Starting phenix.real_space_refine on Tue Sep 24 12:03:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/09_2024/6hn5_0247.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/09_2024/6hn5_0247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/09_2024/6hn5_0247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/09_2024/6hn5_0247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/09_2024/6hn5_0247.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/09_2024/6hn5_0247.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4980 2.51 5 N 1338 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7869 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "E" Number of atoms: 4715 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 584, 4708 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 28, 'TRANS': 555} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 584, 4708 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 28, 'TRANS': 555} Chain breaks: 2 bond proxies already assigned to first conformer: 4812 Chain: "F" Number of atoms: 2625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2625 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR B 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 26 " occ=0.50 Time building chain proxies: 6.82, per 1000 atoms: 0.87 Number of scatterers: 7869 At special positions: 0 Unit cell: (105.04, 108.16, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1492 8.00 N 1338 7.00 C 4980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.02 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.02 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.02 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.04 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.02 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.02 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 524 " - pdb=" SG CYS F 524 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 682 " - pdb=" SG CYS F 685 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN E 111 " " NAG E1001 " - " ASN E 25 " " NAG E1004 " - " ASN E 215 " " NAG E1005 " - " ASN E 255 " " NAG E1006 " - " ASN E 397 " " NAG E1007 " - " ASN E 418 " " NAG E1008 " - " ASN E 16 " " NAG F1001 " - " ASN F 337 " " NAG F1002 " - " ASN F 397 " " NAG F1003 " - " ASN F 514 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 14 sheets defined 15.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.567A pdb=" N CYS A 7 " --> pdb=" O VAL A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 18 Processing helix chain 'B' and resid 9 through 16 Processing helix chain 'E' and resid 17 through 24 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.592A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 350 through 358 Processing helix chain 'E' and resid 378 through 382 removed outlier: 4.380A pdb=" N PHE E 381 " --> pdb=" O SER E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.668A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 328 Processing helix chain 'F' and resid 349 through 359 removed outlier: 3.709A pdb=" N GLU F 353 " --> pdb=" O ASN F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 removed outlier: 3.565A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 688 through 714 removed outlier: 3.615A pdb=" N PHE F 714 " --> pdb=" O HIS F 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8 removed outlier: 7.440A pdb=" N GLU E 6 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE E 29 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS E 8 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.462A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU E 36 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE E 13 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET E 38 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE E 64 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 35 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL E 66 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU E 37 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG E 118 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL E 94 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU E 120 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE E 96 