Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 16:13:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/04_2023/6hn5_0247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/04_2023/6hn5_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_0247/04_2023/6hn5_0247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/04_2023/6hn5_0247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/04_2023/6hn5_0247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn5_0247/04_2023/6hn5_0247.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 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 Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F ARG 539": "NH1" <-> "NH2" Residue "F ARG 717": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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: 6.69, per 1000 atoms: 0.85 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-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: 2.98 Conformation dependent library (CDL) restraints added in 1.7 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: 0.50 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: 2.19 Time building geometry restraints manager: 3.26 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: 96.59 - 104.10: 111 104.10 - 111.61: 3484 111.61 - 119.12: 3073 119.12 - 126.63: 4103 126.63 - 134.14: 133 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: 4496 15.41 - 30.82: 219 30.82 - 46.22: 54 46.22 - 61.63: 10 61.63 - 77.04: 4 Dihedral angle restraints: 4783 sinusoidal: 1998 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 4780 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 2.440 nonbonded pdb=" NH2 ARG E 65 " pdb=" OE2 GLU E 97 " model vdw 2.293 2.520 nonbonded pdb=" OG SER F 399 " pdb=" O GLN F 423 " model vdw 2.336 2.440 nonbonded pdb=" OG SER F 378 " pdb=" OD1 ASP F 522 " model vdw 2.336 2.440 nonbonded pdb=" O ILE E 131 " pdb=" NE2 GLN E 189 " model vdw 2.354 2.520 ... (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 ========== 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: 1.170 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: 5.370 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.000 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- 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 : 9.753 74.824 2920 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 % 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 *********************** 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 : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2753 time to fit residues: 48.0512 Evaluate side-chains 71 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3029 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7512 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 8051 Z= 0.273 Angle : 0.740 16.726 10904 Z= 0.369 Chirality : 0.050 0.392 1214 Planarity : 0.006 0.093 1392 Dihedral : 6.388 41.972 1045 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 1.39 % 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: -3.21 (0.24), residues: 940 helix: -1.94 (0.38), residues: 136 sheet: -1.44 (0.42), residues: 142 loop : -2.51 (0.21), residues: 662 *********************** 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 102 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.2285 time to fit residues: 31.7702 Evaluate side-chains 67 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.029 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0835 time to fit residues: 2.2464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN F 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 8051 Z= 0.389 Angle : 0.807 24.181 10904 Z= 0.389 Chirality : 0.051 0.347 1214 Planarity : 0.006 0.091 1392 Dihedral : 6.247 41.218 1045 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 0.93 % 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: -3.07 (0.24), residues: 940 helix: -1.69 (0.40), residues: 136 sheet: -1.34 (0.41), residues: 142 loop : -2.45 (0.21), residues: 662 *********************** 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 71 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.955 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.2212 time to fit residues: 21.1451 Evaluate side-chains 60 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2261 time to fit residues: 2.1610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 8051 Z= 0.244 Angle : 0.707 16.551 10904 Z= 0.343 Chirality : 0.048 0.273 1214 Planarity : 0.005 0.091 1392 Dihedral : 5.912 39.452 1045 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 0.35 % 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: -2.85 (0.25), residues: 940 helix: -1.36 (0.42), residues: 136 sheet: -1.06 (0.43), residues: 142 loop : -2.37 (0.22), residues: 662 *********************** 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 63 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.117 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.2101 time to fit residues: 18.5077 Evaluate side-chains 54 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0770 time to fit residues: 1.4585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8051 Z= 0.202 Angle : 0.663 15.529 10904 Z= 0.321 Chirality : 0.047 0.268 1214 Planarity : 0.005 0.092 1392 Dihedral : 5.573 37.378 1045 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer Outliers : 0.69 % 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: -2.64 (0.25), residues: 940 helix: -1.07 (0.44), residues: 137 sheet: -0.93 (0.43), residues: 143 loop : -2.26 (0.22), residues: 660 *********************** 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 62 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.1824 time to fit residues: 16.6410 Evaluate side-chains 56 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0832 time to fit residues: 1.6789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 0.0020 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 8051 Z= 0.261 Angle : 0.692 16.015 10904 Z= 0.333 Chirality : 0.048 0.272 1214 Planarity : 0.005 0.092 1392 Dihedral : 5.567 37.405 1045 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 0.58 % 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: -2.59 (0.25), residues: 940 helix: -0.93 (0.44), residues: 138 sheet: -0.92 (0.42), residues: 143 loop : -2.25 (0.22), residues: 659 *********************** 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 62 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.1936 time to fit residues: 16.8154 Evaluate side-chains 55 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0860 time to fit residues: 1.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 HIS ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN F 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8051 Z= 0.166 Angle : 0.639 14.302 10904 Z= 0.310 Chirality : 0.046 0.265 1214 Planarity : 0.004 0.094 1392 Dihedral : 5.370 36.869 1045 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 0.81 % 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: -2.31 (0.26), residues: 940 helix: -0.39 (0.47), residues: 131 sheet: -0.79 (0.45), residues: 133 loop : -2.08 (0.22), residues: 676 *********************** 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 66 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.912 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 0.1854 time to fit residues: 18.0089 Evaluate side-chains 58 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0804 time to fit residues: 1.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.0070 chunk 86 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8051 Z= 0.161 Angle : 0.631 12.745 10904 Z= 0.308 Chirality : 0.046 0.264 1214 Planarity : 0.004 0.093 1392 Dihedral : 5.165 35.729 1045 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 0.35 % 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: -2.20 (0.26), residues: 940 helix: -0.20 (0.48), residues: 133 sheet: -0.63 (0.45), residues: 133 loop : -2.05 (0.22), residues: 674 *********************** 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 69 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.974 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.1717 time to fit residues: 17.4780 Evaluate side-chains 58 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0730 time to fit residues: 1.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 521 GLN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3566 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= 0.171 Angle : 0.642 13.002 10904 Z= 0.309 Chirality : 0.046 0.265 1214 Planarity : 0.004 0.095 1392 Dihedral : 5.118 35.953 1045 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.23 % 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: -2.11 (0.26), residues: 940 helix: -0.18 (0.48), residues: 132 sheet: -0.49 (0.46), residues: 133 loop : -2.00 (0.22), residues: 675 *********************** 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 57 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.960 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.1869 time to fit residues: 16.3279 Evaluate side-chains 54 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0778 time to fit residues: 1.4602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.3980 chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.0770 chunk 45 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 521 GLN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8051 Z= 0.149 Angle : 0.629 12.690 10904 Z= 0.305 Chirality : 0.046 0.262 1214 Planarity : 0.004 0.095 1392 Dihedral : 4.971 35.599 1045 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.12 % 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: -2.06 (0.26), residues: 940 helix: -0.07 (0.48), residues: 133 sheet: -0.38 (0.46), residues: 133 loop : -2.00 (0.22), residues: 674 ********************** 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 58 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.947 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1867 time to fit residues: 16.2509 Evaluate side-chains 54 residues out of total 860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.145881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.116665 restraints weight = 32002.337| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 5.97 r_work: 0.3713 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8051 Z= 0.179 Angle : 0.643 13.121 10904 Z= 0.310 Chirality : 0.046 0.264 1214 Planarity : 0.004 0.095 1392 Dihedral : 4.979 36.188 1045 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.35 % 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: -2.08 (0.26), residues: 940 helix: -0.15 (0.47), residues: 133 sheet: -0.38 (0.46), residues: 133 loop : -2.01 (0.22), residues: 674 =============================================================================== Job complete usr+sys time: 1959.77 seconds wall clock time: 36 minutes 3.66 seconds (2163.66 seconds total)