Starting phenix.real_space_refine on Tue Mar 3 17:52:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gji_51393/03_2026/9gji_51393.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gji_51393/03_2026/9gji_51393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gji_51393/03_2026/9gji_51393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gji_51393/03_2026/9gji_51393.map" model { file = "/net/cci-nas-00/data/ceres_data/9gji_51393/03_2026/9gji_51393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gji_51393/03_2026/9gji_51393.cif" } resolution = 3.4 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= 0.091 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 4697 2.51 5 N 1265 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 7545 Number of models: 1 Model: "" Number of chains: 6 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 Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.20 Number of scatterers: 7545 At special positions: 0 Unit cell: (100.672, 94.016, 113.152, 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 1514 8.00 N 1265 7.00 C 4697 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=2.04 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.02 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=2.04 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: 0.84 Conformation dependent library (CDL) restraints added in 212.8 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 19 sheets defined 17.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.883A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 188 through 196 removed outlier: 3.922A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 236 through 241 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 274 Processing helix chain 'H' and resid 282 through 299 Processing helix chain 'H' and resid 329 through 334 Processing helix chain 'H' and resid 350 through 359 removed outlier: 3.929A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG H 359 " --> pdb=" O ARG H 355 " (cutoff:3.500A) 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 375 through 391 removed outlier: 3.530A pdb=" N THR H 379 " --> pdb=" O GLU H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 586 through 590 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'L' and resid 67 through 71 Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.908A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.514A pdb=" N PHE L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.699A pdb=" N ASN L 187 " --> pdb=" O PRO L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 201 removed outlier: 3.579A pdb=" N TYR L 201 " --> pdb=" O THR L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 226 Processing helix chain 'L' and resid 254 through 258 removed outlier: 3.901A pdb=" N LYS L 258 " --> pdb=" O THR L 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.510A pdb=" N THR H 82 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 131 through 134 removed outlier: 6.615A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 258 through 262 removed outlier: 6.052A pdb=" N THR H 214 " --> pdb=" O LYS H 245 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 247 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU H 249 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE H 218 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR H 314 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 5.940A 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 426 Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 456 removed outlier: 6.780A 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 512 through 515 removed outlier: 6.202A pdb=" N THR H 514 " --> pdb=" O LYS H 524 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS H 524 " --> pdb=" O THR H 514 " (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 573 Processing sheet with id=AB2, first strand: chain 'H' and resid 628 through 630 Processing sheet with id=AB3, first strand: chain 'H' and resid 650 through 651 Processing sheet with id=AB4, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB5, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AB6, first strand: chain 'L' and resid 103 through 107 Processing sheet with id=AB7, first strand: chain 'L' and resid 156 through 160 Processing sheet with id=AB8, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AB9, first strand: chain 'L' and resid 207 through 212 Processing sheet with id=AC1, first strand: chain 'L' and resid 240 through 244 201 hydrogen bonds defined for protein. 