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN E 122 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 146 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 121 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN E 148 " --> pdb=" O LYS E 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 212 through 216 removed outlier: 3.556A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 232 Processing sheet with id=AA5, first strand: chain 'E' and resid 252 through 254 removed outlier: 6.739A pdb=" N HIS E 247 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321 removed outlier: 6.232A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU E 368 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU E 403 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE E 370 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR E 398 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE E 427 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE E 400 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N HIS E 429 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 402 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 475 through 479 removed outlier: 6.454A pdb=" N ARG E 488 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE E 478 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 486 " --> pdb=" O ILE E 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 530 through 534 Processing sheet with id=AB2, first strand: chain 'F' and resid 311 through 313 Processing sheet with id=AB3, first strand: chain 'F' and resid 320 through 321 removed outlier: 3.658A pdb=" N ARG F 371 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS F 429 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 428 " --> pdb=" O ASP F 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 475 through 480 removed outlier: 6.603A pdb=" N ARG F 488 " --> pdb=" O SER F 476 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE F 478 " --> pdb=" O LEU F 486 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 486 " --> pdb=" O ILE F 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.658A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 429 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: 2.39 Time building geometry restraints manager: 2.26 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: 2459 1.33 - 1.46: 2003 1.46 - 1.59: 3518 1.59 - 1.71: 0 1.71 - 1.84: 71 Bond restraints: 8051 Sorted by residual: bond pdb=" CG1 ILE E 370 " pdb=" CD1 ILE E 370 " ideal model delta sigma weight residual 1.513 1.384 0.129 3.90e-02 6.57e+02 1.09e+01 bond pdb=" CG LEU E 36 " pdb=" CD1 LEU E 36 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CG LEU E 137 " pdb=" CD1 LEU E 137 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" C PRO F 494 " pdb=" N PRO F 495 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.26e+00 bond pdb=" CG LEU E 36 " pdb=" CD2 LEU E 36 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.26e+00 ... (remaining 8046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 10303 2.43 - 4.85: 514 4.85 - 7.28: 71 7.28 - 9.70: 10 9.70 - 12.13: 6 Bond angle restraints: 10904 Sorted by residual: angle pdb=" CA THR E 578 " pdb=" CB THR E 578 " pdb=" CG2 THR E 578 " ideal model delta sigma weight residual 110.50 117.90 -7.40 1.70e+00 3.46e-01 1.89e+01 angle pdb=" C TRP E 251 " pdb=" N ARG E 252 " pdb=" CA ARG E 252 " ideal model delta sigma weight residual 122.29 115.75 6.54 1.65e+00 3.67e-01 1.57e+01 angle pdb=" C ILE E 35 " pdb=" N LEU E 36 " pdb=" CA LEU E 36 " ideal model delta sigma weight residual 121.62 114.38 7.24 1.83e+00 2.99e-01 1.56e+01 angle pdb=" C ARG E 577 " pdb=" N THR E 578 " pdb=" CA THR E 578 " ideal model delta sigma weight residual 122.78 128.67 -5.89 1.52e+00 4.33e-01 1.50e+01 angle pdb=" N GLU B 21 " pdb=" CA GLU B 21 " pdb=" C GLU B 21 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 ... (remaining 10899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 4691 15.41 - 30.82: 226 30.82 - 46.22: 64 46.22 - 61.63: 29 61.63 - 77.04: 4 Dihedral angle restraints: 5014 sinusoidal: 2229 harmonic: 2785 Sorted by residual: dihedral pdb=" CA PRO E 243 " pdb=" C PRO E 243 " pdb=" N PRO E 244 " pdb=" CA PRO E 244 " ideal model delta harmonic sigma weight residual 180.00 130.18 49.82 