Starting phenix.real_space_refine on Tue Feb 3 22:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w78_65720/02_2026/9w78_65720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w78_65720/02_2026/9w78_65720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w78_65720/02_2026/9w78_65720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w78_65720/02_2026/9w78_65720.map" model { file = "/net/cci-nas-00/data/ceres_data/9w78_65720/02_2026/9w78_65720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w78_65720/02_2026/9w78_65720.cif" } resolution = 2.3 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= 0.001 sd= 0.020 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 37 5.16 5 C 4636 2.51 5 N 1210 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7299 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "C" Number of atoms: 5734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5734 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 32, 'TRANS': 665} Chain breaks: 1 Chain: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.55, per 1000 atoms: 0.21 Number of scatterers: 7299 At special positions: 0 Unit cell: (73.7751, 96.6709, 128.046, 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 37 16.00 O 1416 8.00 N 1210 7.00 C 4636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 353 " - pdb=" SG CYS D 406 " distance=2.05 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " 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 F 4 " - " MAN F 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 1 " - " ASN C 53 " " NAG B 1 " - " ASN C 690 " " NAG C 801 " - " ASN C 322 " " NAG C 802 " - " ASN C 329 " " NAG E 1 " - " ASN C 546 " " NAG F 1 " - " ASN C 38 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 213.9 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 58.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'D' and resid 312 through 317 removed outlier: 3.790A pdb=" N PHE D 316 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 377 through 385 removed outlier: 3.552A pdb=" N VAL D 381 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG D 382 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.697A pdb=" N GLN D 471 " --> pdb=" O ASP D 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 52 removed outlier: 4.266A pdb=" N ASN C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.839A pdb=" N GLN C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 83 No H-bonds generated for 'chain 'C' and resid 82 through 83' Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.511A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.747A pdb=" N SER C 103 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.562A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 194 Proline residue: C 178 - end of helix removed outlier: 3.655A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 218 through 251 removed outlier: 3.648A pdb=" N LEU C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 4.026A pdb=" N ASP C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.559A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.546A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 387 through 388 No H-bonds generated for 'chain 'C' and resid 387 through 388' Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.528A pdb=" N ARG C 393 " --> pdb=" O TYR C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.672A pdb=" N GLU C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.557A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.961A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.622A pdb=" N CYS C 542 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 4.029A pdb=" N VAL C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 636 through 658 Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 707 Processing helix chain 'C' and resid 707 through 714 removed outlier: 3.590A pdb=" N ILE C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 330 through 332 Processing sheet with id=AA2, first strand: chain 'D' and resid 426 through 428 Processing sheet with id=AA3, first strand: chain 'D' and resid 446 through 449 Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.911A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.327A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 618 through 621 Processing sheet with id=AA8, first strand: chain 'C' and resid 618 through 621 removed outlier: 5.965A pdb=" N ASP C 693 " --> pdb=" O SER C 687 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 981 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: 1.09 Time building geometry restraints manager: 0.95 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: 2309 1.34 - 1.47: 2024 1.47 - 1.59: 3100 1.59 - 1.72: 0 1.72 - 1.84: 62 Bond restraints: 7495 Sorted by residual: bond pdb=" CG1 ILE C 79 " pdb=" CD1 ILE C 79 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.84e+00 bond pdb=" CB PRO C 500 " pdb=" CG PRO C 500 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.73e+00 bond pdb=" C GLU C 589 " pdb=" N PRO C 590 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.60e+00 bond pdb=" C LEU C 450 " pdb=" N PRO C 451 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.59e+00 bond pdb=" C GLU C 145 " pdb=" N PRO C 146 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.56e+00 ... (remaining 7490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 10054 2.68 - 5.35: 91 5.35 - 8.03: 16 8.03 - 10.70: 0 10.70 - 13.38: 1 Bond angle restraints: 10162 Sorted by residual: angle pdb=" CA ILE C 79 " pdb=" CB ILE C 79 " pdb=" CG1 ILE C 79 " ideal model delta sigma weight residual 110.40 116.95 -6.55 1.70e+00 3.46e-01 1.48e+01 angle pdb=" CA LEU C 254 " pdb=" CB LEU C 254 " pdb=" CG LEU C 254 " ideal model delta sigma weight residual 116.30 129.68 -13.38 3.50e+00 8.16e-02 1.46e+01 angle pdb=" CA TYR C 385 " pdb=" CB TYR C 385 " pdb=" CG TYR C 385 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 angle pdb=" C TRP C 168 " pdb=" N ARG C 169 " pdb=" CA ARG C 169 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" CB GLU C 310 " pdb=" CG GLU C 310 " pdb=" CD GLU C 310 " ideal model delta sigma weight residual 112.60 117.72 -5.12 1.70e+00 3.46e-01 9.06e+00 ... (remaining 10157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 4155 24.44 - 48.87: 382 48.87 - 73.31: 68 73.31 - 97.75: 6 97.75 - 122.18: 3 Dihedral angle restraints: 4614 sinusoidal: 2059 harmonic: 2555 Sorted by residual: dihedral pdb=" CB CYS D 353 " pdb=" SG CYS D 353 " pdb=" SG CYS D 406 " pdb=" CB CYS D 406 " ideal model delta sinusoidal sigma weight residual 93.00 57.40 35.60 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" C2 MAN F 5 " pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " pdb=" C5 MAN F 5 " ideal model delta sinusoidal sigma weight residual -57.62 64.56 -122.18 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CA ASP C 250 " pdb=" C ASP C 250 " pdb=" N THR C 251 " pdb=" CA THR C 251 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 970 0.074 - 0.148: 117 0.148 - 0.221: 8 0.221 - 0.295: 0 0.295 - 0.369: 1 Chirality restraints: 1096 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 546 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB THR C 662 " pdb=" CA THR C 662 " pdb=" OG1 THR C 662 " pdb=" CG2 THR C 662 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 9.88e-01 ... (remaining 1093 not shown) Planarity restraints: 1297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 582 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO C 583 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 583 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 583 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 385 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO D 386 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 386 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 386 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 436 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO D 437 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 437 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 437 " 0.027 5.00e-02 4.00e+02 ... (remaining 1294 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2110 2.81 - 3.33: 6432 3.33 - 3.86: 12761 3.86 - 4.38: 