483 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: 1.17 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2417 1.34 - 1.46: 1772 1.46 - 1.58: 3427 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 7701 Sorted by residual: bond pdb=" CB LYS H 229 " pdb=" CG LYS H 229 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CA ASN H 75 " pdb=" CB ASN H 75 " ideal model delta sigma weight residual 1.534 1.561 -0.027 2.33e-02 1.84e+03 1.32e+00 bond pdb=" CB LYS H 268 " pdb=" CG LYS H 268 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CB CYS H 601 " pdb=" SG CYS H 601 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.09e+00 bond pdb=" CB CYS H 613 " pdb=" SG CYS H 613 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.07e+00 ... (remaining 7696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 10232 1.84 - 3.68: 158 3.68 - 5.52: 23 5.52 - 7.35: 5 7.35 - 9.19: 2 Bond angle restraints: 10420 Sorted by residual: angle pdb=" CA LYS H 268 " pdb=" CB LYS H 268 " pdb=" CG LYS H 268 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CB MET H 579 " pdb=" CG MET H 579 " pdb=" SD MET H 579 " ideal model delta sigma weight residual 112.70 103.51 9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CA LYS H 229 " pdb=" CB LYS H 229 " pdb=" CG LYS H 229 " ideal model delta sigma weight residual 114.10 120.08 -5.98 2.00e+00 2.50e-01 8.94e+00 angle pdb=" CB LYS H 229 " pdb=" CG LYS H 229 " pdb=" CD LYS H 229 " ideal model delta sigma weight residual 111.30 118.14 -6.84 2.30e+00 1.89e-01 8.84e+00 angle pdb=" CB LYS H 268 " pdb=" CG LYS H 268 " pdb=" CD LYS H 268 " ideal model delta sigma weight residual 111.30 117.26 -5.96 2.30e+00 1.89e-01 6.72e+00 ... (remaining 10415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4144 17.65 - 35.30: 572 35.30 - 52.95: 126 52.95 - 70.60: 40 70.60 - 88.25: 21 Dihedral angle restraints: 4903 sinusoidal: 2175 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS H 601 " pdb=" SG CYS H 601 " pdb=" SG CYS H 613 " pdb=" CB CYS H 613 " ideal model delta sinusoidal sigma weight residual 93.00 171.23 -78.23 1 1.00e+01 1.00e-02 7.64e+01 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 -160.17 74.17 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS H 395 " pdb=" SG CYS H 395 " pdb=" SG CYS H 404 " pdb=" CB CYS H 404 " ideal model delta sinusoidal sigma weight residual 93.00 165.26 -72.26 1 1.00e+01 1.00e-02 6.67e+01 ... (remaining 4900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 780 0.037 - 0.074: 276 0.074 - 0.111: 85 0.111 - 0.149: 23 0.149 - 0.186: 1 Chirality restraints: 1165 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 -2.21 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE H 338 " pdb=" N ILE H 338 " pdb=" C ILE H 338 " pdb=" CB ILE H 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1162 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.034 5.00e-02 4.00e+02 5.15e-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 GLY H 364 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO H 365 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 384 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C PHE H 384 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE H 384 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS H 385 " -0.008 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 192 2.68 - 3.24: 7079 3.24 - 3.79: 11296 3.79 - 4.35: 15682 4.35 - 4.90: 25885 Nonbonded interactions: 60134 Sorted by model distance: nonbonded pdb=" OG1 THR H 263 " pdb=" OE1 GLN H 266 " model vdw 2.128 3.040 nonbonded pdb=" O TYR H 195 " pdb=" OG1 THR H 199 " model vdw 2.223 3.040 nonbonded pdb=" O LYS L 222 " pdb=" OG1 THR L 225 " model vdw 2.233 3.040 nonbonded pdb=" O VAL H 212 " pdb=" OG1 THR H 243 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG H 394 " pdb=" O ASP H 405 " model vdw 2.276 3.120 ... (remaining 60129 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: 1.120 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.200 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.003 0.036 7739 Z= 0.115 Angle : 0.602 9.192 10508 Z= 0.316 Chirality : 0.043 0.186 1165 Planarity : 0.004 0.052 1328 Dihedral : 17.302 88.253 3075 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.36 % Allowed : 23.35 % Favored : 76.29 % 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: -0.54 (0.27), residues: 915 helix: -1.08 (0.51), residues: 102 sheet: -0.24 (0.37), residues: 188 loop : -0.21 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 273 TYR 0.018 