Starting phenix.real_space_refine on Tue Mar 3 17:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gje_51389/03_2026/9gje_51389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gje_51389/03_2026/9gje_51389.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 { model { file = "/net/cci-nas-00/data/ceres_data/9gje_51389/03_2026/9gje_51389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gje_51389/03_2026/9gje_51389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gje_51389/03_2026/9gje_51389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gje_51389/03_2026/9gje_51389.map" } 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 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= 0.002 sd= 0.113 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 69 5.16 5 C 4691 2.51 5 N 1265 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7533 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 5113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5113 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" 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 Time building chain proxies: 1.60, per 1000 atoms: 0.21 Number of scatterers: 7533 At special positions: 0 Unit cell: (97.344, 99.008, 113.984, 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 69 16.00 O 1508 8.00 N 1265 7.00 C 4691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " distance=2.03 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG H 701 " - " ASN H 468 " " NAG H 702 " - " ASN H 198 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 268.5 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 21 sheets defined 17.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.843A pdb=" N ILE H 129 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 196 removed outlier: 4.103A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 236 removed outlier: 4.560A pdb=" N LYS H 229 " --> pdb=" O SER H 225 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER H 236 " --> pdb=" O GLN H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 273 Processing helix chain 'H' and resid 282 through 299 Processing helix chain 'H' and resid 328 through 334 Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.528A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 361 No H-bonds generated for 'chain 'H' and resid 359 through 361' Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 372 through 374 No H-bonds generated for 'chain 'H' and resid 372 through 374' Processing helix chain 'H' and resid 375 through 391 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 586 through 590 Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.741A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.603A pdb=" N PHE L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.554A pdb=" N ASN L 187 " --> pdb=" O PRO L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 Processing helix chain 'L' and resid 254 through 258 removed outlier: 3.886A pdb=" N LYS L 258 " --> pdb=" O THR L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 281 Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.583A pdb=" N THR H 82 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.583A pdb=" N THR H 82 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 257 through 262 removed outlier: 3.516A pdb=" N PHE H 258 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR H 214 " --> pdb=" O GLY H 246 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N THR H 248 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU H 216 " --> pdb=" O THR H 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR H 250 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE H 218 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N LEU H 252 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N PHE H 220 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS H 215 " --> pdb=" O ARG H 312 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 456 removed outlier: 6.954A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA8, first strand: chain 'H' and resid 511 through 515 removed outlier: 6.607A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 540 through 544 Processing sheet with id=AB1, first strand: chain 'H' and resid 569 through 572 Processing sheet with id=AB2, first strand: chain 'H' and resid 601 through 602 removed outlier: 4.020A pdb=" N LYS H 602 " --> pdb=" O GLN