tt0) REVERT: A 241 ASN cc_start: 0.9128 (t0) cc_final: 0.8738 (t0) REVERT: A 272 GLU cc_start: 0.8046 (tp30) cc_final: 0.7765 (mt-10) REVERT: A 449 GLU cc_start: 0.8220 (tp30) cc_final: 0.8017 (tp30) REVERT: A 455 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7056 (tm-30) REVERT: A 470 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7245 (mtpp) REVERT: A 681 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8115 (pptt) REVERT: B 59 ILE cc_start: 0.8104 (mt) cc_final: 0.7813 (mt) REVERT: B 86 GLN cc_start: 0.7141 (mp10) cc_final: 0.6338 (mp10) REVERT: B 109 LEU cc_start: 0.8771 (mm) cc_final: 0.8487 (mm) REVERT: B 138 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 176 GLU cc_start: 0.8707 (tp30) cc_final: 0.8292 (tp30) REVERT: B 272 GLU cc_start: 0.8008 (tp30) cc_final: 0.7593 (mt-10) REVERT: B 455 GLU cc_start: 0.7980 (tt0) cc_final: 0.6841 (tm-30) REVERT: B 470 LYS cc_start: 0.7556 (mtmm) cc_final: 0.7188 (mtpp) REVERT: B 681 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8142 (pptt) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.0904 time to fit residues: 16.8739 Evaluate side-chains 118 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106899 restraints weight = 13102.177| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.85 r_work: 0.3034 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11169 Z= 0.132 Angle : 0.541 8.579 15129 Z= 0.283 Chirality : 0.041 0.196 1652 Planarity : 0.004 0.050 1926 Dihedral : 4.501 53.642 1418 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 10.46 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.12 (0.24), residues: 1324 helix: 1.68 (0.22), residues: 626 sheet: 0.33 (0.45), residues: 149 loop : -0.16 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.009 0.001 TYR B 160 PHE 0.020 0.001 PHE B 118 TRP 0.013 0.001 TRP A 443 HIS 0.006 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00311 (11167) covalent geometry : angle 0.54069 (15129) hydrogen bonds : bond 0.04041 ( 543) hydrogen bonds : angle 4.11376 ( 1503) metal coordination : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.331 Fit side-chains REVERT: A 55 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8142 (mp10) REVERT: A 162 GLU cc_start: 0.8021 (tp30) cc_final: 0.7696 (tp30) REVERT: A 239 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7452 (mtmm) REVERT: A 241 ASN cc_start: 0.9131 (t0) cc_final: 0.8730 (t0) REVERT: A 272 GLU cc_start: 0.8078 (tp30) cc_final: 0.7808 (mt-10) REVERT: A 449 GLU cc_start: 0.8253 (tp30) cc_final: 0.8002 (tp30) REVERT: A 455 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7009 (tm-30) REVERT: A 470 LYS cc_start: 0.7608 (mtmm) cc_final: 0.7209 (mtpp) REVERT: B 59 ILE cc_start: 0.8050 (mt) cc_final: 0.7768 (mt) REVERT: B 86 GLN cc_start: 0.7175 (mp10) cc_final: 0.6625 (mp-120) REVERT: B 109 LEU cc_start: 0.8757 (mm) cc_final: 0.8439 (mm) REVERT: B 138 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7554 (mm) REVERT: B 176 GLU cc_start: 0.8670 (tp30) cc_final: 0.8355 (tp30) REVERT: B 272 GLU cc_start: 0.8056 (tp30) cc_final: 0.7750 (mt-10) REVERT: B 470 LYS cc_start: 0.7491 (mtmm) cc_final: 0.7134 (mtpp) REVERT: B 681 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8089 (pptt) outliers start: 21 outliers final: 12 residues processed: 132 average time/residue: 0.0898 time to fit residues: 17.6799 Evaluate side-chains 123 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 604 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 0.0000 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 42 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109311 restraints weight = 13157.341| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.85 r_work: 0.3081 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11169 Z= 0.101 Angle : 0.509 9.802 15129 Z= 0.268 Chirality : 0.039 0.204 1652 Planarity : 0.004 0.054 1926 Dihedral : 4.253 51.213 1418 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.24 % Allowed : 11.37 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.32 (0.24), residues: 1324 helix: 1.89 (0.22), residues: 626 sheet: 0.58 (0.46), residues: 147 loop : -0.17 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.005 