0.001 TYR H 269 PHE 0.011 0.001 PHE H 258 TRP 0.011 0.001 TRP L 223 HIS 0.002 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7701) covalent geometry : angle 0.58599 (10420) SS BOND : bond 0.00271 ( 26) SS BOND : angle 1.64957 ( 52) hydrogen bonds : bond 0.17412 ( 193) hydrogen bonds : angle 7.52488 ( 483) link_ALPHA1-2 : bond 0.00545 ( 2) link_ALPHA1-2 : angle 1.27325 ( 6) link_ALPHA1-3 : bond 0.00266 ( 1) link_ALPHA1-3 : angle 1.65438 ( 3) link_ALPHA1-6 : bond 0.00507 ( 1) link_ALPHA1-6 : angle 1.24686 ( 3) link_BETA1-4 : bond 0.00481 ( 4) link_BETA1-4 : angle 1.90423 ( 12) link_NAG-ASN : bond 0.00108 ( 4) link_NAG-ASN : angle 1.32752 ( 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 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 0.1007 time to fit residues: 11.7180 Evaluate side-chains 77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 477 CYS 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: 4.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 HIS H 609 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.194581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152962 restraints weight = 9206.464| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 4.72 r_work: 0.3485 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7739 Z= 0.152 Angle : 0.587 7.241 10508 Z= 0.299 Chirality : 0.045 0.206 1165 Planarity : 0.004 0.051 1328 Dihedral : 9.225 65.771 1281 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.65 % Allowed : 20.70 % Favored : 76.65 % 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: -0.46 (0.28), residues: 915 helix: -0.63 (0.53), residues: 104 sheet: -0.31 (0.37), residues: 190 loop : -0.18 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 347 TYR 0.018 0.001 TYR L 242 PHE 0.016 0.001 PHE H 64 TRP 0.010 0.001 TRP H 66 HIS 0.005 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7701) covalent geometry : angle 0.56924 (10420) SS BOND : bond 0.00241 ( 26) SS BOND : angle 1.21725 ( 52) hydrogen bonds : bond 0.04005 ( 193) hydrogen bonds : angle 6.02374 ( 483) link_ALPHA1-2 : bond 0.00547 ( 2) link_ALPHA1-2 : angle 1.32210 ( 6) link_ALPHA1-3 : bond 0.00457 ( 1) link_ALPHA1-3 : angle 1.47691 ( 3) link_ALPHA1-6 : bond 0.00114 ( 1) link_ALPHA1-6 : angle 1.71827 ( 3) link_BETA1-4 : bond 0.00439 ( 4) link_BETA1-4 : angle 2.89849 ( 12) link_NAG-ASN : bond 0.00224 ( 4) link_NAG-ASN : angle 1.78151 ( 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 104 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 234 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7645 (t0) REVERT: H 490 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7030 (tt0) outliers start: 22 outliers final: 13 residues processed: 94 average time/residue: 0.0957 time to fit residues: 11.8239 Evaluate side-chains 88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 490 GLU Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 255 THR Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 119 ASN ** 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 = 0.4332 r_free = 0.4332 target = 0.194013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144077 restraints weight = 9141.009| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.60 r_work: 0.3552 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7739 Z= 0.136 Angle : 0.557 8.270 10508 Z= 0.284 Chirality : 0.044 0.203 1165 Planarity : 0.004 0.050 1328 Dihedral : 7.551 57.056 1281 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.13 % Allowed : 20.46 % Favored : 76.41 % 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: -0.46 (0.28), residues: 915 helix: -0.45 (0.54), residues: 103 sheet: -0.38 (0.36), residues: 190 loop : -0.19 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 251 TYR 0.027 0.001 TYR L 231 PHE 0.015 0.001 PHE H 64 TRP 0.009 0.001 TRP L 223 HIS 0.004 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7701) covalent geometry : angle 0.54147 (10420) SS BOND : bond 0.00194 ( 26) SS BOND : angle 0.92985 ( 52) hydrogen bonds : bond 0.03288 ( 193) hydrogen bonds : angle 5.70349 ( 483) link_ALPHA1-2 : bond 0.00495 ( 2) link_ALPHA1-2 : angle 1.34135 ( 6) link_ALPHA1-3 : bond 0.00765 ( 1) link_ALPHA1-3 : angle 1.54343 ( 3) link_ALPHA1-6 : bond 0.00141 ( 1) link_ALPHA1-6 : angle 1.78501 ( 3) link_BETA1-4 : bond 0.00594 ( 4) link_BETA1-4 : angle 2.75930 ( 12) link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 1.75944 ( 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 109 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 234 