H 612 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN H 612 " --> pdb=" O LYS H 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 628 through 630 Processing sheet with id=AB4, first strand: chain 'H' and resid 650 through 651 Processing sheet with id=AB5, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.421A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB7, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AB8, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AB9, first strand: chain 'L' and resid 156 through 160 Processing sheet with id=AC1, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC2, first strand: chain 'L' and resid 207 through 212 Processing sheet with id=AC3, first strand: chain 'L' and resid 240 through 244 210 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1261 1.31 - 1.44: 2131 1.44 - 1.57: 4212 1.57 - 1.69: 0 1.69 - 1.82: 85 Bond restraints: 7689 Sorted by residual: bond pdb=" C ASN H 337 " pdb=" O ASN H 337 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.47e-02 4.63e+03 9.38e+00 bond pdb=" C ASN H 337 " pdb=" N ILE H 338 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.32e-02 5.74e+03 3.77e+00 bond pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 1.461 1.480 -0.019 1.41e-02 5.03e+03 1.74e+00 bond pdb=" CA ASN H 337 " pdb=" CB ASN H 337 " ideal model delta sigma weight residual 1.532 1.516 0.016 1.48e-02 4.57e+03 1.12e+00 bond pdb=" CB CYS H 456 " pdb=" SG CYS H 456 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 9.93e-01 ... (remaining 7684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 10285 1.92 - 3.84: 96 3.84 - 5.76: 19 5.76 - 7.68: 2 7.68 - 9.60: 1 Bond angle restraints: 10403 Sorted by residual: angle pdb=" CA ASN H 337 " pdb=" C ASN H 337 " pdb=" O ASN H 337 " ideal model delta sigma weight residual 122.03 117.99 4.04 1.25e+00 6.40e-01 1.04e+01 angle pdb=" C ASN H 337 " pdb=" CA ASN H 337 " pdb=" CB ASN H 337 " ideal model delta sigma weight residual 112.11 116.65 -4.54 1.46e+00 4.69e-01 9.66e+00 angle pdb=" CA ASN H 337 " pdb=" C ASN H 337 " pdb=" N ILE H 338 " ideal model delta sigma weight residual 114.98 118.88 -3.90 1.34e+00 5.57e-01 8.47e+00 angle pdb=" CA LEU H 237 " pdb=" CB LEU H 237 " pdb=" CG LEU H 237 " ideal model delta sigma weight residual 116.30 125.90 -9.60 3.50e+00 8.16e-02 7.53e+00 angle pdb=" N ARG H 146 " pdb=" CA ARG H 146 " pdb=" C ARG H 146 " ideal model delta sigma weight residual 109.81 114.53 -4.72 2.21e+00 2.05e-01 4.56e+00 ... (remaining 10398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 4151 18.09 - 36.18: 544 36.18 - 54.26: 131 54.26 - 72.35: 34 72.35 - 90.44: 21 Dihedral angle restraints: 4881 sinusoidal: 2153 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS H 477 " pdb=" SG CYS H 477 " pdb=" SG CYS H 515 " pdb=" CB CYS H 515 " ideal model delta sinusoidal sigma weight residual -86.00 -165.23 79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS H 592 " pdb=" SG CYS H 592 " pdb=" SG CYS H 630 " pdb=" CB CYS H 630 " ideal model delta sinusoidal sigma weight residual -86.00 -145.18 59.18 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS H 420 " pdb=" SG CYS H 420 " pdb=" SG CYS H 456 " pdb=" CB CYS H 456 " ideal model delta sinusoidal sigma weight residual 93.00 149.57 -56.57 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 4878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 909 0.050 - 0.100: 208 0.100 - 0.150: 40 0.150 - 0.200: 1 0.200 - 0.250: 2 Chirality restraints: 1160 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN H 337 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C1 NAG H 701 " pdb=" ND2 ASN H 468 " pdb=" C2 NAG H 701 " pdb=" O5 NAG H 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASN H 337 " pdb=" N ASN H 337 " pdb=" C ASN H 337 " pdb=" CB ASN H 337 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1157 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 337 " -0.144 2.00e-02 2.50e+03 1.39e-01 2.43e+02 pdb=" CG ASN H 337 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN H 337 " 0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN H 337 " 0.206 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO L 40 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 223 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO L 224 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 224 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 