0.001 TYR A 160 PHE 0.025 0.001 PHE B 118 TRP 0.013 0.001 TRP A 443 HIS 0.002 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00217 (11167) covalent geometry : angle 0.50930 (15129) hydrogen bonds : bond 0.03342 ( 543) hydrogen bonds : angle 3.95621 ( 1503) metal coordination : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.520 Fit side-chains REVERT: A 55 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8198 (mp10) REVERT: A 59 ILE cc_start: 0.8059 (mt) cc_final: 0.7798 (mt) REVERT: A 162 GLU cc_start: 0.8058 (tp30) cc_final: 0.7721 (tp30) REVERT: A 241 ASN cc_start: 0.9107 (t0) cc_final: 0.8689 (t0) REVERT: A 449 GLU cc_start: 0.8240 (tp30) cc_final: 0.8008 (tp30) REVERT: A 455 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7083 (tm-30) REVERT: A 470 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7249 (mtpp) REVERT: A 681 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8201 (pptt) REVERT: B 59 ILE cc_start: 0.8032 (mt) cc_final: 0.7754 (mt) REVERT: B 86 GLN cc_start: 0.7183 (mp10) cc_final: 0.6618 (mp-120) REVERT: B 109 LEU cc_start: 0.8739 (mm) cc_final: 0.8410 (mm) REVERT: B 176 GLU cc_start: 0.8641 (tp30) cc_final: 0.8302 (tp30) REVERT: B 220 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (tt) REVERT: B 455 GLU cc_start: 0.8136 (tt0) cc_final: 0.6970 (tm-30) REVERT: B 470 LYS cc_start: 0.7539 (mtmm) cc_final: 0.6957 (mtpp) REVERT: B 604 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: B 681 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8185 (pptt) outliers start: 15 outliers final: 6 residues processed: 136 average time/residue: 0.0997 time to fit residues: 20.1251 Evaluate side-chains 119 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 604 GLN Chi-restraints excluded: chain B residue 611 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 50 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101434 restraints weight = 13290.999| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.82 r_work: 0.2965 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11169 Z= 0.229 Angle : 0.637 9.331 15129 Z= 0.328 Chirality : 0.045 0.219 1652 Planarity : 0.004 0.044 1926 Dihedral : 4.788 53.100 1418 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.07 % Allowed : 12.85 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.82 (0.24), residues: 1324 helix: 1.50 (0.21), residues: 631 sheet: 0.31 (0.45), residues: 146 loop : -0.48 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 632 TYR 0.015 0.002 TYR A 575 PHE 0.020 0.002 PHE B 118 TRP 0.018 0.002 TRP B 651 HIS 0.007 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00572 (11167) covalent geometry : angle 0.63705 (15129) hydrogen bonds : bond 0.05203 ( 543) hydrogen bonds : angle 4.26105 ( 1503) metal coordination : bond 0.00307 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8081 (mp10) REVERT: A 162 GLU cc_start: 0.8109 (tp30) cc_final: 0.7751 (tp30) REVERT: A 241 ASN cc_start: 0.9145 (t0) cc_final: 0.8735 (t0) REVERT: A 449 GLU cc_start: 0.8220 (tp30) cc_final: 0.7990 (tp30) REVERT: A 455 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7030 (tm-30) REVERT: A 470 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7238 (mtpp) REVERT: A 681 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8151 (pptt) REVERT: B 86 GLN cc_start: 0.7288 (mp10) cc_final: 0.6721 (mp-120) REVERT: B 109 LEU cc_start: 0.8730 (mm) cc_final: 0.8407 (mm) REVERT: B 176 GLU cc_start: 0.8689 (tp30) cc_final: 0.8371 (tp30) REVERT: B 281 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7414 (mp) REVERT: B 470 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7234 (mtpp) REVERT: B 604 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: B 681 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8207 (pptt) outliers start: 13 outliers final: 8 residues processed: 122 average time/residue: 0.0992 time to fit residues: 17.8839 Evaluate side-chains 118 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 604 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105473 restraints weight = 13084.246| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.85 r_work: 0.3031 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11169 