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7696 (t0) REVERT: H 485 ASP cc_start: 0.8220 (m-30) cc_final: 0.8018 (p0) REVERT: H 490 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: H 507 ASP cc_start: 0.8147 (t0) cc_final: 0.7772 (t0) REVERT: H 581 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5715 (mp0) outliers start: 26 outliers final: 13 residues processed: 101 average time/residue: 0.0957 time to fit residues: 13.0029 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 490 GLU Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.193277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143942 restraints weight = 9299.456| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.55 r_work: 0.3552 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7739 Z= 0.123 Angle : 0.546 8.466 10508 Z= 0.277 Chirality : 0.044 0.205 1165 Planarity : 0.004 0.050 1328 Dihedral : 6.749 51.447 1281 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.21 % Allowed : 19.74 % Favored : 76.05 % 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: -0.48 (0.28), residues: 915 helix: -0.44 (0.54), residues: 103 sheet: -0.39 (0.37), residues: 190 loop : -0.21 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 273 TYR 0.031 0.001 TYR L 242 PHE 0.014 0.001 PHE H 64 TRP 0.009 0.001 TRP L 223 HIS 0.003 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7701) covalent geometry : angle 0.53203 (10420) SS BOND : bond 0.00180 ( 26) SS BOND : angle 0.80738 ( 52) hydrogen bonds : bond 0.03011 ( 193) hydrogen bonds : angle 5.51856 ( 483) link_ALPHA1-2 : bond 0.00458 ( 2) link_ALPHA1-2 : angle 1.36584 ( 6) link_ALPHA1-3 : bond 0.00798 ( 1) link_ALPHA1-3 : angle 1.54380 ( 3) link_ALPHA1-6 : bond 0.00036 ( 1) link_ALPHA1-6 : angle 1.92727 ( 3) link_BETA1-4 : bond 0.00544 ( 4) link_BETA1-4 : angle 2.60683 ( 12) link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 1.72255 ( 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 118 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 234 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7680 (t0) REVERT: H 327 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7267 (t80) REVERT: H 393 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: H 485 ASP cc_start: 0.8276 (m-30) cc_final: 0.8050 (p0) REVERT: H 490 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6962 (tt0) REVERT: H 507 ASP cc_start: 0.8147 (t0) cc_final: 0.7761 (t0) REVERT: H 531 MET cc_start: 0.5694 (tpt) cc_final: 0.5325 (tpt) REVERT: H 569 TYR cc_start: 0.8081 (m-80) cc_final: 0.7735 (m-80) REVERT: H 581 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5766 (mp0) outliers start: 35 outliers final: 21 residues processed: 108 average time/residue: 0.0884 time to fit residues: 13.0328 Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 490 GLU Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141475 restraints weight = 9308.469| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.50 r_work: 0.3504 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7739 Z= 0.169 Angle : 0.571 7.934 10508 Z= 0.292 Chirality : 0.045 0.205 1165 Planarity : 0.004 0.051 1328 Dihedral : 6.647 51.623 1281 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.97 % Allowed : 21.06 % Favored : 74.97 % 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: -0.62 (0.27), residues: 915 helix: -0.45 (0.54), residues: 103 sheet: -0.49 (0.37), residues: 190 loop : -0.33 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 273 TYR 0.039 0.002 TYR L 242 PHE 0.018 0.002 PHE H 64 TRP 0.014 0.001 TRP L 223 HIS 0.004 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7701) covalent geometry : angle 0.55755 (10420) SS BOND : bond 0.00208 ( 26) SS BOND : angle 0.86887 ( 52) hydrogen bonds : bond 0.03061 ( 193) hydrogen bonds : angle 5.63822 ( 483) link_ALPHA1-2 : bond 0.00446 ( 2) link_ALPHA1-2 : angle 1.33328 ( 6) link_ALPHA1-3 : bond 0.00726 ( 1) link_ALPHA1-3 : angle 1.58868 ( 3) link_ALPHA1-6 : bond 0.00032 ( 1) link_ALPHA1-6 : angle 1.72065 ( 3) link_BETA1-4 : bond 0.00583 ( 4) link_BETA1-4 : angle 2.54659 ( 12) link_NAG-ASN : bond 0.00215 ( 4) link_NAG-ASN : angle 1.81710 ( 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 116 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 229 LYS cc_start: 0.8574 (tppt) cc_final: 0.8234 (tptt) REVERT: H 327 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7296 (t80) REVERT: H 485 ASP cc_start: 0.8223 (m-30) cc_final: 0.8016 (p0) REVERT: H 507 ASP cc_start: 0.8155 (t0) cc_final: 0.7763 (t0) REVERT: H 531 MET cc_start: 