Starting phenix.real_space_refine on Sun Mar 10 22:50:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv3_34282/03_2024/8gv3_34282_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.002 sd= 0.238 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 4 5.49 5 S 46 5.16 5 C 3634 2.51 5 N 954 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 222": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5720 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} Conformer: "B" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} bond proxies already assigned to first conformer: 2822 Chain: "B" Number of atoms: 2778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} Conformer: "B" Number of residues, atoms: 373, 2775 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 356} bond proxies already assigned to first conformer: 2822 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' ZN': 2, 'NAD': 1, 'WKZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' ZN': 2, 'NAD': 1, 'WKZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 696 SG CYS A 96 83.998 27.246 17.420 1.00 53.43 S ATOM 715 SG CYS A 99 80.541 26.704 19.076 1.00 59.54 S ATOM 741 SG CYS A 102 81.036 29.728 17.005 1.00 49.33 S ATOM 802 SG CYS A 110 82.922 29.536 20.183 1.00 47.97 S ATOM 323 SG CYS A 44 83.107 47.740 31.478 1.00 59.70 S ATOM 1275 SG CYS A 173 81.944 45.551 28.014 1.00 47.81 S ATOM 3474 SG CYS B 96 36.999 47.553 17.420 1.00 53.45 S ATOM 3493 SG CYS B 99 40.458 48.095 19.072 1.00 60.78 S ATOM 3519 SG CYS B 102 39.962 45.071 17.004 1.00 50.91 S ATOM 3580 SG CYS B 110 38.078 45.265 20.184 1.00 48.57 S ATOM 3101 SG CYS B 44 37.894 27.060 31.479 1.00 60.48 S ATOM 4053 SG CYS B 173 39.057 29.247 28.014 1.00 47.65 S Time building chain proxies: 6.17, per 1000 atoms: 1.08 Number of scatterers: 5720 At special positions: 0 Unit cell: (122.1, 75.9, 58.3, 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 46 16.00 P 4 15.00 O 1078 8.00 N 954 7.00 C 3634 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 - 3.50 Amino acid : False - 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: 2.07 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 110 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 102 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 99 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 96 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 173 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 44 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 66 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 102 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 99 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 96 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 173 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 44 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 66 " Number of angles added : 12 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 28.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.665A pdb=" N LYS A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.359A pdb=" N ALA A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 249 through 257 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 323 through 335 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.762A pdb=" N PHE A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.666A pdb=" N LYS B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 201 through 213 Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.357A pdb=" N ALA B 229 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 323 through 335 Proline residue: B 328 - end of helix Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.766A pdb=" N PHE B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 148 through 152 removed outlier: 3.802A pdb=" N SER A 74 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS A 37 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 72 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.868A pdb=" N THR A 369 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 370 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN A 348 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS A 372 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A 350 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 129 through 131 removed outlier: 4.292A pdb=" N PHE A 129 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.250A pdb=" N SER A 288 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 217 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL A 196 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 219 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU A 238 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 5 through 11 Processing sheet with id= G, first strand: chain 'B' and resid 148 through 152 removed outlier: 3.799A pdb=" N SER B 74 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 37 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 72 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.874A pdb=" N THR B 369 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 370 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 348 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS B 372 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER B 350 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.291A pdb=" N PHE B 129 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 