Z= 0.114 Angle : 0.534 9.145 15129 Z= 0.278 Chirality : 0.040 0.203 1652 Planarity : 0.004 0.045 1926 Dihedral : 4.399 52.378 1418 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.91 % Allowed : 13.01 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.12 (0.24), residues: 1324 helix: 1.83 (0.22), residues: 632 sheet: 0.42 (0.46), residues: 146 loop : -0.41 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.006 0.001 TYR A 231 PHE 0.027 0.001 PHE A 118 TRP 0.014 0.001 TRP B 443 HIS 0.004 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00254 (11167) covalent geometry : angle 0.53396 (15129) hydrogen bonds : bond 0.03799 ( 543) hydrogen bonds : angle 4.00178 ( 1503) metal coordination : bond 0.00191 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8168 (mp10) REVERT: A 59 ILE cc_start: 0.8053 (mt) cc_final: 0.7816 (mt) REVERT: A 162 GLU cc_start: 0.8053 (tp30) cc_final: 0.7716 (tp30) REVERT: A 220 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 241 ASN cc_start: 0.9137 (t0) cc_final: 0.8728 (t0) REVERT: A 449 GLU cc_start: 0.8181 (tp30) cc_final: 0.7970 (tp30) REVERT: A 455 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7094 (tm-30) REVERT: A 470 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7264 (mtpp) REVERT: A 510 TYR cc_start: 0.8134 (m-80) cc_final: 0.7893 (m-80) REVERT: A 681 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8173 (pptt) REVERT: B 59 ILE cc_start: 0.8047 (mt) cc_final: 0.7800 (mt) REVERT: B 74 ASP cc_start: 0.7245 (t0) cc_final: 0.7001 (p0) REVERT: B 86 GLN cc_start: 0.7274 (mp10) cc_final: 0.6696 (mp-120) REVERT: B 109 LEU cc_start: 0.8756 (mm) cc_final: 0.8431 (mm) REVERT: B 176 GLU cc_start: 0.8661 (tp30) cc_final: 0.8064 (tt0) REVERT: B 281 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7296 (mp) REVERT: B 455 GLU cc_start: 0.8193 (tt0) cc_final: 0.6926 (tm-30) REVERT: B 470 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7020 (mtpp) REVERT: B 510 TYR cc_start: 0.8233 (m-80) cc_final: 0.8025 (m-80) REVERT: B 604 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: B 681 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8220 (pptt) outliers start: 11 outliers final: 6 residues processed: 120 average time/residue: 0.0981 time to fit residues: 17.4227 Evaluate side-chains 113 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 604 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104745 restraints weight = 12966.910| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.79 r_work: 0.3027 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11169 Z= 0.134 Angle : 0.546 9.128 15129 Z= 0.282 Chirality : 0.041 0.204 1652 Planarity : 0.004 0.042 1926 Dihedral : 4.364 52.395 1418 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.99 % Allowed : 12.77 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.13 (0.24), residues: 1324 helix: 1.82 (0.22), residues: 632 sheet: 0.42 (0.46), residues: 146 loop : -0.39 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.010 0.001 TYR A 231 PHE 0.029 0.001 PHE A 118 TRP 0.018 0.001 TRP B 443 HIS 0.005 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00321 (11167) covalent geometry : angle 0.54641 (15129) hydrogen bonds : bond 0.03946 ( 543) hydrogen bonds : angle 3.98694 ( 1503) metal coordination : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8166 (mp10) REVERT: A 59 ILE cc_start: 0.8038 (mt) cc_final: 0.7804 (mt) REVERT: A 74 ASP cc_start: 0.7269 (t0) cc_final: 0.6832 (p0) REVERT: A 121 GLN cc_start: 0.6302 (tt0) cc_final: 0.6055 (tt0) REVERT: A 162 GLU cc_start: 0.8082 (tp30) cc_final: 0.7746 (tp30) REVERT: A 220 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 241 ASN cc_start: 0.9130 (t0) cc_final: 0.8714 (t0) REVERT: A 449 GLU cc_start: 0.8202 (tp30) cc_final: 0.7976 (tp30) REVERT: A 455 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7065 (tm-30) REVERT: A 470 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7046 (mtpp) REVERT: A 510 TYR cc_start: 0.8182 (m-80) cc_final: 0.7969 (m-80) REVERT: A 681 LYS cc_start: 0.8789 (mtmm) cc_final: 0.8160 (pptt) REVERT: B 59 ILE cc_start: 0.8066 (mt) cc_final: 0.7814 (mt) REVERT: B 74 ASP cc_start: 0.7290 (t0) cc_final: 0.7034 (p0) REVERT: B 86 GLN cc_start: 0.7275 (mp10) cc_final: 0.6697 (mp-120) REVERT: B 109 LEU cc_start: 0.8739 (mm) cc_final: 0.8408 (mm) REVERT: B 176 GLU cc_start: 0.8642 (tp30) cc_final: 0.8107 (tt0) REVERT: B 281 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7313 (mp) REVERT: B 455 GLU cc_start: 0.8173 (tt0) cc_final: 0.6927 (tm-30) REVERT: B 470 LYS cc_start: 0.7598 (mtmm) cc_final: 0.7030 (mtpp) REVERT: B 510 TYR cc_start: 0.8190 (m-80) cc_final: 0.7989 (m-80) REVERT: B 604 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7703 (pt0) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 0.0939 time to fit residues: 17.0265 Evaluate side-chains 118 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 604 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107882 restraints weight = 13309.165| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.92 r_work: 0.3096 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11169 Z= 0.105 Angle : 0.518 9.045 15129 Z= 0.271 Chirality : 0.040 0.199 1652 Planarity : 0.004 0.042 1926 Dihedral : 4.141 51.784 1418 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.82 % Allowed : 12.77 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.21 (0.25), residues: 1324 helix: 1.88 (0.22), residues: 639 sheet: 0.56 (0.47), residues: 146 loop : -0.42 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.006 0.001 TYR A 231 PHE 0.029 0.001 PHE B 118 TRP 0.023 0.001 TRP B 443 HIS 0.003 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00232 (11167) covalent geometry : angle 0.51831 (15129) hydrogen bonds : bond 0.03355 ( 543) hydrogen bonds : angle 3.86362 ( 1503) metal coordination : bond 0.00148 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8220 (mp10) REVERT: A 59 ILE cc_start: 0.8091 (mt) cc_final: 0.7842 (mt) REVERT: A 74 ASP cc_start: 0.7273 (t0) cc_final: 0.6967 (p0) REVERT: A 162 GLU cc_start: 0.8115 (tp30) cc_final: 0.7742 (tp30) REVERT: A 220 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 241 ASN cc_start: 0.9067 (t0) cc_final: 0.8631 (t0) REVERT: A 455 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7212 (tm-30) REVERT: A 470 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7226 (mtpp) REVERT: A 510 TYR cc_start: 0.8186 (m-80) cc_final: 0.7763 (m-80) REVERT: A 681 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8187 (pptt) REVERT: B 59 ILE cc_start: 0.8093 (mt) cc_final: 0.7851 (mt) REVERT: B 74 ASP cc_start: 0.7294 (t0) cc_final: 0.7053 (p0) REVERT: B 86 GLN cc_start: 0.7335 (mp10) cc_final: 0.6943 (mm110) REVERT: B 109 LEU cc_start: 0.8780 (mm) cc_final: 0.8448 (mm) REVERT: B 132 PHE cc_start: 0.7678 (p90) cc_final: 0.7441 (p90) REVERT: B 176 GLU cc_start: 0.8625 (tp30) cc_final: 0.8135 (tt0) REVERT: B 240 ASP cc_start: 0.8699 (p0) cc_final: 0.8177 (m-30) REVERT: B 281 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7441 (mp) REVERT: B 455 GLU cc_start: 0.8255 (tt0) cc_final: 0.7086 (tm-30) REVERT: B 470 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7198 (mtpp) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.0987 time to fit residues: 18.1930 Evaluate side-chains 111 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108166 restraints weight = 13248.776| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.85 r_work: 0.3078 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11169 Z= 0.119 Angle : 0.530 9.128 15129 Z= 0.275 Chirality : 0.040 0.205 1652 Planarity : 0.004 0.040 1926 Dihedral : 4.144 51.989 1418 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.99 % Allowed : 13.18 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.16 (0.25), residues: 1324 helix: 1.84 (0.22), residues: 639 sheet: 0.52 (0.46), residues: 146 loop : -0.43 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.008 0.001 TYR A 231 PHE 0.030 0.001 PHE A 118 TRP 0.021 0.001 TRP B 443 HIS 0.004 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00276 (11167) covalent geometry : angle 0.52965 (15129) hydrogen bonds : bond 0.03569 ( 543) hydrogen bonds : angle 3.86848 ( 1503) metal coordination : bond 0.00165 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.66 seconds wall clock time: 39 minutes 29.10 seconds (2369.10 seconds total)