224 " -0.020 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 32 2.43 - 3.05: 4527 3.05 - 3.66: 10615 3.66 - 4.28: 16404 4.28 - 4.90: 28707 Nonbonded interactions: 60285 Sorted by model distance: nonbonded pdb=" OD1 ASP H 398 " pdb=" O6 NAG A 1 " model vdw 1.810 3.040 nonbonded pdb=" OG SER H 605 " pdb=" O3 NAG H 702 " model vdw 2.215 3.040 nonbonded pdb=" O TYR H 195 " pdb=" OG1 THR H 199 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR H 367 " pdb=" OE1 GLU H 369 " model vdw 2.251 3.040 nonbonded pdb=" O4 BMA B 3 " pdb=" O6 MAN B 6 " model vdw 2.272 3.040 ... (remaining 60280 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.005 0.217 7727 Z= 0.206 Angle : 0.602 21.987 10491 Z= 0.288 Chirality : 0.044 0.250 1160 Planarity : 0.004 0.052 1328 Dihedral : 17.474 90.436 3053 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.48 % Allowed : 19.74 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.28), residues: 915 helix: -0.33 (0.52), residues: 103 sheet: -0.09 (0.40), residues: 172 loop : -0.08 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 273 TYR 0.010 0.001 TYR H 166 PHE 0.011 0.001 PHE H 64 TRP 0.007 0.001 TRP H 435 HIS 0.003 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7689) covalent geometry : angle 0.52250 (10403) SS BOND : bond 0.00203 ( 26) SS BOND : angle 0.99100 ( 52) hydrogen bonds : bond 0.23274 ( 186) hydrogen bonds : angle 9.03873 ( 528) link_ALPHA1-2 : bond 0.00313 ( 2) link_ALPHA1-2 : angle 1.53988 ( 6) link_ALPHA1-3 : bond 0.00157 ( 1) link_ALPHA1-3 : angle 1.83409 ( 3) link_ALPHA1-6 : bond 0.00048 ( 1) link_ALPHA1-6 : angle 1.67521 ( 3) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 2.13078 ( 12) link_NAG-ASN : bond 0.10873 ( 4) link_NAG-ASN : angle 8.28822 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.261 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.1135 time to fit residues: 10.9351 Evaluate side-chains 68 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 283 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106665 restraints weight = 8539.731| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.44 r_work: 0.2958 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7727 Z= 0.124 Angle : 0.548 7.225 10491 Z= 0.278 Chirality : 0.045 0.235 1160 Planarity : 0.004 0.047 1328 Dihedral : 9.329 73.283 1266 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.93 % Allowed : 18.41 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 915 helix: -0.18 (0.53), residues: 103 sheet: -0.26 (0.38), residues: 190 loop : 0.06 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 549 TYR 0.017 0.001 TYR H 27 PHE 0.011 0.001 PHE H 64 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7689) covalent geometry : angle 0.52862 (10403) SS BOND : bond 0.00196 ( 26) SS BOND : angle 0.81621 ( 52) hydrogen bonds : bond 0.04027 ( 186) hydrogen bonds : angle 5.97685 ( 528) link_ALPHA1-2 : bond 0.00322 ( 2) link_ALPHA1-2 : angle 1.45614 ( 6) link_ALPHA1-3 : bond 0.00671 ( 1) link_ALPHA1-3 : angle 1.36684 ( 3) link_ALPHA1-6 : bond 0.00323 ( 1) link_ALPHA1-6 : angle 2.19074 ( 3) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 2.95863 ( 12) link_NAG-ASN : bond 0.00178 ( 4) link_NAG-ASN : angle 2.48473 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: H 266 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: L 237 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7620 (p0) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.1069 time to fit residues: 12.3068 Evaluate side-chains 82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain L residue 237 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 HIS H 88 ASN H 627 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101673 restraints weight = 8589.154| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.57 r_work: 0.2856 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7727 Z= 0.245 Angle : 0.607 7.182 10491 Z= 0.309 Chirality : 0.048 0.231 1160 Planarity : 0.004 0.043 1328 Dihedral : 8.542 73.082 1258 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.21 % Allowed : 17.21 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.28), residues: 915 helix: -0.31 (0.52), residues: 105 sheet: -0.14 (0.38), residues: 196 loop : -0.11 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 549 TYR 0.020 0.002 TYR H 27 PHE 0.015 0.002 PHE H 64 TRP 0.011 0.002 