Starting phenix.real_space_refine on Tue Feb 13 12:35:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mx2_24070/02_2024/7mx2_24070_updated.pdb" } resolution = 3.64 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= 0.004 sd= 0.093 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 40 5.16 5 C 3978 2.51 5 N 1078 2.21 5 O 1060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 575": "OE1" <-> "OE2" Residue "A ARG 294": "NH1" <-> "NH2" 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: 6159 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4515 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 617} Chain breaks: 5 Unresolved non-hydrogen bonds: 730 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 586 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 23, 'TYR:plan': 3, 'ASN:plan1': 10, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 411 Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 451 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1115 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 148} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 91 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 78 Unusual residues: {'CMC': 1} Classifications: {'peptide': 4, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="PRO D 405 " pdbres="CMC D 501 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.97, per 1000 atoms: 0.64 Number of scatterers: 6159 At special positions: 0 Unit cell: (80.64, 99.12, 106.68, 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 40 16.00 P 3 15.00 O 1060 8.00 N 1078 7.00 C 3978 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 2 sheets defined 53.3% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.631A pdb=" N GLU B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.991A pdb=" N LYS B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 125 through 128 No H-bonds generated for 'chain 'B' and resid 125 through 128' 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 210 removed outlier: 3.587A pdb=" N ARG B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 Processing helix chain 'B' and resid 256 through 277 removed outlier: 3.641A pdb=" N GLU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 269 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 343 removed outlier: 3.864A pdb=" N GLU B 341 " --> pdb=" O LYS B 337 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 361 removed outlier: 3.728A 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 388 through 399 Processing helix chain 'B' and resid 415 through 439 removed outlier: 4.342A 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 443 through 475 removed outlier: 4.321A pdb=" N ARG B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 509 removed outlier: 3.671A pdb=" N GLY B 507 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 527 removed outlier: 3.729A pdb=" N TRP B 523 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 573 through 599 Processing helix chain 'B' and resid 612 through 619 Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 634 through 641 removed outlier: 3.652A pdb=" N GLU B 639 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 652 through 671 Processing helix chain 'B' and resid 678 through 699 removed outlier: 3.511A pdb=" N ILE B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Proline residue: B 689 - end of helix removed outlier: 3.621A pdb=" N GLY B 699 " --> pdb=" O LYS B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'A' and resid 221 through 234 Proline residue: A 225 - end of helix removed outlier: 3.522A pdb=" N MET A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 229 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 232 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' 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 Processing helix chain 'A' and resid 327 through 336 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 214 through 217 removed outlier: 6.597A pdb=" N LYS A 271 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE A 284 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP A 273 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY A 282 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS A 275 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG A 280 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 317 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE A 284 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 319 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N MET A 286 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N GLU A 321 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 10.645A pdb=" N ALA A 288 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 15.045A pdb=" N GLU A 323 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 342 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS A 358 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG A 340 " --> pdb=" O LYS A 358 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 936 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: 1.72 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 