0.5941 (tpt) cc_final: 0.5466 (tpt) REVERT: H 554 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8578 (p0) REVERT: L 242 TYR cc_start: 0.8689 (m-10) cc_final: 0.8424 (m-10) outliers start: 33 outliers final: 21 residues processed: 106 average time/residue: 0.0917 time to fit residues: 12.9965 Evaluate side-chains 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 458 ASP Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.189243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137772 restraints weight = 9321.522| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.45 r_work: 0.3502 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7739 Z= 0.168 Angle : 0.574 7.577 10508 Z= 0.293 Chirality : 0.045 0.212 1165 Planarity : 0.004 0.051 1328 Dihedral : 6.505 51.037 1281 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.21 % Allowed : 21.66 % Favored : 74.13 % 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: -0.69 (0.27), residues: 915 helix: -0.48 (0.53), residues: 103 sheet: -0.53 (0.37), residues: 190 loop : -0.38 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 273 TYR 0.032 0.001 TYR L 231 PHE 0.017 0.002 PHE H 64 TRP 0.010 0.001 TRP L 223 HIS 0.004 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7701) covalent geometry : angle 0.56190 (10420) SS BOND : bond 0.00210 ( 26) SS BOND : angle 0.83501 ( 52) hydrogen bonds : bond 0.02975 ( 193) hydrogen bonds : angle 5.61163 ( 483) link_ALPHA1-2 : bond 0.00442 ( 2) link_ALPHA1-2 : angle 1.33008 ( 6) link_ALPHA1-3 : bond 0.00764 ( 1) link_ALPHA1-3 : angle 1.57780 ( 3) link_ALPHA1-6 : bond 0.00067 ( 1) link_ALPHA1-6 : angle 1.64820 ( 3) link_BETA1-4 : bond 0.00598 ( 4) link_BETA1-4 : angle 2.49769 ( 12) link_NAG-ASN : bond 0.00148 ( 4) link_NAG-ASN : angle 1.81883 ( 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 115 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 327 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7248 (t80) REVERT: H 485 ASP cc_start: 0.8186 (m-30) cc_final: 0.7952 (p0) REVERT: H 507 ASP cc_start: 0.8146 (t0) cc_final: 0.7740 (t0) REVERT: H 531 MET cc_start: 0.6116 (tpt) cc_final: 0.5793 (tpt) REVERT: H 554 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8593 (p0) REVERT: L 218 ILE cc_start: 0.6136 (OUTLIER) cc_final: 0.5843 (mp) outliers start: 35 outliers final: 27 residues processed: 105 average time/residue: 0.0940 time to fit residues: 13.2338 Evaluate side-chains 108 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 308 ASP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 218 ILE Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.0030 chunk 60 optimal weight: 30.0000 chunk 61 optimal weight: 0.0050 chunk 86 optimal weight: 0.9990 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 210 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.192625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141578 restraints weight = 9231.550| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.42 r_work: 0.3552 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7739 Z= 0.102 Angle : 0.539 5.771 10508 Z= 0.277 Chirality : 0.044 0.213 1165 Planarity : 0.004 0.050 1328 Dihedral : 5.887 49.663 1281 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.25 % Allowed : 22.74 % Favored : 74.01 % 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: -0.56 (0.28), residues: 915 helix: -0.45 (0.54), residues: 103 sheet: -0.46 (0.37), residues: 193 loop : -0.26 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 273 TYR 0.014 0.001 TYR H 50 PHE 0.011 0.001 PHE H 64 TRP 0.011 0.001 TRP L 223 HIS 0.002 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7701) covalent geometry : angle 0.52830 (10420) SS BOND : bond 0.00170 ( 26) SS BOND : angle 0.67714 ( 52) hydrogen bonds : bond 0.02743 ( 193) hydrogen bonds : angle 5.40846 ( 483) link_ALPHA1-2 : bond 0.00422 ( 2) link_ALPHA1-2 : angle 1.38086 ( 6) link_ALPHA1-3 : bond 0.00994 ( 1) link_ALPHA1-3 : angle 1.56995 ( 3) link_ALPHA1-6 : bond 0.00442 ( 1) link_ALPHA1-6 : angle 1.56873 ( 3) link_BETA1-4 : bond 0.00566 ( 4) link_BETA1-4 : angle 2.24682 ( 12) link_NAG-ASN : bond 0.00124 ( 4) link_NAG-ASN : angle 1.70971 ( 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 113 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 393 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: H 485 ASP cc_start: 0.8241 (m-30) cc_final: 0.7950 (p0) REVERT: H 507 ASP cc_start: 0.8097 (t0) cc_final: 0.7707 (t0) REVERT: H 531 MET cc_start: 0.6027 (tpt) cc_final: 0.5421 (tpt) REVERT: H 554 