TRP H 66 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 7689) covalent geometry : angle 0.58674 (10403) SS BOND : bond 0.00419 ( 26) SS BOND : angle 1.19129 ( 52) hydrogen bonds : bond 0.03921 ( 186) hydrogen bonds : angle 5.74750 ( 528) link_ALPHA1-2 : bond 0.00227 ( 2) link_ALPHA1-2 : angle 1.68674 ( 6) link_ALPHA1-3 : bond 0.00383 ( 1) link_ALPHA1-3 : angle 1.69280 ( 3) link_ALPHA1-6 : bond 0.00786 ( 1) link_ALPHA1-6 : angle 2.33993 ( 3) link_BETA1-4 : bond 0.00344 ( 4) link_BETA1-4 : angle 2.95177 ( 12) link_NAG-ASN : bond 0.00323 ( 4) link_NAG-ASN : angle 2.28586 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: H 266 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: H 405 ASP cc_start: 0.9059 (t0) cc_final: 0.8578 (t0) REVERT: L 91 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8021 (t80) REVERT: L 237 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7739 (p0) outliers start: 35 outliers final: 22 residues processed: 99 average time/residue: 0.0852 time to fit residues: 11.6642 Evaluate side-chains 91 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 262 ILE Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 498 CYS Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107527 restraints weight = 8579.869| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.48 r_work: 0.2941 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7727 Z= 0.108 Angle : 0.521 7.521 10491 Z= 0.262 Chirality : 0.044 0.220 1160 Planarity : 0.003 0.042 1328 Dihedral : 7.531 65.565 1258 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.13 % Allowed : 18.29 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 915 helix: -0.32 (0.51), residues: 109 sheet: -0.07 (0.38), residues: 198 loop : -0.02 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 397 TYR 0.014 0.001 TYR H 27 PHE 0.011 0.001 PHE H 64 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7689) covalent geometry : angle 0.50368 (10403) SS BOND : bond 0.00205 ( 26) SS BOND : angle 0.77913 ( 52) hydrogen bonds : bond 0.03109 ( 186) hydrogen bonds : angle 5.25715 ( 528) link_ALPHA1-2 : bond 0.00296 ( 2) link_ALPHA1-2 : angle 1.54537 ( 6) link_ALPHA1-3 : bond 0.00801 ( 1) link_ALPHA1-3 : angle 1.32454 ( 3) link_ALPHA1-6 : bond 0.00270 ( 1) link_ALPHA1-6 : angle 2.24451 ( 3) link_BETA1-4 : bond 0.00417 ( 4) link_BETA1-4 : angle 2.70079 ( 12) link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 2.17622 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.287 Fit side-chains REVERT: H 224 ASP cc_start: 0.7649 (m-30) cc_final: 0.7199 (m-30) REVERT: H 266 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: H 405 ASP cc_start: 0.8898 (t0) cc_final: 0.8603 (t0) REVERT: L 91 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.7996 (t80) REVERT: L 237 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7745 (p0) outliers start: 26 outliers final: 18 residues processed: 93 average time/residue: 0.1021 time to fit residues: 12.7590 Evaluate side-chains 90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 249 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 69 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107182 restraints weight = 8583.731| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.43 r_work: 0.2970 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7727 Z= 0.093 Angle : 0.509 7.561 10491 Z= 0.256 Chirality : 0.044 0.214 1160 Planarity : 0.003 0.043 1328 Dihedral : 7.107 61.508 1258 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.61 % Allowed : 17.93 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 915 helix: -0.17 (0.51), residues: 109 sheet: -0.24 (0.37), residues: 200 loop : 0.06 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 128 TYR 0.014 0.001 TYR H 27 PHE 0.010 0.001 PHE H 370 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7689) covalent geometry : angle 0.49146 (10403) SS BOND : bond 0.00195 ( 26) SS BOND : angle 0.78585 ( 52) hydrogen bonds : bond 0.02879 ( 186) hydrogen bonds : angle 5.01469 ( 528) link_ALPHA1-2 : bond 0.00352 ( 2) link_ALPHA1-2 : angle 1.52772 ( 6) link_ALPHA1-3 : bond 0.00806 ( 1) link_ALPHA1-3 : angle 1.32868 ( 3) link_ALPHA1-6 : bond 0.00317 ( 1) link_ALPHA1-6 : angle 2.10042 ( 3) link_BETA1-4 : bond 0.00402 ( 4) link_BETA1-4 : angle 2.57885 ( 12) link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 2.15992 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 