959 1.30 - 1.43: 1680 1.43 - 1.56: 3587 1.56 - 1.69: 5 1.69 - 1.82: 64 Bond restraints: 6295 Sorted by residual: bond pdb=" C5P CMC D 501 " pdb=" N4P CMC D 501 " ideal model delta sigma weight residual 1.493 1.316 0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C9P CMC D 501 " pdb=" N8P CMC D 501 " ideal model delta sigma weight residual 1.485 1.310 0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" O6A CMC D 501 " pdb=" P2A CMC D 501 " ideal model delta sigma weight residual 1.717 1.548 0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C3B CMC D 501 " pdb=" C4B CMC D 501 " ideal model delta sigma weight residual 1.347 1.512 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" C4B CMC D 501 " pdb=" O4B CMC D 501 " ideal model delta sigma weight residual 1.596 1.445 0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6290 not shown) Histogram of bond angle deviations from ideal: 79.21 - 90.16: 1 90.16 - 101.11: 26 101.11 - 112.06: 3328 112.06 - 123.01: 4962 123.01 - 133.96: 298 Bond angle restraints: 8615 Sorted by residual: angle pdb=" C1 CMC D 501 " pdb=" C2 CMC D 501 " pdb=" O21 CMC D 501 " ideal model delta sigma weight residual 119.98 79.21 40.77 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C1B CMC D 501 " pdb=" N9A CMC D 501 " pdb=" C4A CMC D 501 " ideal model delta sigma weight residual 90.87 124.99 -34.12 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N1A CMC D 501 " pdb=" C6A CMC D 501 " pdb=" N6A CMC D 501 " ideal model delta sigma weight residual 94.05 118.87 -24.82 3.00e+00 1.11e-01 6.84e+01 angle pdb=" C5A CMC D 501 " pdb=" C6A CMC D 501 " pdb=" N6A CMC D 501 " ideal model delta sigma weight residual 145.98 123.59 22.39 3.00e+00 1.11e-01 5.57e+01 angle pdb=" C2 CMC D 501 " pdb=" C1 CMC D 501 " pdb=" S1P CMC D 501 " ideal model delta sigma weight residual 109.50 128.39 -18.89 3.00e+00 1.11e-01 3.97e+01 ... (remaining 8610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.41: 3539 30.41 - 60.81: 143 60.81 - 91.22: 6 91.22 - 121.63: 0 121.63 - 152.03: 1 Dihedral angle restraints: 3689 sinusoidal: 1114 harmonic: 2575 Sorted by residual: dihedral pdb=" CG ARG A 294 " pdb=" CD ARG A 294 " pdb=" NE ARG A 294 " pdb=" CZ ARG A 294 " ideal model delta sinusoidal sigma weight residual 90.00 6.24 83.76 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CDP CMC D 501 " pdb=" CBP CMC D 501 " pdb=" CCP CMC D 501 " pdb=" O6A CMC D 501 " ideal model delta sinusoidal sigma weight residual 329.01 176.98 152.03 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA GLY B 55 " pdb=" C GLY B 55 " pdb=" N LEU B 56 " pdb=" CA LEU B 56 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 888 0.057 - 0.113: 132 0.113 - 0.170: 10 0.170 - 0.227: 0 0.227 - 0.284: 3 Chirality restraints: 1033 Sorted by residual: chirality pdb=" C3B CMC D 501 " pdb=" C2B CMC D 501 " pdb=" C4B CMC D 501 " pdb=" O3B CMC D 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA MET D 402 " pdb=" N MET D 402 " pdb=" C MET D 402 " pdb=" CB MET D 402 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2B CMC D 501 " pdb=" C1B CMC D 501 " pdb=" C3B CMC D 501 " pdb=" O2B CMC D 501 " both_signs ideal model delta sigma weight residual False -2.57 -2.33 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1030 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC D 501 " 0.268 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" C9P CMC D 501 " -0.012 2.00e-02 2.50e+03 pdb=" CAP CMC D 501 " 0.145 2.00e-02 2.50e+03 pdb=" N8P CMC D 501 " -0.417 2.00e-02 2.50e+03 pdb=" O9P CMC D 501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC D 501 " -0.073 2.00e-02 2.50e+03 6.23e-02 4.85e+01 pdb=" C5P CMC D 501 " -0.010 2.00e-02 2.50e+03 pdb=" C6P CMC D 501 " 0.029 2.00e-02 2.50e+03 pdb=" N4P CMC D 501 " 0.103 2.00e-02 2.50e+03 pdb=" O5P CMC D 501 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 652 " -0.080 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO B 653 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 653 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 653 " -0.062 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 32 2.60 - 3.17: 5179 3.17 - 3.75: 9567 3.75 - 4.32: 11728 4.32 - 4.90: 20046 Nonbonded interactions: 46552 Sorted by model distance: nonbonded pdb=" O2B CMC D 501 " pdb=" O9A CMC D 501 " model vdw 2.021 2.440 nonbonded pdb=" OH TYR A 283 " pdb=" OE1 GLU A 321 " model vdw 2.248 2.440 nonbonded pdb=" O LYS B 96 " pdb=" OH TYR B 134 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR A 239 " pdb=" N LEU D 403 " model vdw 2.297 2.520 nonbonded pdb=" O SER B 124 " pdb=" OG1 THR B 128 " model vdw 2.313 2.440 ... (remaining 46547 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.010 Extract box with map and model: 2.150 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.120 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 6295 Z= 0.497 Angle : 1.063 40.770 8615 Z= 0.436 Chirality : 0.042 0.284 1033 Planarity : 0.009 0.231 1094 Dihedral : 15.721 152.034 2009 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.40 % Allowed : 22.95 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.30), residues: 