Starting phenix.real_space_refine on Tue Feb 13 09:53:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb3_24393/02_2024/7rb3_24393_neut_updated.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.080 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 P 3 5.49 5 S 31 5.16 5 C 3297 2.51 5 N 906 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 679": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5110 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4053 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 557} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 665 Unresolved non-hydrogen angles: 821 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 10, 'ASP:plan': 21, 'PHE:plan': 1, 'GLU:plan': 32, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 336 Chain: "A" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1057 Unusual residues: {'CMC': 1} Classifications: {'peptide': 147, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 143, None: 2} Not linked: pdbres="ARG A 362 " pdbres="CMC A 401 " Not linked: pdbres="CMC A 401 " pdbres="MET A 402 " Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'CMC:plan-5': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 3.86, per 1000 atoms: 0.76 Number of scatterers: 5110 At special positions: 0 Unit cell: (65.52, 104.16, 104.16, 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 31 16.00 P 3 15.00 O 873 8.00 N 906 7.00 C 3297 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 2 sheets defined 60.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 102 through 121 Processing helix chain 'B' and resid 133 through 136 No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 144 through 167 Processing helix chain 'B' and resid 190 through 211 removed outlier: 4.452A pdb=" N ARG B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 251 removed outlier: 3.668A pdb=" N THR B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 262 through 279 removed outlier: 3.577A pdb=" N VAL B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ALA B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 344 removed outlier: 4.261A pdb=" N VAL B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 327 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 343 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 361 removed outlier: 3.798A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 388 through 399 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 418 through 440 removed outlier: 4.655A pdb=" N SER B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) Proline residue: B 431 - end of helix Processing helix chain 'B' and resid 445 through 474 removed outlier: 3.745A pdb=" N LEU B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 removed outlier: 3.746A pdb=" N GLY B 507 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 removed outlier: 4.539A pdb=" N TYR B 519 " --> pdb=" O HIS B 516 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 520 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 522 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B 527 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 Processing helix chain 'B' and resid 573 through 599 Processing helix chain 'B' and resid 612 through 619 Processing helix chain 'B' and resid 621 through 624 Processing helix chain 'B' and resid 634 through 641 Processing helix chain 'B' and resid 652 through 672 removed outlier: 4.035A pdb=" N ASN B 672 " --> pdb=" O MET B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 699 Proline residue: B 689 - end of helix removed outlier: 3.566A pdb=" N VAL B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 699 " --> pdb=" O LYS B 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 312 removed outlier: 4.181A pdb=" N ALA A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 Processing sheet with id= A, first strand: chain 'B' and resid 710 through 712 Processing sheet with id= B, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.113A pdb=" N VAL A 260 " --> pdb=" O CYS A 264 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N CYS A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS A 271 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE A 284 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP A 273 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY A 282 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU A 317 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 284 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A 319 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N MET A 286 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU A 321 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N ALA A 288 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 14.998A pdb=" N GLU A 323 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 342 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS A 358 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ARG A 340 " --> pdb=" O LYS A 358 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 858 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: 1.34 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1253 1.33 - 1.46: 1135 1.46 - 1.58: 2786 