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8623 (p0) REVERT: H 581 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: L 218 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5774 (mp) outliers start: 27 outliers final: 21 residues processed: 107 average time/residue: 0.0974 time to fit residues: 13.7877 Evaluate side-chains 105 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 308 ASP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 458 ASP Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.191528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140422 restraints weight = 9282.276| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.30 r_work: 0.3519 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7739 Z= 0.148 Angle : 0.577 7.616 10508 Z= 0.294 Chirality : 0.044 0.210 1165 Planarity : 0.004 0.052 1328 Dihedral : 6.044 50.675 1281 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.61 % Allowed : 22.62 % Favored : 73.77 % 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: -0.65 (0.27), residues: 915 helix: -0.50 (0.53), residues: 103 sheet: -0.54 (0.36), residues: 193 loop : -0.33 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 273 TYR 0.034 0.001 TYR L 231 PHE 0.016 0.001 PHE H 64 TRP 0.012 0.001 TRP L 223 HIS 0.004 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7701) covalent geometry : angle 0.56616 (10420) SS BOND : bond 0.00191 ( 26) SS BOND : angle 0.74327 ( 52) hydrogen bonds : bond 0.02932 ( 193) hydrogen bonds : angle 5.47993 ( 483) link_ALPHA1-2 : bond 0.00410 ( 2) link_ALPHA1-2 : angle 1.33512 ( 6) link_ALPHA1-3 : bond 0.00756 ( 1) link_ALPHA1-3 : angle 1.62516 ( 3) link_ALPHA1-6 : bond 0.00149 ( 1) link_ALPHA1-6 : angle 1.53000 ( 3) link_BETA1-4 : bond 0.00586 ( 4) link_BETA1-4 : angle 2.40995 ( 12) link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 1.66756 ( 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 115 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 460 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: H 485 ASP cc_start: 0.8233 (m-30) cc_final: 0.7955 (p0) REVERT: H 507 ASP cc_start: 0.8131 (t0) cc_final: 0.7751 (t0) REVERT: H 531 MET cc_start: 0.6254 (tpt) cc_final: 0.5479 (tpt) REVERT: H 554 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8627 (p0) REVERT: L 218 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5880 (mp) outliers start: 30 outliers final: 25 residues processed: 108 average time/residue: 0.0916 time to fit residues: 13.3672 Evaluate side-chains 106 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 308 ASP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 458 ASP Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.192715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142019 restraints weight = 9319.091| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.31 r_work: 0.3554 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7739 Z= 0.108 Angle : 0.565 7.269 10508 Z= 0.290 Chirality : 0.044 0.215 1165 Planarity : 0.004 0.057 1328 Dihedral : 5.729 50.027 1281 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.85 % Allowed : 22.98 % Favored : 73.16 % 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: -0.63 (0.27), residues: 915 helix: -0.65 (0.52), residues: 103 sheet: -0.50 (0.37), residues: 193 loop : -0.28 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 273 TYR 0.014 0.001 TYR L 242 PHE 0.011 0.001 PHE H 64 TRP 0.011 0.001 TRP L 223 HIS 0.002 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7701) covalent geometry : angle 0.55558 (10420) SS BOND : bond 0.00172 ( 26) SS BOND : angle 0.64025 ( 52) hydrogen bonds : bond 0.02798 ( 193) hydrogen bonds : angle 5.38301 ( 483) link_ALPHA1-2 : bond 0.00389 ( 2) link_ALPHA1-2 : angle 1.35864 ( 6) link_ALPHA1-3 : bond 0.00962 ( 1) link_ALPHA1-3 : angle 1.56458 ( 3) link_ALPHA1-6 : bond 0.00416 ( 1) link_ALPHA1-6 : angle 1.45278 ( 3) link_BETA1-4 : bond 0.00593 ( 4) link_BETA1-4 : angle 2.24004 ( 12) link_NAG-ASN : bond 0.00151 ( 4) link_NAG-ASN : angle 1.62256 ( 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 112 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 460 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: H 485 ASP cc_start: 0.8236 (m-30) cc_final: 0.7957 (p0) REVERT: H 507 ASP cc_start: 0.8133 (t0) cc_final: 0.7724 (t0) REVERT: H 509 TYR cc_start: 0.7215 (m-10) cc_final: 0.6925 (m-10) REVERT: H 531 MET cc_start: 0.6228 (tpt) cc_final: 0.5406 (tpt) REVERT: H 554 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8642 (p0) REVERT: H 581 