855 helix: 2.69 (0.24), residues: 471 sheet: -1.67 (0.67), residues: 53 loop : -1.21 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 119 HIS 0.003 0.001 HIS B 495 PHE 0.015 0.001 PHE B 432 TYR 0.010 0.001 TYR B 616 ARG 0.032 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.732 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.1325 time to fit residues: 19.7549 Evaluate side-chains 97 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6295 Z= 0.198 Angle : 0.504 9.816 8615 Z= 0.248 Chirality : 0.039 0.192 1033 Planarity : 0.003 0.063 1094 Dihedral : 7.310 155.328 946 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 4.39 % Allowed : 20.36 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.31), residues: 855 helix: 2.69 (0.24), residues: 477 sheet: -1.59 (0.60), residues: 62 loop : -1.16 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 523 HIS 0.003 0.000 HIS B 495 PHE 0.014 0.001 PHE B 432 TYR 0.011 0.001 TYR A 348 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.745 Fit side-chains REVERT: B 329 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.9007 (m-80) REVERT: B 597 ASP cc_start: 0.8825 (t0) cc_final: 0.8544 (t0) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.1204 time to fit residues: 20.5673 Evaluate side-chains 112 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6295 Z= 0.390 Angle : 0.595 8.513 8615 Z= 0.298 Chirality : 0.042 0.206 1033 Planarity : 0.004 0.061 1094 Dihedral : 7.520 151.144 946 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 6.79 % Allowed : 18.56 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.20 (0.30), residues: 855 helix: 2.50 (0.24), residues: 471 sheet: -1.60 (0.61), residues: 52 loop : -1.41 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 523 HIS 0.004 0.001 HIS B 495 PHE 0.020 0.002 PHE B 432 TYR 0.015 0.002 TYR B 520 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 0.665 Fit side-chains REVERT: B 60 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: B 591 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7548 (mppt) REVERT: B 627 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6538 (tmm) outliers start: 34 outliers final: 22 residues processed: 124 average time/residue: 0.1261 time to fit residues: 22.8514 Evaluate side-chains 117 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6295 Z= 0.167 Angle : 0.495 8.257 8615 Z= 0.242 Chirality : 0.039 0.218 1033 Planarity : 0.003 0.057 1094 Dihedral : 7.211 148.709 946 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 3.99 % Allowed : 22.16 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.55 (0.30), residues: 855 helix: 2.76 (0.24), residues: 473 sheet: -1.46 (0.61), residues: 52 loop : -1.25 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 119 HIS 0.002 0.000 HIS B 495 PHE 0.017 0.001 PHE B 432 TYR 0.015 0.001 TYR A 347 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.726 Fit side-chains REVERT: B 60 MET cc_start: 0.8396 (tpp) cc_final: 0.7829 (mtm) REVERT: B 325 MET cc_start: 0.8771 (tmm) cc_final: 0.8502 (tmm) REVERT: B 627 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6960 (tmm) outliers start: 20 outliers final: 14 residues processed: 111 average time/residue: 0.1334 time to fit residues: 21.4569 Evaluate side-chains 109 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6295 Z= 0.349 Angle : 0.574 8.156 8615 Z= 0.281 Chirality : 0.041 0.211 1033 Planarity : 0.003 0.056 1094 Dihedral : 7.139 145.011 946 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 5.79 % Allowed : 20.56 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.35 (0.30), residues: 855 helix: 2.61 (0.24), residues: 470 sheet: -1.69 (0.61), residues: 52 loop : -1.30 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 532 HIS 0.003 0.001 HIS B 495 PHE 0.017 0.002 PHE B 432 TYR 0.016 0.002 TYR B 520 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.713 Fit side-chains REVERT: B 60 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8002 (ttm) REVERT: B 476 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 627 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6586 (tmm) outliers start: 29 outliers final: 22 residues processed: 114 average time/residue: 0.1174 time to fit residues: 20.2957 Evaluate side-chains 118 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6295 Z= 0.161 Angle : 0.498 8.340 8615 Z= 0.240 Chirality : 0.038 0.205 1033 Planarity : 0.003 0.053 1094 Dihedral : 6.852 142.680 946 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 3.79 % Allowed : 23.15 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.30), residues: 855 helix: 2.84 (0.24), residues: 469 sheet: -1.52 (0.63), residues: 52 loop : -1.15 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 119 HIS 0.002 0.000 HIS B 495 PHE 0.013 0.001 PHE B 432 TYR 0.013 0.001 TYR B 520 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.748 Fit side-chains REVERT: B 60 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: B 627 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6528 (tmm) REVERT: A 361 LEU cc_start: 0.8964 (mm) cc_final: 0.8748 (mt) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.1190 time to fit residues: 19.6220 Evaluate side-chains 111 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.0050 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6295 Z= 0.138 Angle : 0.497 8.431 8615 Z= 0.237 Chirality : 0.038 0.212 1033 Planarity : 0.003 0.051 1094 Dihedral : 6.458 137.223 946 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.91 % Rotamer: Outliers : 4.39 % Allowed : 23.75 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.83 (0.30), residues: 855 helix: 2.98 (0.24), residues: 469 sheet: -1.24 (0.63), residues: 52 loop : -1.06 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 119 HIS 0.002 0.000 HIS B 495 PHE 0.011 0.001 PHE B 383 TYR 0.020 0.001 TYR B 519 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.713 Fit side-chains REVERT: B 60 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7737 (mtp) REVERT: B 627 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6499 (tmm) REVERT: A 361 LEU cc_start: 0.8957 (mm) cc_final: 0.8753 (mt) outliers start: 22 outliers final: 17 residues processed: 114 average time/residue: 0.1240 time to fit residues: 21.0766 Evaluate side-chains 115 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6295 Z= 0.306 Angle : 0.560 10.208 8615 Z= 0.272 Chirality : 0.041 0.224 1033 Planarity : 0.003 0.051 1094 Dihedral : 6.518 133.526 946 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 4.39 % Allowed : 23.75 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.64 (0.30), residues: 855 helix: 2.84 (0.24), residues: 468 sheet: -1.39 (0.62), residues: 52 loop : -1.14 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 523 HIS 0.003 0.001 HIS B 495 PHE 0.016 0.001 PHE B 432 TYR 0.023 0.002 TYR B 519 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.732 Fit side-chains REVERT: B 60 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7922 (mtp) outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.1434 time to fit residues: 22.7360 Evaluate side-chains 112 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 49 optimal weight: 0.0170 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6295 Z= 0.165 Angle : 0.526 12.279 8615 Z= 0.250 Chirality : 0.039 0.222 1033 Planarity : 0.003 0.050 1094 Dihedral : 6.307 131.514 946 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 3.59 % Allowed : 24.95 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.77 (0.30), residues: 855 helix: 2.94 (0.24), residues: 469 sheet: -1.26 (0.63), residues: 52 loop : -1.10 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 119 HIS 0.002 0.000 HIS B 495 PHE 0.012 0.001 PHE B 432 TYR 0.022 0.001 TYR B 519 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.761 Fit side-chains REVERT: B 60 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7843 (mtp) REVERT: B 272 LEU cc_start: 0.8750 (mt) cc_final: 0.8544 (mt) REVERT: B 627 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6472 (tmm) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.1173 time to fit residues: 19.4427 Evaluate side-chains 115 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8433 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 6295 Z= 0.404 Angle : 0.621 15.338 8615 Z= 0.303 Chirality : 0.042 0.224 1033 Planarity : 0.004 0.050 1094 Dihedral : 6.516 130.022 946 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 3.59 % Allowed : 24.35 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.30), residues: 855 helix: 2.67 (0.24), residues: 468 sheet: -1.55 (0.62), residues: 52 loop : -1.21 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 523 HIS 0.004 0.001 HIS B 495 PHE 0.018 0.002 PHE B 432 TYR 0.028 0.002 TYR B 519 ARG 0.004 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.945 Fit side-chains REVERT: B 60 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: B 627 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6514 (tmm) outliers start: 18 outliers final: 16 residues processed: 108 average time/residue: 0.1196 time to fit residues: 19.7533 Evaluate side-chains 114 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 386 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086788 restraints weight = 11482.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089729 restraints weight = 6202.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091760 restraints weight = 4114.432| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6295 Z= 0.306 Angle : 0.591 16.009 8615 Z= 0.284 Chirality : 0.041 0.214 1033 Planarity : 0.003 0.050 1094 Dihedral : 6.489 128.075 946 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 3.59 % Allowed : 25.15 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.43 (0.30), residues: 855 helix: 2.68 (0.24), residues: 467 sheet: -1.59 (0.62), residues: 52 loop : -1.23 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 532 HIS 0.003 0.001 HIS B 495 PHE 0.018 0.001 PHE B 432 TYR 0.026 0.002 TYR B 519 ARG 0.003 0.000 ARG A 294 =============================================================================== Job complete usr+sys time: 1358.06 seconds wall clock time: 25 minutes 17.31 seconds (1517.31 seconds total)