1.58 - 1.70: 1 1.70 - 1.82: 51 Bond restraints: 5226 Sorted by residual: bond pdb=" C5P CMC A 401 " pdb=" N4P CMC A 401 " ideal model delta sigma weight residual 1.493 1.316 0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C9P CMC A 401 " pdb=" N8P CMC A 401 " ideal model delta sigma weight residual 1.485 1.310 0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" O6A CMC A 401 " pdb=" P2A CMC A 401 " ideal model delta sigma weight residual 1.717 1.547 0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" C3B CMC A 401 " pdb=" C4B CMC A 401 " ideal model delta sigma weight residual 1.347 1.512 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C4B CMC A 401 " pdb=" O4B CMC A 401 " ideal model delta sigma weight residual 1.596 1.445 0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 5221 not shown) Histogram of bond angle deviations from ideal: 79.24 - 90.19: 1 90.19 - 101.14: 17 101.14 - 112.10: 2748 112.10 - 123.05: 4141 123.05 - 134.00: 239 Bond angle restraints: 7146 Sorted by residual: angle pdb=" C1 CMC A 401 " pdb=" C2 CMC A 401 " pdb=" O21 CMC A 401 " ideal model delta sigma weight residual 119.98 79.24 40.74 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C1B CMC A 401 " pdb=" N9A CMC A 401 " pdb=" C4A CMC A 401 " ideal model delta sigma weight residual 90.87 125.06 -34.19 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N1A CMC A 401 " pdb=" C6A CMC A 401 " pdb=" N6A CMC A 401 " ideal model delta sigma weight residual 94.05 118.88 -24.83 3.00e+00 1.11e-01 6.85e+01 angle pdb=" C5A CMC A 401 " pdb=" C6A CMC A 401 " pdb=" N6A CMC A 401 " ideal model delta sigma weight residual 145.98 123.58 22.40 3.00e+00 1.11e-01 5.58e+01 angle pdb=" C2 CMC A 401 " pdb=" C1 CMC A 401 " pdb=" S1P CMC A 401 " ideal model delta sigma weight residual 109.50 128.38 -18.88 3.00e+00 1.11e-01 3.96e+01 ... (remaining 7141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.41: 2904 30.41 - 60.82: 122 60.82 - 91.23: 7 91.23 - 121.65: 0 121.65 - 152.06: 1 Dihedral angle restraints: 3034 sinusoidal: 880 harmonic: 2154 Sorted by residual: dihedral pdb=" C MET A 402 " pdb=" N MET A 402 " pdb=" CA MET A 402 " pdb=" CB MET A 402 " ideal model delta harmonic sigma weight residual -122.60 -111.25 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" CDP CMC A 401 " pdb=" CBP CMC A 401 " pdb=" CCP CMC A 401 " pdb=" O6A CMC A 401 " ideal model delta sinusoidal sigma weight residual 329.01 176.95 152.06 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA SER A 220 " pdb=" C SER A 220 " pdb=" N GLU A 221 " pdb=" CA GLU A 221 " ideal model delta harmonic sigma weight residual 180.00 157.96 22.04 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 3031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 756 0.068 - 0.135: 78 0.135 - 0.203: 2 0.203 - 0.270: 3 0.270 - 0.338: 2 Chirality restraints: 841 Sorted by residual: chirality pdb=" CA MET A 402 " pdb=" N MET A 402 " pdb=" C MET A 402 " pdb=" CB MET A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C3B CMC A 401 " pdb=" C2B CMC A 401 " pdb=" C4B CMC A 401 " pdb=" O3B CMC A 401 " both_signs ideal model delta sigma weight residual False -2.35 -2.64 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2B CMC A 401 " pdb=" C1B CMC A 401 " pdb=" C3B CMC A 401 " pdb=" O2B CMC A 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.33 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 838 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC A 401 " -0.268 2.00e-02 2.50e+03 2.31e-01 6.69e+02 pdb=" C9P CMC A 401 " 0.012 2.00e-02 2.50e+03 pdb=" CAP CMC A 401 " -0.145 2.00e-02 2.50e+03 pdb=" N8P CMC A 401 " 0.417 2.00e-02 2.50e+03 pdb=" O9P CMC A 401 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC A 401 " 0.073 2.00e-02 2.50e+03 6.20e-02 4.81e+01 pdb=" C5P CMC A 401 " 0.010 2.00e-02 2.50e+03 pdb=" C6P CMC A 401 " -0.029 2.00e-02 2.50e+03 pdb=" N4P CMC A 401 " -0.103 2.00e-02 2.50e+03 pdb=" O5P CMC A 401 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B CMC A 401 " 0.058 2.00e-02 2.50e+03 2.40e-02 1.58e+01 pdb=" C2A CMC A 401 " -0.007 2.00e-02 2.50e+03 pdb=" C4A CMC A 401 " -0.012 2.00e-02 2.50e+03 pdb=" C5A CMC A 401 " -0.007 2.00e-02 2.50e+03 pdb=" C6A CMC A 401 " -0.007 2.00e-02 2.50e+03 pdb=" C8A CMC A 401 " -0.010 2.00e-02 2.50e+03 pdb=" N1A CMC A 401 " 0.008 2.00e-02 2.50e+03 pdb=" N3A CMC A 401 " -0.016 2.00e-02 2.50e+03 pdb=" N6A CMC A 401 " 0.034 2.00e-02 2.50e+03 pdb=" N7A CMC A 401 " -0.011 2.00e-02 2.50e+03 pdb=" N9A CMC A 401 " -0.031 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 28 2.60 - 3.17: 4308 3.17 - 3.75: 8017 3.75 - 4.32: 10045 4.32 - 4.90: 17043 Nonbonded interactions: 39441 Sorted by model distance: nonbonded pdb=" O2B CMC A 401 " pdb=" O9A CMC A 401 " model vdw 2.021 2.440 nonbonded pdb=" O TYR B 412 " pdb=" NZ LYS B 418 " model vdw 2.280 2.520 nonbonded pdb=" O LYS B 96 " pdb=" OH TYR B 134 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR A 348 " pdb=" O MET A 402 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR B 582 " pdb=" OE2 GLU B 679 " model vdw 2.391 2.440 ... (remaining 39436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.910 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.008 0.177 5226 