118 ASP cc_start: 0.8613 (t0) cc_final: 0.8360 (t0) REVERT: H 128 ARG cc_start: 0.8844 (ttm-80) cc_final: 0.8566 (ttm-80) REVERT: H 224 ASP cc_start: 0.7612 (m-30) cc_final: 0.7157 (m-30) REVERT: H 266 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: H 405 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8527 (t0) REVERT: H 455 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: H 478 MET cc_start: 0.7491 (mmt) cc_final: 0.6652 (mmp) REVERT: L 91 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7785 (t80) REVERT: L 237 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7626 (p0) outliers start: 30 outliers final: 20 residues processed: 97 average time/residue: 0.0951 time to fit residues: 12.6032 Evaluate side-chains 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 249 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106499 restraints weight = 8620.841| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.42 r_work: 0.2944 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7727 Z= 0.115 Angle : 0.505 6.334 10491 Z= 0.256 Chirality : 0.044 0.214 1160 Planarity : 0.003 0.042 1328 Dihedral : 6.836 57.770 1258 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.49 % Allowed : 18.05 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.28), residues: 915 helix: -0.10 (0.52), residues: 109 sheet: 0.05 (0.38), residues: 198 loop : -0.00 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 128 TYR 0.014 0.001 TYR H 27 PHE 0.011 0.001 PHE H 64 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS H 368 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7689) covalent geometry : angle 0.48905 (10403) SS BOND : bond 0.00196 ( 26) SS BOND : angle 0.80410 ( 52) hydrogen bonds : bond 0.02833 ( 186) hydrogen bonds : angle 4.94479 ( 528) link_ALPHA1-2 : bond 0.00288 ( 2) link_ALPHA1-2 : angle 1.54245 ( 6) link_ALPHA1-3 : bond 0.00723 ( 1) link_ALPHA1-3 : angle 1.39681 ( 3) link_ALPHA1-6 : bond 0.00247 ( 1) link_ALPHA1-6 : angle 2.08725 ( 3) link_BETA1-4 : bond 0.00400 ( 4) link_BETA1-4 : angle 2.51302 ( 12) link_NAG-ASN : bond 0.00201 ( 4) link_NAG-ASN : angle 1.84920 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: H 118 ASP cc_start: 0.8626 (t0) cc_final: 0.8360 (t0) REVERT: H 224 ASP cc_start: 0.7641 (m-30) cc_final: 0.7128 (m-30) REVERT: H 266 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: H 405 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8624 (t0) REVERT: H 455 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: H 478 MET cc_start: 0.7470 (mmt) cc_final: 0.6648 (mmm) REVERT: L 91 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.7819 (t80) REVERT: L 237 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7598 (p0) outliers start: 29 outliers final: 19 residues processed: 95 average time/residue: 0.0934 time to fit residues: 12.2617 Evaluate side-chains 91 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 455 GLU Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 249 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103442 restraints weight = 8674.036| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.49 r_work: 0.2888 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7727 Z= 0.145 Angle : 0.528 8.289 10491 Z= 0.267 Chirality : 0.045 0.223 1160 Planarity : 0.004 0.041 1328 Dihedral : 6.770 55.106 1258 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.73 % Allowed : 18.29 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.28), residues: 915 helix: -0.12 (0.52), residues: 109 sheet: 0.04 (0.38), residues: 198 loop : -0.04 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 128 TYR 0.015 0.001 TYR H 27 PHE 0.013 0.001 PHE H 64 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7689) covalent geometry : angle 0.51110 (10403) SS BOND : bond 0.00212 ( 26) SS BOND : angle 0.91822 ( 52) hydrogen bonds : bond 0.02887 ( 186) hydrogen bonds : angle 4.99052 ( 528) link_ALPHA1-2 : bond 0.00251 ( 2) link_ALPHA1-2 : angle 1.58872 ( 6) link_ALPHA1-3 : bond 0.00683 ( 1) link_ALPHA1-3 : angle 1.45635 ( 3) link_ALPHA1-6 : bond 0.00199 ( 1) link_ALPHA1-6 : angle 2.08419 ( 3) link_BETA1-4 : bond 0.00391 ( 4) link_BETA1-4 : angle 2.50467 ( 12) link_NAG-ASN : bond 0.00288 ( 4) link_NAG-ASN : angle 2.20513 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: H 224 ASP cc_start: 0.7619 (m-30) cc_final: 0.7077 (m-30) REVERT: H 242 