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: L 218 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5873 (mp) outliers start: 32 outliers final: 25 residues processed: 106 average time/residue: 0.0952 time to fit residues: 13.5160 Evaluate side-chains 104 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 308 ASP Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 458 ASP Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 40.0000 chunk 84 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 ASN H 210 ASN H 281 GLN H 373 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.185606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135895 restraints weight = 9348.048| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.29 r_work: 0.3451 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7739 Z= 0.267 Angle : 0.705 12.193 10508 Z= 0.363 Chirality : 0.048 0.204 1165 Planarity : 0.005 0.056 1328 Dihedral : 6.774 51.840 1281 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.61 % Allowed : 22.98 % Favored : 73.41 % 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: -1.06 (0.27), residues: 915 helix: -0.93 (0.50), residues: 103 sheet: -0.55 (0.38), residues: 186 loop : -0.69 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 273 TYR 0.045 0.002 TYR L 242 PHE 0.023 0.002 PHE H 64 TRP 0.014 0.002 TRP H 435 HIS 0.006 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 7701) covalent geometry : angle 0.69307 (10420) SS BOND : bond 0.00275 ( 26) SS BOND : angle 1.01201 ( 52) hydrogen bonds : bond 0.03295 ( 193) hydrogen bonds : angle 5.94243 ( 483) link_ALPHA1-2 : bond 0.00504 ( 2) link_ALPHA1-2 : angle 1.37885 ( 6) link_ALPHA1-3 : bond 0.00411 ( 1) link_ALPHA1-3 : angle 1.75865 ( 3) link_ALPHA1-6 : bond 0.00310 ( 1) link_ALPHA1-6 : angle 1.73320 ( 3) link_BETA1-4 : bond 0.00649 ( 4) link_BETA1-4 : angle 2.74746 ( 12) link_NAG-ASN : bond 0.00327 ( 4) link_NAG-ASN : angle 1.86574 ( 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 115 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 229 LYS cc_start: 0.8798 (mppt) cc_final: 0.8263 (tptt) REVERT: H 352 LYS cc_start: 0.9096 (mttt) cc_final: 0.8850 (mmtm) REVERT: H 460 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: H 507 ASP cc_start: 0.8140 (t0) cc_final: 0.7757 (t0) REVERT: H 554 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8647 (p0) REVERT: H 566 MET cc_start: 0.7121 (mtp) cc_final: 0.6781 (mtp) REVERT: L 218 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6229 (mp) outliers start: 30 outliers final: 24 residues processed: 111 average time/residue: 0.0940 time to fit residues: 13.9057 Evaluate side-chains 105 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 261 ASN Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 458 ASP Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 581 GLU Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 147 MET Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 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 = 0.4246 r_free = 0.4246 target = 0.185700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136086 restraints weight = 9258.795| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.41 r_work: 0.3465 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 7739 Z= 0.280 Angle : 1.042 59.166 10508 Z= 0.608 Chirality : 0.050 0.621 1165 Planarity : 0.005 0.058 1328 Dihedral : 6.790 52.129 1281 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.73 % Allowed : 23.23 % Favored : 73.04 % Cbeta Deviations : 0.11 % 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: -1.08 (0.27), residues: 915 helix: -0.93 (0.50), residues: 103 sheet: -0.54 (0.38), residues: 186 loop : -0.72 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 273 TYR 0.049 0.002 TYR L 242 PHE 0.041 0.003 PHE H 258 TRP 0.013 0.002 TRP H 66 HIS 0.006 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 7701) covalent geometry : angle 1.03643 (10420) SS BOND : bond 0.00230 ( 26) SS BOND : angle 1.00833 ( 52) hydrogen bonds : bond 0.03271 ( 193) hydrogen bonds : angle 5.93947 ( 483) link_ALPHA1-2 : bond 0.00413 ( 2) link_ALPHA1-2 : angle 1.38370 ( 6) link_ALPHA1-3 : bond 0.00464 ( 1) link_ALPHA1-3 : angle 1.82045 ( 3) link_ALPHA1-6 : bond 0.00256 ( 1) link_ALPHA1-6 : angle 1.69604 ( 3) link_BETA1-4 : bond 0.00768 ( 4) link_BETA1-4 : angle 2.72089 ( 12) link_NAG-ASN : bond 0.00325 ( 4) link_NAG-ASN : angle 1.86386 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.56 seconds wall clock time: 34 minutes 5.68 seconds (2045.68 seconds total)