Starting phenix.real_space_refine on Tue Aug 6 11:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/08_2024/8wmq_37658_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/08_2024/8wmq_37658.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/08_2024/8wmq_37658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/08_2024/8wmq_37658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/08_2024/8wmq_37658_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/08_2024/8wmq_37658_trim.cif" } resolution = 3.3 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= 0.000 sd= 0.003 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 S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16348 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.59, per 1000 atoms: 0.46 Number of scatterers: 16348 At special positions: 0 Unit cell: (96.163, 114.885, 101.269, 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) S 52 16.00 O 1472 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 12.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 67.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 73 removed outlier: 4.203A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 149 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.760A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.542A pdb=" N ILE B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.510A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 removed outlier: 3.509A pdb=" N TRP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.861A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.728A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.268A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 4.000A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 524 Proline residue: B 512 - end of helix removed outlier: 3.637A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 554 removed outlier: 5.159A pdb=" N TRP B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.200A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.862A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 202 Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.852A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.510A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.862A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 406 removed outlier: 3.735A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.006A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 Proline residue: A 512 - end of helix removed outlier: 3.634A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 3.543A pdb=" N GLY A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.664A pdb=" N THR B 250 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.766A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 removed outlier: 4.104A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 513 hydrogen bonds defined for protein. 1458 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: 5.58 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3414 1.42 - 1.62: 4820 1.62 - 1.81: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 1.500 1.557 -0.057 2.00e-02 2.50e+03 8.08e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 79.62 - 97.20: 4 97.20 - 114.79: 20971 114.79 - 132.38: 8927 132.38 - 149.96: 18 149.96 - 167.55: 2 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.91 34.01 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.94 33.98 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.62 32.88 3.00e+00 1.11e-01 1.20e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 7404 24.94 - 49.87: 339 49.87 - 74.80: 132 74.80 - 99.74: 4 99.74 - 124.67: 3 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual -86.00 -144.84 58.84 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1137 0.053 - 0.105: 191 0.105 - 0.158: 27 0.158 - 0.210: 0 0.210 - 0.263: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 362 " pdb=" N ILE A 362 " pdb=" C ILE A 362 " pdb=" CB ILE A 362 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO B 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 340 " 0.043 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 341 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 766 2.19 - 2.79: 32112 2.79 - 3.39: 45274 3.39 - 4.00: 56801 4.00 - 4.60: 89965 Nonbonded interactions: 224918 Sorted by model distance: nonbonded pdb=" O LEU A 519 " pdb=" HG1 THR A 523 " model vdw 1.583 2.450 nonbonded pdb=" O LEU B 519 " pdb=" HG1 THR B 523 " model vdw 1.584 2.450 nonbonded pdb=" HG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 1.608 2.450 nonbonded pdb=" O SER B 88 " pdb="HD21 ASN A 270 " model vdw 1.630 2.450 nonbonded pdb=" O PHE B 332 " pdb=" HG1 THR B 338 " model vdw 1.633 2.450 ... (remaining 224913 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.580 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: 0.250 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 53.310 Find NCS groups from input model: 0.540 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.004 0.130 8328 Z= 0.249 Angle : 1.070 41.971 11334 Z= 0.456 Chirality : 0.040 0.263 1356 Planarity : 0.005 0.065 1400 Dihedral : 14.040 124.675 2938 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.89 (0.26), residues: 1076 helix: 1.65 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 482 HIS 0.003 0.001 HIS A 360 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR B 309 ARG 0.017 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.306 Fit side-chains REVERT: B 390 ASP cc_start: 0.7078 (m-30) cc_final: 0.6821 (m-30) REVERT: B 444 GLU cc_start: 0.6848 (mp0) cc_final: 0.6634 (mp0) REVERT: A 390 ASP cc_start: 0.7144 (m-30) cc_final: 0.6882 (m-30) REVERT: A 444 GLU cc_start: 0.6869 (mp0) cc_final: 0.6630 (mp0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2822 time to fit residues: 58.3610 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8328 Z= 0.202 Angle : 1.001 37.429 11334 Z= 0.409 Chirality : 0.039 0.204 1356 Planarity : 0.005 0.066 1400 Dihedral : 8.653 111.989 1236 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.47 % Allowed : 6.06 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.26), residues: 1076 helix: 1.81 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS B 360 PHE 0.012 0.001 PHE B 46 TYR 0.010 0.001 TYR B 524 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.322 Fit side-chains REVERT: B 390 ASP cc_start: 0.7163 (m-30) cc_final: 0.6873 (m-30) REVERT: B 444 GLU cc_start: 0.7035 (mp0) cc_final: 0.6780 (mp0) REVERT: A 390 ASP cc_start: 0.7168 (m-30) cc_final: 0.6895 (m-30) outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.3058 time to fit residues: 54.8274 Evaluate side-chains 110 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8328 