LYS cc_start: 0.8948 (mttt) cc_final: 0.8158 (tptp) REVERT: H 266 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: H 405 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8665 (t0) REVERT: H 478 MET cc_start: 0.7453 (mmt) cc_final: 0.6630 (mmm) REVERT: L 91 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7890 (t80) REVERT: L 237 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7619 (p0) outliers start: 31 outliers final: 24 residues processed: 94 average time/residue: 0.0934 time to fit residues: 12.1123 Evaluate side-chains 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102049 restraints weight = 8626.867| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.49 r_work: 0.2847 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7727 Z= 0.181 Angle : 0.553 8.354 10491 Z= 0.282 Chirality : 0.046 0.238 1160 Planarity : 0.004 0.041 1328 Dihedral : 6.822 53.169 1258 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.73 % Allowed : 17.93 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 915 helix: -0.15 (0.52), residues: 109 sheet: -0.02 (0.38), residues: 198 loop : -0.08 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 245 TYR 0.016 0.001 TYR H 27 PHE 0.013 0.002 PHE H 64 TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7689) covalent geometry : angle 0.53602 (10403) SS BOND : bond 0.00235 ( 26) SS BOND : angle 1.07575 ( 52) hydrogen bonds : bond 0.03012 ( 186) hydrogen bonds : angle 5.12280 ( 528) link_ALPHA1-2 : bond 0.00198 ( 2) link_ALPHA1-2 : angle 1.66147 ( 6) link_ALPHA1-3 : bond 0.00626 ( 1) link_ALPHA1-3 : angle 1.52108 ( 3) link_ALPHA1-6 : bond 0.00188 ( 1) link_ALPHA1-6 : angle 2.02234 ( 3) link_BETA1-4 : bond 0.00383 ( 4) link_BETA1-4 : angle 2.55729 ( 12) link_NAG-ASN : bond 0.00210 ( 4) link_NAG-ASN : angle 2.02974 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 224 ASP cc_start: 0.7541 (m-30) cc_final: 0.7191 (m-30) REVERT: H 242 LYS cc_start: 0.8960 (mttt) cc_final: 0.8151 (tptp) REVERT: H 405 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8648 (t0) REVERT: H 478 MET cc_start: 0.7506 (mmt) cc_final: 0.6702 (mmm) REVERT: L 91 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7746 (t80) REVERT: L 237 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7626 (p0) outliers start: 31 outliers final: 24 residues processed: 90 average time/residue: 0.0929 time to fit residues: 11.5332 Evaluate side-chains 93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain H residue 405 ASP Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 58 optimal weight: 0.0040 chunk 85 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 158 HIS ** 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 = 0.3840 r_free = 0.3840 target = 0.164485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113082 restraints weight = 8468.489| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.59 r_work: 0.2968 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7727 Z= 0.088 Angle : 0.500 8.654 10491 Z= 0.253 Chirality : 0.044 0.222 1160 Planarity : 0.003 0.041 1328 Dihedral : 5.993 49.181 1258 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.13 % Allowed : 18.65 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.28), residues: 915 helix: 0.00 (0.52), residues: 109 sheet: -0.23 (0.36), residues: 222 loop : 0.01 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 128 TYR 0.013 0.001 TYR H 27 PHE 0.010 0.001 PHE H 64 TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 7689) covalent geometry : angle 0.48700 (10403) SS BOND : bond 0.00178 ( 26) SS BOND : angle 0.68252 ( 52) hydrogen bonds : bond 0.02592 ( 186) hydrogen bonds : angle 4.82325 ( 528) link_ALPHA1-2 : bond 0.00364 ( 2) link_ALPHA1-2 : angle 1.54260 ( 6) link_ALPHA1-3 : bond 0.01058 ( 1) link_ALPHA1-3 : angle 1.08208 ( 3) link_ALPHA1-6 : bond 0.00335 ( 1) link_ALPHA1-6 : angle 1.75586 ( 3) link_BETA1-4 : bond 0.00428 ( 4) link_BETA1-4 : angle 2.26838 ( 12) link_NAG-ASN : bond 0.00252 ( 4) link_NAG-ASN : angle 1.89337 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: H 118 ASP cc_start: 0.8740 (t0) cc_final: 0.8063 (t70) REVERT: H 224 ASP cc_start: 0.7660 (m-30) cc_final: 0.7358 (m-30) REVERT: H 233 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7857 (tm-30) REVERT: H 242 LYS cc_start: 0.8918 (mttt) cc_final: 0.8239 (tptp) REVERT: H 266 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: H 308 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6111 (p0) REVERT: H 478 MET cc_start: 0.7566 (mmt) cc_final: 0.6806 (mmm) REVERT: L 91 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8043 (t80) REVERT: L 237 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (p0) outliers start: 26 outliers final: 18 residues processed: 90 average time/residue: 0.1068 time to fit residues: 12.7915 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 225 SER Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 308 ASP Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.0070 chunk 57 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.102738 restraints weight = 8639.307| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.41 r_work: 0.2901 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7727 Z= 0.096 Angle : 0.504 11.113 10491 Z= 0.254 Chirality : 0.044 0.219 1160 Planarity : 0.003 0.041 1328 Dihedral : 5.762 49.254 1258 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.77 % Allowed : 18.89 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 915 helix: 0.12 (0.52), residues: 110 sheet: -0.20 (0.37), residues: 218 loop : 0.04 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 397 TYR 0.013 0.001 TYR H 27 PHE 0.010 0.001 PHE H 370 TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7689) covalent geometry : angle 0.49125 (10403) SS BOND : bond 0.00171 ( 26) SS BOND : angle 0.73288 ( 52) hydrogen bonds : bond 0.02617 ( 186) hydrogen bonds : angle 4.79646 ( 528) link_ALPHA1-2 : bond 0.00306 ( 2) link_ALPHA1-2 : angle 1.53790 ( 6) link_ALPHA1-3 : bond 0.00993 ( 1) link_ALPHA1-3 : angle 1.23568 ( 3) link_ALPHA1-6 : bond 0.00287 ( 1) link_ALPHA1-6 : angle 1.73220 ( 3) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 2.29639 ( 12) link_NAG-ASN : bond 0.00234 ( 4) link_NAG-ASN : angle 1.73200 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: H 118 ASP cc_start: 0.8724 (t0) cc_final: 0.8020 (t70) REVERT: H 224 ASP cc_start: 0.7645 (m-30) cc_final: 0.7334 (m-30) REVERT: H 233 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7838 (tm-30) REVERT: H 242 LYS cc_start: 0.8935 (mttt) cc_final: 0.8213 (tptp) REVERT: H 266 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: H 308 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6027 (p0) REVERT: H 478 MET cc_start: 0.7587 (mmt) cc_final: 0.6802 (mmm) REVERT: L 91 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8043 (t80) REVERT: L 237 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7745 (p0) outliers start: 23 outliers final: 17 residues processed: 86 average time/residue: 0.0945 time to fit residues: 11.2479 Evaluate side-chains 86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 308 ASP Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 512 SER Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 chunk 33 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 158 HIS ** 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 = 0.3870 r_free = 0.3870 target = 0.166740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117384 restraints weight = 8484.474| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.29 r_work: 0.3045 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7727 Z= 0.079 Angle : 0.488 10.520 10491 Z= 0.245 Chirality : 0.043 0.209 1160 Planarity : 0.003 0.041 1328 Dihedral : 5.097 49.276 1258 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.89 % Allowed : 19.37 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 915 helix: 0.20 (0.52), residues: 110 sheet: 0.03 (0.39), residues: 196 loop : 0.06 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 397 TYR 0.012 0.001 TYR H 27 PHE 0.008 0.001 PHE H 370 TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 7689) covalent geometry : angle 0.47837 (10403) SS BOND : bond 0.00158 ( 26) SS BOND : angle 0.54628 ( 52) hydrogen bonds : bond 0.02444 ( 186) hydrogen bonds : angle 4.59380 ( 528) link_ALPHA1-2 : bond 0.00353 ( 2) link_ALPHA1-2 : angle 1.48717 ( 6) link_ALPHA1-3 : bond 0.01175 ( 1) link_ALPHA1-3 : angle 1.01243 ( 3) link_ALPHA1-6 : bond 0.00543 ( 1) link_ALPHA1-6 : angle 1.64131 ( 3) link_BETA1-4 : bond 0.00428 ( 4) link_BETA1-4 : angle 2.10362 ( 12) link_NAG-ASN : bond 0.00279 ( 4) link_NAG-ASN : angle 1.55641 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.05 seconds wall clock time: 40 minutes 48.69 seconds (2448.69 seconds total)