0 5.00e+00 4.00e-02 9.93e+01 dihedral pdb=" CB CYS E 524 " pdb=" SG CYS E 524 " pdb=" SG CYS F 524 " pdb=" CB CYS F 524 " ideal model delta sinusoidal sigma weight residual 93.00 170.04 -77.04 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 155 " pdb=" CB CYS E 155 " ideal model delta sinusoidal sigma weight residual 93.00 36.84 56.16 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 5011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1095 0.113 - 0.225: 113 0.225 - 0.338: 3 0.338 - 0.450: 2 0.450 - 0.563: 1 Chirality restraints: 1214 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN E 111 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" C2 NAG E1007 " pdb=" C1 NAG E1007 " pdb=" C3 NAG E1007 " pdb=" N2 NAG E1007 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C2 NAG F1002 " pdb=" C1 NAG F1002 " pdb=" C3 NAG F1002 " pdb=" N2 NAG F1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1211 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 370 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ILE F 370 " 0.081 2.00e-02 2.50e+03 pdb=" O ILE F 370 " -0.031 2.00e-02 2.50e+03 pdb=" N ARG F 371 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 243 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO E 244 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 242 " -0.064 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO E 243 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.053 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2130 2.80 - 3.33: 6748 3.33 - 3.85: 13004 3.85 - 4.38: 15070 4.38 - 4.90: 25846 Nonbonded interactions: 62798 Sorted by model distance: nonbonded pdb=" O MET F 442 " pdb=" OG SER F 446 " model vdw 2.281 3.040 nonbonded pdb=" NH2 ARG E 65 " pdb=" OE2 GLU E 97 " model vdw 2.293 3.120 nonbonded pdb=" OG SER F 399 " pdb=" O GLN F 423 " model vdw 2.336 3.040 nonbonded pdb=" OG SER F 378 " pdb=" OD1 ASP F 522 " model vdw 2.336 3.040 nonbonded pdb=" O ILE E 131 " pdb=" NE2 GLN E 189 " model vdw 2.354 3.120 ... (remaining 62793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.012 0.129 8051 Z= 0.792 Angle : 1.200 12.131 10904 Z= 0.620 Chirality : 0.071 0.563 1214 Planarity : 0.008 0.101 1392 Dihedral : 10.560 74.824 3151 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 0.12 % Allowed : 2.78 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -3.94 (0.22), residues: 940 helix: -3.18 (0.29), residues: 143 sheet: -1.88 (0.40), residues: 147 loop : -2.85 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP F 529 HIS 0.023 0.004 HIS E 264 PHE 0.042 0.006 PHE F 701 TYR 0.035 0.004 TYR E 277 ARG 0.017 0.002 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 460 LYS cc_start: 0.7294 (mtpt) cc_final: 0.6543 (pttt) REVERT: E 509 GLU cc_start: 0.8125 (tt0) cc_final: 0.7750 (tt0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2789 time to fit residues: 48.5894 Evaluate side-chains 71 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN E 187 HIS E 247 HIS E 295 ASN E 313 HIS E 405 ASN E 561 GLN F 561 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8051 Z= 0.269 Angle : 0.747 16.887 10904 Z= 0.375 Chirality : 0.050 0.331 1214 Planarity : 0.006 0.093 1392 Dihedral : 9.382 59.122 1276 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.27 % Allowed : 7.87 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -3.11 (0.24), residues: 940 helix: -1.79 (0.40), residues: 130 sheet: -1.48 (0.43), residues: 140 loop : -2.43 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 414 HIS 0.009 0.001 HIS E 264 PHE 0.029 0.002 PHE E 258 TYR 0.015 0.002 TYR F 401 ARG 0.007 0.001 ARG E 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7879 (m-30) cc_final: 0.7678 (m-30) REVERT: E 78 ASN cc_start: 0.8207 (m-40) cc_final: 0.7949 (m-40) REVERT: E 460 LYS cc_start: 0.7284 (mtpt) cc_final: 0.6557 (pttt) REVERT: E 509 GLU cc_start: 0.8219 (tt0) cc_final: 0.7654 (tt0) REVERT: E 557 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8101 (ptpt) REVERT: F 357 ASN cc_start: 0.8829 (m-40) cc_final: 0.8585 (m-40) REVERT: F 438 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7958 (mm-30) REVERT: F 504 MET cc_start: 0.7890 (mtt) cc_final: 0.7636 (mtp) REVERT: F 522 ASP cc_start: 0.6097 (m-30) cc_final: 0.5644 (t0) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.1976 time to fit residues: 27.2535 Evaluate side-chains 68 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 337 ASN E 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8051 Z= 0.291 Angle : 0.764 20.618 10904 Z= 0.373 Chirality : 0.051 0.524 1214 Planarity : 0.005 0.091 1392 Dihedral : 8.811 58.413 1276 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.27 % Allowed : 9.14 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.88 (0.25), residues: 940 helix: -1.43 (0.43), residues: 129 sheet: -1.26 (0.43), residues: 142 loop : -2.33 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 414 HIS 0.016 0.001 HIS E 264 PHE 0.037 0.002 PHE E 258 TYR 0.029 0.002 TYR B 16 ARG 0.007 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7908 (m-30) cc_final: 0.7664 (m-30) REVERT: E 78 ASN cc_start: 0.8287 (m-40) cc_final: 0.7993 (m-40) REVERT: E 337 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8220 (t0) REVERT: E 460 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6489 (pttt) REVERT: E 509 GLU cc_start: 0.8220 (tt0) cc_final: 0.7972 (tt0) REVERT: E 557 LYS cc_start: 0.8766 (ptpt) cc_final: 0.8332 (ptpp) REVERT: F 423 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7807 (pm20) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.2059 time to fit residues: 22.9417 Evaluate side-chains 72 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 524 CYS Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 509 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 0.0670 chunk 90 optimal weight: 0.0370 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 GLN E 337 ASN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8051 Z= 0.197 Angle : 0.700 16.991 10904 Z= 0.339 Chirality : 0.050 0.542 1214 Planarity : 0.005 0.092 1392 Dihedral : 8.401 59.006 1276 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.50 % Allowed : 9.49 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.72 (0.25), residues: 940 helix: -1.25 (0.43), residues: 131 sheet: -1.18 (0.45), residues: 133 loop : -2.21 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 412 HIS 0.007 0.001 HIS E 264 PHE 0.031 0.002 PHE E 258 TYR 0.023 0.001 TYR B 16 ARG 0.005 0.001 ARG E 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7676 (m-30) cc_final: 0.7456 (m-30) REVERT: E 78 ASN cc_start: 0.8258 (m-40) cc_final: 0.8010 (m-40) REVERT: E 211 GLU cc_start: 0.7559 (tt0) cc_final: 0.6942 (tm-30) REVERT: E 460 LYS cc_start: 0.7163 (mtpt) cc_final: 0.6459 (pttt) REVERT: F 423 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: F 582 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8206 (tmtt) outliers start: 12 outliers final: 6 residues processed: 79 average time/residue: 0.2056 time to fit residues: 22.5969 Evaluate side-chains 74 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 524 CYS Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 576 ARG Chi-restraints excluded: chain F residue 582 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 0.0370 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8051 Z= 0.309 Angle : 0.726 17.896 10904 Z= 0.354 Chirality : 0.051 0.554 1214 Planarity : 0.005 0.089 1392 Dihedral : 8.153 57.766 1276 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.43 % Allowed : 9.03 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.67 (0.25), residues: 940 helix: -1.10 (0.44), residues: 131 sheet: -1.19 (0.43), residues: 138 loop : -2.20 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 412 HIS 0.007 0.001 HIS E 264 PHE 0.027 0.002 PHE E 258 TYR 0.034 0.002 TYR B 16 ARG 0.006 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7856 (m-30) cc_final: 0.7579 (m-30) REVERT: E 78 ASN cc_start: 0.8362 (m-40) cc_final: 0.8106 (m-40) REVERT: E 239 GLU cc_start: 0.4671 (pm20) cc_final: 0.4371 (pm20) REVERT: E 460 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6420 (pttt) REVERT: E 509 GLU cc_start: 0.8254 (tt0) cc_final: 0.7720 (tt0) REVERT: E 557 LYS cc_start: 0.8757 (ptpt) cc_final: 0.8294 (pttm) REVERT: F 411 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8444 (tt) REVERT: F 423 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: F 582 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8268 (tmtt) outliers start: 20 