Z= 0.588 Angle : 1.166 40.739 7146 Z= 0.490 Chirality : 0.045 0.338 841 Planarity : 0.009 0.231 908 Dihedral : 16.705 152.056 1626 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.30 % Allowed : 25.39 % Favored : 73.32 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 8.00 % 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: 1.44 (0.32), residues: 706 helix: 2.01 (0.25), residues: 449 sheet: -0.92 (0.71), residues: 57 loop : -0.90 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 491 HIS 0.005 0.001 HIS B 472 PHE 0.014 0.001 PHE B 607 TYR 0.024 0.002 TYR B 520 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.607 Fit side-chains REVERT: A 301 ASN cc_start: 0.8692 (m-40) cc_final: 0.8486 (m110) outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.1303 time to fit residues: 21.3142 Evaluate side-chains 116 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 overall best weight: 1.1858 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5226 Z= 0.196 Angle : 0.535 9.439 7146 Z= 0.258 Chirality : 0.038 0.127 841 Planarity : 0.004 0.047 908 Dihedral : 8.325 171.043 794 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.44 % Allowed : 19.17 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.60 (0.32), residues: 706 helix: 2.13 (0.25), residues: 448 sheet: -0.95 (0.70), residues: 57 loop : -0.79 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 491 HIS 0.004 0.001 HIS B 495 PHE 0.007 0.001 PHE B 354 TYR 0.024 0.001 TYR B 520 ARG 0.002 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.615 Fit side-chains REVERT: A 231 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (tt) REVERT: A 301 ASN cc_start: 0.8715 (m-40) cc_final: 0.8507 (m110) outliers start: 21 outliers final: 15 residues processed: 127 average time/residue: 0.1135 time to fit residues: 20.5112 Evaluate side-chains 131 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5226 Z= 0.263 Angle : 0.531 8.278 7146 Z= 0.261 Chirality : 0.039 0.142 841 Planarity : 0.004 0.044 908 Dihedral : 8.312 172.285 794 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.44 % Allowed : 20.47 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.47 (0.32), residues: 706 helix: 2.01 (0.25), residues: 447 sheet: -0.98 (0.71), residues: 57 loop : -0.77 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 491 HIS 0.004 0.001 HIS B 472 PHE 0.010 0.001 PHE B 620 TYR 0.026 0.001 TYR B 520 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.611 Fit side-chains REVERT: B 394 ASP cc_start: 0.7802 (t0) cc_final: 0.7298 (t0) REVERT: A 231 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8153 (tt) outliers start: 21 outliers final: 17 residues processed: 127 average time/residue: 0.1261 time to fit residues: 22.4304 Evaluate side-chains 133 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5226 Z= 0.201 Angle : 0.506 8.181 7146 Z= 0.245 Chirality : 0.038 0.127 841 Planarity : 0.003 0.042 908 Dihedral : 8.282 175.127 794 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.18 % Allowed : 21.24 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.50 (0.32), residues: 706 helix: 2.02 (0.25), residues: 448 sheet: -0.95 (0.71), residues: 57 loop : -0.76 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 491 HIS 0.004 0.001 HIS B 495 PHE 0.008 0.001 PHE B 620 TYR 0.022 0.001 TYR B 520 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.510 Fit side-chains REVERT: B 394 ASP cc_start: 0.7799 (t0) cc_final: 0.7290 (t0) REVERT: A 213 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6417 (pt) REVERT: A 231 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8165 (tt) outliers start: 20 outliers final: 17 residues processed: 129 average time/residue: 0.1284 time to fit residues: 22.8997 Evaluate side-chains 136 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 5226 Z= 0.531 Angle : 0.663 8.229 7146 Z= 0.329 Chirality : 0.043 0.189 841 Planarity : 0.004 0.043 908 Dihedral : 8.593 170.374 794 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.99 % Allowed : 20.47 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.82 (0.31), residues: 706 helix: 1.52 (0.24), residues: 444 sheet: -0.94 (0.70), residues: 57 loop : -1.12 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 119 HIS 0.004 0.001 HIS B 123 PHE 0.017 0.002 PHE B 354 TYR 0.033 0.002 TYR B 520 ARG 0.004 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.637 Fit side-chains REVERT: B 352 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8323 (mt) REVERT: B 394 ASP cc_start: 0.7828 (t0) cc_final: 0.7330 (t0) REVERT: A 231 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8267 (tt) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.1341 time to fit residues: 23.1986 Evaluate side-chains 129 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 36 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 584 ASN B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5226 Z= 0.130 Angle : 0.525 9.439 7146 Z= 0.247 Chirality : 0.037 0.119 841 Planarity : 0.003 0.041 908 Dihedral : 8.390 176.982 794 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.89 % Allowed : 23.06 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.42 (0.32), residues: 706 helix: 2.09 (0.25), residues: 