313 through 315 removed outlier: 6.249A pdb=" N SER B 288 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 217 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL B 196 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 219 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 238 " --> pdb=" O GLY B 220 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 420 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: 1.52 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 958 1.31 - 1.43: 1399 1.43 - 1.56: 3393 1.56 - 1.68: 28 1.68 - 1.81: 58 Bond restraints: 5836 Sorted by residual: bond pdb=" C3B NAD A 403 " pdb=" C4B NAD A 403 " ideal model delta sigma weight residual 1.523 1.253 0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C3B NAD B 403 " pdb=" C4B NAD B 403 " ideal model delta sigma weight residual 1.523 1.253 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1B NAD B 403 " pdb=" C2B NAD B 403 " ideal model delta sigma weight residual 1.534 1.272 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C1B NAD A 403 " pdb=" C2B NAD A 403 " ideal model delta sigma weight residual 1.534 1.272 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAD A 403 " pdb=" C2D NAD A 403 " ideal model delta sigma weight residual 1.528 1.269 0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 5831 not shown) Histogram of bond angle deviations from ideal: 97.99 - 106.94: 191 106.94 - 115.90: 3768 115.90 - 124.86: 3850 124.86 - 133.82: 99 133.82 - 142.77: 10 Bond angle restraints: 7918 Sorted by residual: angle pdb=" C1B NAD B 403 " pdb=" N9A NAD B 403 " pdb=" C4A NAD B 403 " ideal model delta sigma weight residual 126.46 108.58 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1B NAD A 403 " pdb=" N9A NAD A 403 " pdb=" C4A NAD A 403 " ideal model delta sigma weight residual 126.46 108.60 17.86 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1B NAD B 403 " pdb=" N9A NAD B 403 " pdb=" C8A NAD B 403 " ideal model delta sigma weight residual 127.40 142.77 -15.37 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C1B NAD A 403 " pdb=" N9A NAD A 403 " pdb=" C8A NAD A 403 " ideal model delta sigma weight residual 127.40 142.71 -15.31 3.00e+00 1.11e-01 2.60e+01 angle pdb=" O1A NAD A 403 " pdb=" PA NAD A 403 " pdb=" O2A NAD A 403 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 ... (remaining 7913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 3076 15.55 - 31.10: 335 31.10 - 46.65: 65 46.65 - 62.20: 40 62.20 - 77.75: 8 Dihedral angle restraints: 3524 sinusoidal: 1426 harmonic: 2098 Sorted by residual: dihedral pdb=" CA LYS A 322 " pdb=" C LYS A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LYS B 322 " pdb=" C LYS B 322 " pdb=" N SER B 323 " pdb=" CA SER B 323 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA THR A 312 " pdb=" C THR A 312 " pdb=" N TRP A 313 " pdb=" CA TRP A 313 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 3521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 697 0.060 - 0.119: 187 0.119 - 0.179: 20 0.179 - 0.239: 2 0.239 - 0.298: 2 Chirality restraints: 908 Sorted by residual: chirality pdb=" C3D NAD A 403 " pdb=" C2D NAD A 403 " pdb=" C4D NAD A 403 " pdb=" O3D NAD A 403 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3D NAD B 403 " pdb=" C2D NAD B 403 " pdb=" C4D NAD B 403 " pdb=" O3D NAD B 403 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3B NAD A 403 " pdb=" C2B NAD A 403 " pdb=" C4B NAD A 403 " pdb=" O3B NAD A 403 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 905 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 313 " -0.003 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP B 313 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 313 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP B 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 313 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 313 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 313 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 313 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 313 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.003 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP A 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 373 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C ILE A 373 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE A 373 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 374 " 0.010 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 643 2.75 - 3.28: 5210 3.28 - 3.82: 8583 3.82 - 4.36: 10911 4.36 - 4.90: 19161 Nonbonded interactions: 44508 Sorted by model distance: nonbonded pdb=" OD2 ASP B 124 " pdb=" NH2 ARG B 128 " model vdw 2.208 2.520 nonbonded pdb=" OD2 ASP A 124 " pdb=" NH2 ARG A 128 " model vdw 2.209 2.520 nonbonded pdb=" O CYS A 173 " pdb=" OG1 THR A 177 " model vdw 2.223 2.440 nonbonded pdb=" O CYS B 173 " pdb=" OG1 THR B 177 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP B 222 " pdb=" N ILE B 223 " model vdw 2.265 2.520 ... (remaining 44503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 335 or resid 337 through 374 or resid 401 throug \ h 404)) selection = (chain 'B' and (resid 2 through 335 or resid 337 through 374 or resid 401 throug \ h 404)) } 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=0.50 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: 0.260 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: 