outliers final: 10 residues processed: 83 average time/residue: 0.2270 time to fit residues: 25.8173 Evaluate side-chains 74 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 524 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 576 ARG Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 75 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 HIS E 337 ASN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8051 Z= 0.193 Angle : 0.667 15.935 10904 Z= 0.326 Chirality : 0.049 0.569 1214 Planarity : 0.005 0.091 1392 Dihedral : 7.786 56.081 1276 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.74 % Allowed : 9.72 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.54 (0.25), residues: 940 helix: -0.89 (0.45), residues: 132 sheet: -1.03 (0.44), residues: 133 loop : -2.15 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 412 HIS 0.007 0.001 HIS E 264 PHE 0.027 0.002 PHE E 258 TYR 0.021 0.001 TYR B 16 ARG 0.007 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7874 (tp30) cc_final: 0.7633 (tp30) REVERT: B 22 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6810 (ttp-110) REVERT: E 59 ASP cc_start: 0.7665 (m-30) cc_final: 0.7375 (m-30) REVERT: E 78 ASN cc_start: 0.8323 (m-40) cc_final: 0.8069 (m-40) REVERT: E 258 PHE cc_start: 0.8681 (t80) cc_final: 0.8269 (t80) REVERT: E 460 LYS cc_start: 0.7044 (mtpt) cc_final: 0.6338 (pttt) REVERT: E 509 GLU cc_start: 0.8275 (tt0) cc_final: 0.7927 (tt0) REVERT: E 557 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8272 (ptpt) REVERT: F 423 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: F 582 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8153 (tmtt) outliers start: 14 outliers final: 7 residues processed: 77 average time/residue: 0.2037 time to fit residues: 21.9093 Evaluate side-chains 70 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 524 CYS Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.0010 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8051 Z= 0.198 Angle : 0.660 15.373 10904 Z= 0.323 Chirality : 0.050 0.577 1214 Planarity : 0.005 0.092 1392 Dihedral : 7.549 55.953 1276 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.85 % Allowed : 10.53 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.40 (0.25), residues: 940 helix: -0.80 (0.45), residues: 132 sheet: -0.75 (0.46), residues: 123 loop : -2.08 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 412 HIS 0.007 0.001 HIS E 264 PHE 0.024 0.002 PHE E 258 TYR 0.020 0.001 TYR B 16 ARG 0.005 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7859 (tp30) cc_final: 0.7573 (tp30) REVERT: E 59 ASP cc_start: 0.7694 (m-30) cc_final: 0.7216 (m-30) REVERT: E 78 ASN cc_start: 0.8342 (m-40) cc_final: 0.8077 (m-40) REVERT: E 258 PHE cc_start: 0.8683 (t80) cc_final: 0.8293 (t80) REVERT: E 460 LYS cc_start: 0.6999 (mtpt) cc_final: 0.6271 (pttt) REVERT: E 509 GLU cc_start: 0.8264 (tt0) cc_final: 0.7932 (tt0) REVERT: E 557 LYS cc_start: 0.8753 (ptpt) cc_final: 0.8319 (ptpt) REVERT: F 423 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: F 582 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8140 (tmtt) REVERT: F 693 LEU cc_start: 0.8656 (tp) cc_final: 0.8406 (mm) outliers start: 15 outliers final: 8 residues processed: 80 average time/residue: 0.1979 time to fit residues: 22.2104 Evaluate side-chains 70 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 524 CYS Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8051 Z= 0.193 Angle : 0.655 14.433 10904 Z= 0.324 Chirality : 0.049 0.583 1214 Planarity : 0.005 0.091 1392 Dihedral : 7.367 56.117 1276 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.62 % Allowed : 10.76 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.34 (0.25), residues: 940 helix: -0.71 (0.46), residues: 132 sheet: -0.67 (0.46), residues: 123 loop : -2.05 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 412 HIS 0.006 0.001 HIS E 264 PHE 0.024 0.002 PHE E 258 TYR 0.029 0.001 TYR B 16 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7574 (m-30) cc_final: 0.7288 (m-30) REVERT: E 78 ASN cc_start: 0.8344 (m-40) cc_final: 0.8079 (m-40) REVERT: E 258 PHE cc_start: 0.8655 (t80) cc_final: 0.8275 (t80) REVERT: E 460 LYS cc_start: 0.7002 (mtpt) cc_final: 0.6257 (pttt) REVERT: E 504 MET cc_start: 0.8426 (mtm) cc_final: 