Z= 0.296 Angle : 1.021 37.633 11334 Z= 0.423 Chirality : 0.041 0.208 1356 Planarity : 0.005 0.069 1400 Dihedral : 8.311 103.161 1236 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.52 % Allowed : 8.51 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.81 (0.26), residues: 1076 helix: 1.62 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.003 0.001 HIS B 350 PHE 0.017 0.002 PHE B 189 TYR 0.009 0.001 TYR B 524 ARG 0.001 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.249 Fit side-chains REVERT: B 390 ASP cc_start: 0.7180 (m-30) cc_final: 0.6917 (m-30) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.3240 time to fit residues: 52.7226 Evaluate side-chains 110 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8328 Z= 0.163 Angle : 0.983 36.740 11334 Z= 0.392 Chirality : 0.039 0.210 1356 Planarity : 0.005 0.066 1400 Dihedral : 7.831 96.199 1236 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.93 % Allowed : 9.32 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.25 (0.26), residues: 1076 helix: 1.95 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.94 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 PHE 0.012 0.001 PHE A 189 TYR 0.009 0.001 TYR A 181 ARG 0.001 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.334 Fit side-chains REVERT: B 390 ASP cc_start: 0.7168 (m-30) cc_final: 0.6928 (m-30) outliers start: 8 outliers final: 7 residues processed: 110 average time/residue: 0.3119 time to fit residues: 52.7146 Evaluate side-chains 110 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8328 Z= 0.368 Angle : 1.039 36.735 11334 Z= 0.437 Chirality : 0.043 0.221 1356 Planarity : 0.006 0.070 1400 Dihedral : 8.078 92.969 1236 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.48 % Favored : 94.33 % Rotamer: Outliers : 1.28 % Allowed : 10.84 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.68 (0.25), residues: 1076 helix: 1.54 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 543 HIS 0.004 0.002 HIS A 350 PHE 0.021 0.002 PHE A 189 TYR 0.009 0.002 TYR A 181 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7723 (m-80) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.3581 time to fit residues: 58.1953 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.8164 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8328 Z= 0.261 Angle : 1.007 36.761 11334 Z= 0.413 Chirality : 0.041 0.215 1356 Planarity : 0.005 0.068 1400 Dihedral : 7.824 88.936 1236 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.40 % Allowed : 11.89 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.81 (0.26), residues: 1076 helix: 1.63 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.21 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS A 289 PHE 0.016 0.002 PHE B 555 TYR 0.009 0.001 TYR B 524 ARG 0.001 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7934 (m-80) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.3571 time to fit residues: 54.4998 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8328 Z= 0.182 Angle : 0.986 36.562 11334 Z= 0.394 Chirality : 0.039 0.209 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.317 79.730 1236 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.17 % Allowed : 12.47 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.14 (0.26), residues: 1076 helix: 1.92 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 PHE 0.023 0.001 PHE A 555 TYR 0.009 0.001 TYR A 181 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: A 236 GLN cc_start: 0.6330 (mp10) cc_final: 0.6110 (mp10) outliers start: 10 outliers final: 9 residues processed: 110 average time/residue: 0.3829 time to fit residues: 62.2177 Evaluate side-chains 111 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8328 Z= 0.284 Angle : 1.010 36.683 11334 Z= 0.413 Chirality : 0.040 0.211 1356 Planarity : 0.005 0.068 1400 Dihedral : 7.191 72.208 1236 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.63 % Allowed : 12.59 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.97 (0.26), residues: 1076 helix: 1.78 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.003 0.001 HIS A 350 PHE 0.017 0.002 PHE A 189 TYR 0.009 0.001 TYR A 181 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: A 524 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7587 (m-80) outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.3650 time to fit residues: 58.7423 Evaluate side-chains 112 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8328 Z= 0.158 Angle : 0.985 36.538 11334 Z= 0.391 Chirality : 0.039 0.200 1356 Planarity : 0.005 0.067 1400 Dihedral : 6.377 55.949 1236 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.52 % Allowed : 13.17 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.36 (0.26), residues: 1076 helix: 2.09 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.01 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS A 289 PHE 0.011 0.001 PHE A 466 TYR 0.009 0.001 TYR A 181 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: A 524 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7640 (m-80) outliers start: 13 outliers final: 11 residues processed: 109 average time/residue: 0.3523 time to fit residues: 56.0584 Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8328 Z= 0.143 Angle : 0.973 36.419 11334 Z= 0.383 Chirality : 0.038 0.198 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.726 53.619 1236 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.28 % Allowed : 13.87 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.57 (0.26), residues: 1076 helix: 2.24 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 289 PHE 0.009 0.001 PHE A 189 TYR 0.009 0.001 TYR A 181 ARG 0.003 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: A 524 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7705 (m-80) outliers start: 11 outliers final: 9 residues processed: 111 average time/residue: 0.3233 time to fit residues: 53.3615 Evaluate side-chains 112 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094869 restraints weight = 40531.051| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.38 r_work: 0.3176 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8328 Z= 0.255 Angle : 0.996 36.537 11334 Z= 0.405 Chirality : 0.040 0.207 1356 Planarity : 0.005 0.067 1400 Dihedral : 5.962 54.860 1236 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.63 % Allowed : 13.64 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.30 (0.26), residues: 1076 helix: 2.05 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 380 HIS 0.003 0.001 HIS A 350 PHE 0.016 0.002 PHE A 189 TYR 0.010 0.001 TYR A 181 ARG 0.002 0.000 ARG A 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.60 seconds wall clock time: 59 minutes 41.94 seconds (3581.94 seconds total)