441 sheet: -0.81 (0.78), residues: 50 loop : -1.07 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 491 HIS 0.004 0.001 HIS B 495 PHE 0.006 0.001 PHE B 457 TYR 0.018 0.001 TYR B 520 ARG 0.001 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.632 Fit side-chains REVERT: A 231 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8107 (tt) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.1335 time to fit residues: 23.2524 Evaluate side-chains 124 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.8322 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5226 Z= 0.249 Angle : 0.547 8.309 7146 Z= 0.260 Chirality : 0.039 0.132 841 Planarity : 0.003 0.041 908 Dihedral : 8.366 175.187 794 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.15 % Allowed : 22.80 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.38 (0.32), residues: 706 helix: 1.96 (0.25), residues: 447 sheet: -0.81 (0.72), residues: 57 loop : -0.92 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 491 HIS 0.003 0.001 HIS B 495 PHE 0.009 0.001 PHE B 620 TYR 0.023 0.001 TYR B 520 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.597 Fit side-chains REVERT: B 394 ASP cc_start: 0.7812 (t0) cc_final: 0.7311 (t0) REVERT: A 231 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8131 (tt) outliers start: 16 outliers final: 14 residues processed: 121 average time/residue: 0.1321 time to fit residues: 21.8771 Evaluate side-chains 127 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5226 Z= 0.161 Angle : 0.526 9.852 7146 Z= 0.245 Chirality : 0.038 0.119 841 Planarity : 0.003 0.040 908 Dihedral : 8.302 177.486 794 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.15 % Allowed : 23.83 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.53 (0.32), residues: 706 helix: 2.09 (0.25), residues: 447 sheet: -0.80 (0.77), residues: 50 loop : -0.91 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 491 HIS 0.003 0.000 HIS B 495 PHE 0.006 0.001 PHE B 457 TYR 0.018 0.001 TYR B 520 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.612 Fit side-chains REVERT: A 231 ILE cc_start: 0.8346 (mm) cc_final: 0.8115 (tt) outliers start: 16 outliers final: 15 residues processed: 127 average time/residue: 0.1534 time to fit residues: 26.4448 Evaluate side-chains 129 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 19 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5226 Z= 0.148 Angle : 0.517 9.312 7146 Z= 0.240 Chirality : 0.037 0.118 841 Planarity : 0.003 0.040 908 Dihedral : 8.246 179.270 794 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.11 % Allowed : 24.35 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.74 (0.32), residues: 706 helix: 2.24 (0.25), residues: 446 sheet: -0.68 (0.75), residues: 56 loop : -0.78 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 491 HIS 0.002 0.000 HIS B 495 PHE 0.005 0.001 PHE B 719 TYR 0.015 0.001 TYR B 520 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.552 Fit side-chains REVERT: A 214 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7090 (mtm110) REVERT: A 231 ILE cc_start: 0.8347 (mm) cc_final: 0.8085 (tt) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.1355 time to fit residues: 22.8745 Evaluate side-chains 127 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5226 Z= 0.310 Angle : 0.580 10.000 7146 Z= 0.279 Chirality : 0.040 0.155 841 Planarity : 0.004 0.040 908 Dihedral : 8.159 174.400 792 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.89 % Allowed : 23.83 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.46 (0.32), residues: 706 helix: 2.00 (0.25), residues: 446 sheet: -0.76 (0.72), residues: 57 loop : -0.82 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 491 HIS 0.003 0.001 HIS B 495 PHE 0.010 0.001 PHE B 620 TYR 0.029 0.002 TYR B 520 ARG 0.002 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.595 Fit side-chains REVERT: B 394 ASP cc_start: 0.7812 (t0) cc_final: 0.7364 (t0) REVERT: A 214 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7105 (mtm110) REVERT: A 231 ILE cc_start: 0.8420 (mm) cc_final: 0.8184 (tt) outliers start: 15 outliers final: 15 residues processed: 123 average time/residue: 0.1323 time to fit residues: 21.9511 Evaluate side-chains 128 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.124283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110513 restraints weight = 9332.495| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.84 r_work: 0.3318 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5226 Z= 0.189 Angle : 0.539 9.850 7146 Z= 0.252 Chirality : 0.038 0.122 841 Planarity : 0.003 0.040 908 Dihedral : 8.151 177.443 792 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.15 % Allowed : 23.58 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.63 (0.32), residues: 706 helix: 2.12 (0.25), residues: 446 sheet: -0.70 (0.73), residues: 57 loop : -0.73 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 491 HIS 0.003 0.001 HIS B 495 PHE 0.007 0.001 PHE B 432 TYR 0.020 0.001 TYR B 520 ARG 0.002 0.000 ARG A 214 =============================================================================== Job complete usr+sys time: 1397.36 seconds wall clock time: 25 minutes 57.62 seconds (1557.62 seconds total)