0.8133 (mtm) REVERT: E 509 GLU cc_start: 0.8265 (tt0) cc_final: 0.7927 (tt0) REVERT: E 557 LYS cc_start: 0.8746 (ptpt) cc_final: 0.8319 (ptpt) REVERT: F 423 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: F 582 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8041 (tmtt) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.1811 time to fit residues: 18.5723 Evaluate side-chains 69 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 524 CYS Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8051 Z= 0.272 Angle : 0.691 15.377 10904 Z= 0.341 Chirality : 0.051 0.585 1214 Planarity : 0.005 0.091 1392 Dihedral : 7.365 56.071 1276 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.74 % Allowed : 11.00 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.40 (0.26), residues: 940 helix: -0.91 (0.44), residues: 135 sheet: -0.87 (0.43), residues: 137 loop : -2.04 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 412 HIS 0.006 0.001 HIS E 264 PHE 0.022 0.002 PHE E 258 TYR 0.029 0.002 TYR B 16 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7809 (m-30) cc_final: 0.7526 (m-30) REVERT: E 78 ASN cc_start: 0.8411 (m-40) cc_final: 0.8133 (m-40) REVERT: E 110 MET cc_start: 0.7625 (mmm) cc_final: 0.7423 (mmm) REVERT: E 258 PHE cc_start: 0.8663 (t80) cc_final: 0.8311 (t80) REVERT: E 460 LYS cc_start: 0.7035 (mtpt) cc_final: 0.6284 (pttt) REVERT: E 509 GLU cc_start: 0.8260 (tt0) cc_final: 0.8023 (tt0) REVERT: E 556 LEU cc_start: 0.8569 (mp) cc_final: 0.8271 (mp) REVERT: E 557 LYS cc_start: 0.8674 (ptpt) cc_final: 0.8306 (ptpp) REVERT: F 423 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: F 582 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8108 (tmtt) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.2060 time to fit residues: 20.0489 Evaluate side-chains 64 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 313 HIS E 337 ASN F 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8051 Z= 0.243 Angle : 0.689 15.161 10904 Z= 0.337 Chirality : 0.050 0.589 1214 Planarity : 0.005 0.091 1392 Dihedral : 7.318 56.122 1276 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.39 % Allowed : 11.69 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.44 (0.25), residues: 940 helix: -0.90 (0.44), residues: 141 sheet: -0.84 (0.44), residues: 137 loop : -2.10 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 412 HIS 0.006 0.001 HIS E 264 PHE 0.022 0.002 PHE E 258 TYR 0.029 0.002 TYR B 16 ARG 0.007 0.001 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 ASP cc_start: 0.7768 (m-30) cc_final: 0.7471 (m-30) REVERT: E 78 ASN cc_start: 0.8388 (m-40) cc_final: 0.8108 (m-40) REVERT: E 258 PHE cc_start: 0.8656 (t80) cc_final: 0.8340 (t80) REVERT: E 460 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6264 (pttt) REVERT: E 509 GLU cc_start: 0.8242 (tt0) cc_final: 0.7896 (tt0) REVERT: E 556 LEU cc_start: 0.8543 (mp) cc_final: 0.8252 (mp) REVERT: E 557 LYS cc_start: 0.8665 (ptpt) cc_final: 0.8259 (ptpt) REVERT: F 423 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: F 582 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8101 (tmtt) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.1856 time to fit residues: 18.4319 Evaluate side-chains 66 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 685 CYS Chi-restraints excluded: chain F residue 688 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.142870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.113762 restraints weight = 31872.445| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 6.00 r_work: 0.3667 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8051 Z= 0.219 Angle : 0.683 14.973 10904 Z= 0.332 Chirality : 0.050 0.590 1214 Planarity : 0.005 0.092 1392 Dihedral : 7.258 56.159 1276 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.62 % Allowed : 12.04 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.38 (0.26), residues: 940 helix: -0.84 (0.45), residues: 135 sheet: -0.83 (0.44), residues: 132 loop : -2.04 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 412 HIS 0.006 0.001 HIS E 264 PHE 0.022 0.002 PHE E 258 TYR 0.028 0.002 TYR B 16 ARG 0.006 0.001 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.39 seconds wall clock time: 36 minutes 34.05 seconds (2194.05 seconds total)