1.610 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 0.270 5836 Z= 1.012 Angle : 0.974 17.881 7918 Z= 0.429 Chirality : 0.055 0.298 908 Planarity : 0.005 0.044 992 Dihedral : 14.998 77.754 2188 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.29), residues: 744 helix: -0.80 (0.33), residues: 220 sheet: 0.35 (0.44), residues: 140 loop : -1.05 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 313 HIS 0.004 0.001 HIS A 138 PHE 0.017 0.002 PHE B 351 TYR 0.014 0.002 TYR A 179 ARG 0.003 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.593 Fit side-chains REVERT: A 365 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7740 (tppt) REVERT: B 233 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6990 (tm-30) REVERT: B 365 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7734 (tppt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1815 time to fit residues: 19.8965 Evaluate side-chains 71 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5836 Z= 0.242 Angle : 0.533 5.749 7918 Z= 0.272 Chirality : 0.046 0.133 908 Planarity : 0.004 0.038 992 Dihedral : 9.493 54.427 906 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.00 % Allowed : 4.49 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.29), residues: 744 helix: -0.34 (0.34), residues: 224 sheet: 0.56 (0.45), residues: 140 loop : -0.98 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 313 HIS 0.002 0.001 HIS B 138 PHE 0.005 0.001 PHE A 351 TYR 0.011 0.001 TYR A 179 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.579 Fit side-chains REVERT: A 365 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7524 (tppt) REVERT: B 233 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 365 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7534 (tppt) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.1950 time to fit residues: 19.6583 Evaluate side-chains 74 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5836 Z= 0.355 Angle : 0.578 6.331 7918 Z= 0.295 Chirality : 0.048 0.138 908 Planarity : 0.005 0.039 992 Dihedral : 9.424 57.732 906 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.99 % Allowed : 5.32 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.29), residues: 744 helix: -0.35 (0.34), residues: 224 sheet: 0.45 (0.45), residues: 140 loop : -1.03 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 313 HIS 0.003 0.001 HIS A 138 PHE 0.007 0.001 PHE B 351 TYR 0.013 0.002 TYR B 179 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.647 Fit side-chains REVERT: A 365 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7559 (tppt) REVERT: B 233 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 365 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7561 (tppt) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.2026 time to fit residues: 19.7854 Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5836 Z= 0.277 Angle : 0.536 5.953 7918 Z= 0.273 Chirality : 0.046 0.132 908 Planarity : 0.004 0.038 992 Dihedral : 9.296 59.934 906 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.50 % Allowed : 6.48 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.30), residues: 744 helix: -0.16 (0.35), residues: 224 sheet: 0.51 (0.45), residues: 140 loop : -0.98 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 313 HIS 0.003 0.001 HIS B 138 PHE 0.005 0.001 PHE B 351 TYR 0.012 0.001 TYR B 179 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.667 Fit side-chains REVERT: A 365 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7605 (tppt) REVERT: B 233 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6991 (tm-30) REVERT: B 365 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7613 (tppt) outliers start: 9 outliers final: 9 residues processed: 72 average time/residue: 0.1903 time to fit residues: 17.9269 Evaluate side-chains 74 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5836 Z= 0.277 Angle : 0.534 6.017 7918 Z= 0.271 Chirality : 0.046 0.132 908 Planarity : 0.004 0.037 992 Dihedral : 9.206 57.994 906 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.99 % Allowed : 7.97 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.30), residues: 744 helix: -0.11 (0.35), residues: 224 sheet: 0.48 (0.45), residues: 140 loop : -0.96 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 313 HIS 0.003 0.001 HIS B 138 PHE 0.005 0.001 PHE A 351 TYR 0.011 0.001 TYR B 179 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.640 Fit side-chains REVERT: A 365 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7609 (tppt) REVERT: B 233 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 365 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7634 (tppt) outliers start: 12 outliers final: 12 residues processed: 75 average time/residue: 0.1855 time to fit residues: 18.2289 Evaluate side-chains 77 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5836 Z= 0.212 Angle : 0.498 5.598 7918 Z= 0.252 Chirality : 0.045 0.127 908 Planarity : 0.004 0.036 992 Dihedral : 9.074 56.229 906 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.83 % Allowed : 9.30 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.30), residues: 744 helix: 0.05 (0.35), residues: 224 sheet: 0.55 (0.45), residues: 140 loop : -0.92 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 313 HIS 0.002 0.000 HIS A 138 PHE 0.004 0.001 PHE A 351 TYR 0.010 0.001 TYR B 179 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.661 Fit side-chains REVERT: A 365 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7613 (tppt) REVERT: B 233 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6928 (tm-30) REVERT: B 365 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7619 (tppt) outliers start: 11 outliers final: 11 residues processed: 76 average time/residue: 0.1868 time to fit residues: 18.6081 Evaluate side-chains 77 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5836 Z= 0.132 Angle : 0.453 5.151 7918 Z= 0.228 Chirality : 0.044 0.120 908 Planarity : 0.004 0.034 992 Dihedral : 8.882 56.044 906 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.33 % Allowed : 10.13 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.31), residues: 744 helix: 0.22 (0.36), residues: 226 sheet: 0.64 (0.45), residues: 140 loop : -0.83 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 313 HIS 0.002 0.000 HIS B 138 PHE 0.004 0.001 PHE B 318 TYR 0.007 0.001 TYR A 92 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.600 Fit side-chains REVERT: A 365 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7550 (tppt) REVERT: B 233 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6973 (tm-30) REVERT: B 365 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7587 (tppt) outliers start: 8 outliers final: 8 residues processed: 75 average time/residue: 0.2014 time to fit residues: 19.6409 Evaluate side-chains 77 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.0020 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5836 Z= 0.124 Angle : 0.436 4.783 7918 Z= 0.220 Chirality : 0.044 0.119 908 Planarity : 0.004 0.032 992 Dihedral : 8.725 57.060 906 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.33 % Allowed : 11.13 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.31), residues: 744 helix: 0.21 (0.36), residues: 228 sheet: 0.70 (0.45), residues: 140 loop : -0.75 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 313 HIS 0.002 0.000 HIS B 138 PHE 0.003 0.000 PHE A 318 TYR 0.007 0.001 TYR B 179 ARG 0.001 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.655 Fit side-chains REVERT: A 365 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7428 (tppt) REVERT: B 233 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6965 (tm-30) REVERT: B 365 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7428 (tppt) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.2010 time to fit residues: 20.2653 Evaluate side-chains 78 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5836 Z= 0.226 Angle : 0.488 5.263 7918 Z= 0.247 Chirality : 0.046 0.127 908 Planarity : 0.004 0.034 992 Dihedral : 8.824 57.410 906 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.99 % Allowed : 10.30 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.31), residues: 744 helix: 0.13 (0.36), residues: 226 sheet: 0.66 (0.45), residues: 140 loop : -0.81 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 313 HIS 0.002 0.001 HIS A 138 PHE 0.004 0.001 PHE A 351 TYR 0.011 0.001 TYR B 179 ARG 0.001 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.619 Fit side-chains REVERT: A 365 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7498 (tppt) REVERT: B 233 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6965 (tm-30) REVERT: B 365 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7502 (tppt) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.2021 time to fit residues: 20.2578 Evaluate side-chains 79 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5836 Z= 0.219 Angle : 0.489 5.420 7918 Z= 0.247 Chirality : 0.045 0.127 908 Planarity : 0.004 0.034 992 Dihedral : 8.851 57.949 906 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.99 % Allowed : 10.13 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 744 helix: 0.15 (0.36), residues: 224 sheet: 0.62 (0.45), residues: 140 loop : -0.81 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 313 HIS 0.002 0.001 HIS A 138 PHE 0.004 0.001 PHE B 351 TYR 0.014 0.001 TYR A 179 ARG 0.001 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.637 Fit side-chains REVERT: A 365 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7536 (tppt) REVERT: B 233 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6947 (tm-30) REVERT: B 365 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7537 (tppt) outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 0.1998 time to fit residues: 19.7635 Evaluate side-chains 79 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 313 TRP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.140436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104312 restraints weight = 16981.167| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.03 r_work: 0.2875 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5836 Z= 0.332 Angle : 0.557 6.349 7918 Z= 0.282 Chirality : 0.048 0.138 908 Planarity : 0.004 0.036 992 Dihedral : 9.015 58.813 906 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 10.13 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.30), residues: 744 helix: -0.04 (0.35), residues: 224 sheet: 0.51 (0.46), residues: 140 loop : -0.88 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 313 HIS 0.003 0.001 HIS A 138 PHE 0.005 0.001 PHE B 197 TYR 0.014 0.002 TYR A 179 ARG 0.001 0.000 ARG B 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.70 seconds wall clock time: 26 minutes 37.36 seconds (1597.36 seconds total)