14868 4.38 - 4.90: 25199 Nonbonded interactions: 61370 Sorted by model distance: nonbonded pdb=" O SER D 465 " pdb=" OH TYR C 41 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR D 447 " pdb=" OD2 ASP C 31 " model vdw 2.295 3.040 nonbonded pdb=" O PHE C 327 " pdb=" OG SER C 331 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR C 183 " pdb=" OD1 ASP C 509 " model vdw 2.320 3.040 nonbonded pdb=" OG SER C 109 " pdb=" OD1 ASP C 111 " model vdw 2.320 3.040 ... (remaining 61365 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.004 0.066 7513 Z= 0.166 Angle : 0.713 13.378 10212 Z= 0.357 Chirality : 0.048 0.369 1096 Planarity : 0.005 0.059 1291 Dihedral : 17.982 122.182 2960 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 25.26 % Favored : 72.04 % 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: -0.55 (0.26), residues: 862 helix: -0.11 (0.23), residues: 440 sheet: 0.80 (0.60), residues: 67 loop : -0.77 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 621 TYR 0.020 0.002 TYR C 385 PHE 0.024 0.002 PHE D 480 TRP 0.009 0.001 TRP C 163 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7495) covalent geometry : angle 0.68070 (10162) SS BOND : bond 0.00872 ( 4) SS BOND : angle 1.47132 ( 8) hydrogen bonds : bond 0.14338 ( 337) hydrogen bonds : angle 6.26747 ( 981) link_ALPHA1-2 : bond 0.00703 ( 1) link_ALPHA1-2 : angle 1.79117 ( 3) link_ALPHA1-3 : bond 0.01112 ( 1) link_ALPHA1-3 : angle 1.31916 ( 3) link_ALPHA1-6 : bond 0.00047 ( 1) link_ALPHA1-6 : angle 1.83624 ( 3) link_BETA1-4 : bond 0.01085 ( 5) link_BETA1-4 : angle 3.76588 ( 15) link_NAG-ASN : bond 0.00278 ( 6) link_NAG-ASN : angle 3.61215 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: D 330 LYS cc_start: 0.8272 (tppp) cc_final: 0.7991 (tppp) REVERT: D 374 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7255 (p90) REVERT: C 85 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 351 LEU cc_start: 0.8903 (mt) cc_final: 0.8666 (mp) REVERT: C 360 MET cc_start: 0.8696 (ptm) cc_final: 0.8360 (ttt) REVERT: C 597 GLU cc_start: 0.7895 (tp30) cc_final: 0.7488 (tp30) REVERT: C 600 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7299 (mtm-85) REVERT: C 668 GLU cc_start: 0.7464 (pm20) cc_final: 0.6972 (pm20) outliers start: 21 outliers final: 13 residues processed: 161 average time/residue: 0.5178 time to fit residues: 87.4811 Evaluate side-chains 166 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 459 ASN Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 611 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS C 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114189 restraints weight = 9178.284| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.74 r_work: 0.3433 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7513 Z= 0.169 Angle : 0.596 10.262 10212 Z= 0.292 Chirality : 0.045 0.362 1096 Planarity : 0.005 0.047 1291 Dihedral : 9.673 108.926 1271 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.22 % Allowed : 22.81 % Favored : 73.97 % 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: 0.25 (0.28), residues: 862 helix: 0.74 (0.24), residues: 445 sheet: 0.64 (0.60), residues: 67 loop : -0.57 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 428 TYR 0.021 0.002 TYR C 385 PHE 0.019 0.001 PHE C 523 TRP 0.012 0.001 TRP C 163 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7495) covalent geometry : angle 0.55994 (10162) SS BOND : bond 0.00588 ( 4) SS BOND : angle 1.16298 ( 8) hydrogen bonds : bond 0.05132 ( 337) hydrogen bonds : angle 4.84574 ( 981) link_ALPHA1-2 : bond 0.00641 ( 1) link_ALPHA1-2 : angle 2.20281 ( 3) link_ALPHA1-3 : bond 0.01129 ( 1) link_ALPHA1-3 : angle 1.42134 ( 3) link_ALPHA1-6 : bond 0.00013 ( 1) link_ALPHA1-6 : angle 1.95284 ( 3) link_BETA1-4 : bond 0.00743 ( 5) link_BETA1-4 : angle 3.35093 ( 15) link_NAG-ASN : bond 0.00307 ( 6) link_NAG-ASN : angle 3.56165 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.300 Fit side-chains REVERT: D 374 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7571 (p90) REVERT: C 79 ILE cc_start: 0.8560 (mp) cc_final: 0.8346 (mp) REVERT: C 343 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7621 (m) REVERT: C 597 GLU cc_start: 0.7964 (tp30) cc_final: 0.7402 (tp30) REVERT: C 600 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.7311 (mtm-85) REVERT: C 668 GLU cc_start: 0.7437 (pm20) cc_final: 0.6964 (pm20) REVERT: C 701 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7086 (mt-10) outliers start: 25 outliers final: 11 residues processed: 164 average time/residue: 0.6066 time to fit residues: 104.2677 Evaluate side-chains 163 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 701 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 GLN C 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113048 restraints weight = 9215.120| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.75 r_work: 0.3423 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7513 Z= 0.184 Angle : 0.605 9.563 10212 Z= 0.293 Chirality : 0.046 0.366 1096 Planarity : 0.004 0.045 1291 Dihedral : 9.112 103.588 1258 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.48 % Allowed : 22.94 % Favored : 73.58 % 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: 0.50 (0.28), residues: 862 helix: 0.90 (0.25), residues: 452 sheet: 0.50 (0.60), residues: 67 loop : -0.34 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 428 TYR 0.019 0.002 TYR C 385 PHE 0.021 0.002 PHE C 523 TRP 0.012 0.001 TRP C 163 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 7495) covalent geometry : angle 0.56806 (10162) SS BOND : bond 0.00657 ( 4) SS BOND : angle 1.35783 ( 8) hydrogen bonds : bond 0.05101 ( 337) hydrogen bonds : angle 4.65954 ( 981) link_ALPHA1-2 : bond 0.00803 ( 1) link_ALPHA1-2 : angle 2.58182 ( 3) link_ALPHA1-3 : bond 0.00960 ( 1) link_ALPHA1-3 : angle 1.21263 ( 3) link_ALPHA1-6 : bond 0.00045 ( 1) link_ALPHA1-6 : angle 1.94535 ( 3) link_BETA1-4 : bond 0.00834 ( 5) link_BETA1-4 : angle 3.33687 ( 15) link_NAG-ASN : bond 0.00391 ( 6) link_NAG-ASN : angle 3.63129 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.263 Fit side-chains REVERT: D 374 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (p90) REVERT: D 434 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7813 (ttmm) REVERT: C 79 ILE cc_start: 0.8536 (mp) cc_final: 0.8312 (mp) REVERT: C 343 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7640 (m) REVERT: C 597 GLU cc_start: 0.8000 (tp30) cc_final: 0.7345 (tp30) REVERT: C 600 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7296 (mtm-85) REVERT: C 621 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: C 668 GLU cc_start: 0.7438 (pm20) cc_final: 0.6964 (pm20) outliers start: 27 outliers final: 10 residues processed: 171 average time/residue: 0.6496 time to fit residues: 116.7630 Evaluate side-chains 165 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 621 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 388 GLN C 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.135062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113635 restraints weight = 9314.578| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.76 r_work: 0.3427 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7513 Z= 0.166 Angle : 0.597 9.378 10212 Z= 0.288 Chirality : 0.045 0.355 1096 Planarity : 0.004 0.043 1291 Dihedral : 8.754 100.183 1256 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.87 % Allowed : 21.91 % Favored : 74.23 % 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: 0.66 (0.28), residues: 862 helix: 1.01 (0.25), residues: 452 sheet: 0.72 (0.61), residues: 66 loop : -0.29 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 428 TYR 0.018 0.002 TYR C 385 PHE 0.019 0.001 PHE C 523 TRP 0.011 0.001 TRP C 163 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7495) covalent geometry : angle 0.55795 (10162) SS BOND : bond 0.00629 ( 4) SS BOND : angle 1.31425 ( 8) hydrogen bonds : bond 0.04847 ( 337) hydrogen bonds : angle 4.56238 ( 981) link_ALPHA1-2 : bond 0.00867 ( 1) link_ALPHA1-2 : angle 2.76476 ( 3) link_ALPHA1-3 : bond 0.01028 ( 1) link_ALPHA1-3 : angle 1.35201 ( 3) link_ALPHA1-6 : bond 0.00045 ( 1) link_ALPHA1-6 : angle 2.03733 ( 3) link_BETA1-4 : bond 0.00842 ( 5) link_BETA1-4 : angle 3.32185 ( 15) link_NAG-ASN : bond 0.00651 ( 6) link_NAG-ASN : angle 3.76559 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.356 Fit side-chains REVERT: C 79 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8319 (mp) REVERT: C 343 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7656 (m) REVERT: C 597 GLU cc_start: 0.8021 (tp30) cc_final: 0.7386 (tp30) REVERT: C 600 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7273 (mtm-85) REVERT: C 621 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7617 (ttp-170) REVERT: C 668 GLU cc_start: 0.7421 (pm20) cc_final: 0.6956 (pm20) outliers start: 30 outliers final: 12 residues processed: 174 average time/residue: 0.5554 time to fit residues: 101.5204 Evaluate side-chains 173 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 366 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.2980 chunk 72 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.136578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115385 restraints weight = 9232.803| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.74 r_work: 0.3453 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7513 Z= 0.113 Angle : 0.563 10.260 10212 Z= 0.269 Chirality : 0.042 0.326 1096 Planarity : 0.004 0.041 1291 Dihedral : 8.296 96.370 1254 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.71 % Allowed : 23.20 % Favored : 74.10 % 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: 0.85 (0.29), residues: 862 helix: 1.27 (0.25), residues: 447 sheet: 0.73 (0.62), residues: 66 loop : -0.30 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 697 TYR 0.016 0.001 TYR C 385 PHE 0.011 0.001 PHE C 523 TRP 0.011 0.001 TRP C 163 HIS 0.004 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7495) covalent geometry : angle 0.52984 (10162) SS BOND : bond 0.00536 ( 4) SS BOND : angle 1.07036 ( 8) hydrogen bonds : bond 0.04199 ( 337) hydrogen bonds : angle 4.46853 ( 981) link_ALPHA1-2 : bond 0.01160 ( 1) link_ALPHA1-2 : angle 2.96650 ( 3) link_ALPHA1-3 : bond 0.00970 ( 1) link_ALPHA1-3 : angle 1.33649 ( 3) link_ALPHA1-6 : bond 0.00152 ( 1) link_ALPHA1-6 : angle 1.98269 ( 3) link_BETA1-4 : bond 0.00919 ( 5) link_BETA1-4 : angle 3.23687 ( 15) link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 3.15166 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.299 Fit side-chains REVERT: D 380 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: C 201 ASP cc_start: 0.8014 (t0) cc_final: 0.7794 (t0) REVERT: C 343 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7619 (m) REVERT: C 391 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8350 (mt) REVERT: C 597 GLU cc_start: 0.7965 (tp30) cc_final: 0.7436 (tp30) REVERT: C 600 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7247 (mtm-85) REVERT: C 621 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7589 (ttp-170) REVERT: C 668 GLU cc_start: 0.7411 (pm20) cc_final: 0.6959 (pm20) outliers start: 21 outliers final: 8 residues processed: 177 average time/residue: 0.5894 time to fit residues: 109.8659 Evaluate side-chains 170 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN D 388 GLN ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.134969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.113535 restraints weight = 9233.389| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.75 r_work: 0.3424 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7513 Z= 0.186 Angle : 0.612 9.980 10212 Z= 0.294 Chirality : 0.046 0.364 1096 Planarity : 0.004 0.043 1291 Dihedral : 8.128 95.202 1252 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.09 % Allowed : 22.42 % Favored : 74.48 % 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: 0.81 (0.29), residues: 862 helix: 1.16 (0.25), residues: 452 sheet: 0.78 (0.62), residues: 66 loop : -0.24 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 428 TYR 0.019 0.002 TYR C 385 PHE 0.020 0.001 PHE C 523 TRP 0.010 0.001 TRP C 163 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7495) covalent geometry : angle 0.57423 (10162) SS BOND : bond 0.00635 ( 4) SS BOND : angle 1.35026 ( 8) hydrogen bonds : bond 0.04924 ( 337) hydrogen bonds : angle 4.52520 ( 981) link_ALPHA1-2 : bond 0.00912 ( 1) link_ALPHA1-2 : angle 2.99216 ( 3) link_ALPHA1-3 : bond 0.00949 ( 1) link_ALPHA1-3 : angle 1.32020 ( 3) link_ALPHA1-6 : bond 0.00017 ( 1) link_ALPHA1-6 : angle 2.00110 ( 3) link_BETA1-4 : bond 0.00824 ( 5) link_BETA1-4 : angle 3.28663 ( 15) link_NAG-ASN : bond 0.00702 ( 6) link_NAG-ASN : angle 3.70597 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.293 Fit side-chains REVERT: D 380 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: D 388 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: C 343 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7602 (m) REVERT: C 391 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 597 GLU cc_start: 0.8022 (tp30) cc_final: 0.7417 (tp30) REVERT: C 600 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7269 (mtm-85) REVERT: C 621 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7572 (ttp-170) REVERT: C 668 GLU cc_start: 0.7421 (pm20) cc_final: 0.6962 (pm20) outliers start: 24 outliers final: 11 residues processed: 174 average time/residue: 0.5948 time to fit residues: 108.6415 Evaluate side-chains 174 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN D 388 GLN C 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.135652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114282 restraints weight = 9294.163| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.74 r_work: 0.3435 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7513 Z= 0.151 Angle : 0.593 9.762 10212 Z= 0.286 Chirality : 0.044 0.348 1096 Planarity : 0.004 0.046 1291 Dihedral : 7.966 93.369 1252 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.58 % Allowed : 23.20 % Favored : 74.23 % 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: 0.84 (0.28), residues: 862 helix: 1.24 (0.25), residues: 447 sheet: 0.73 (0.62), residues: 66 loop : -0.28 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 697 TYR 0.018 0.002 TYR C 385 PHE 0.017 0.001 PHE C 523 TRP 0.009 0.001 TRP C 478 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7495) covalent geometry : angle 0.55788 (10162) SS BOND : bond 0.00601 ( 4) SS BOND : angle 1.22597 ( 8) hydrogen bonds : bond 0.04625 ( 337) hydrogen bonds : angle 4.51722 ( 981) link_ALPHA1-2 : bond 0.01030 ( 1) link_ALPHA1-2 : angle 3.05158 ( 3) link_ALPHA1-3 : bond 0.01072 ( 1) link_ALPHA1-3 : angle 1.38448 ( 3) link_ALPHA1-6 : bond 0.00075 ( 1) link_ALPHA1-6 : angle 1.94658 ( 3) link_BETA1-4 : bond 0.00877 ( 5) link_BETA1-4 : angle 3.27930 ( 15) link_NAG-ASN : bond 0.00319 ( 6) link_NAG-ASN : angle 3.42256 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.244 Fit side-chains REVERT: D 347 SER cc_start: 0.7804 (p) cc_final: 0.7600 (p) REVERT: D 380 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: C 343 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7574 (m) REVERT: C 391 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 597 GLU cc_start: 0.7995 (tp30) cc_final: 0.7399 (tp30) REVERT: C 600 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.7261 (mtm-85) REVERT: C 621 ARG cc_start: 0.7860 (ttp-170) cc_final: 0.7566 (ttp-170) REVERT: C 668 GLU cc_start: 0.7408 (pm20) cc_final: 0.6954 (pm20) outliers start: 20 outliers final: 11 residues processed: 176 average time/residue: 0.6014 time to fit residues: 110.9696 Evaluate side-chains 174 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN D 388 GLN C 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.135843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114431 restraints weight = 9327.405| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.76 r_work: 0.3441 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7513 Z= 0.134 Angle : 0.586 9.607 10212 Z= 0.283 Chirality : 0.043 0.336 1096 Planarity : 0.004 0.057 1291 Dihedral : 7.799 90.510 1252 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.32 % Allowed : 23.07 % Favored : 74.61 % 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: 0.89 (0.29), residues: 862 helix: 1.27 (0.25), residues: 449 sheet: 0.69 (0.62), residues: 66 loop : -0.24 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 697 TYR 0.019 0.001 TYR C 385 PHE 0.014 0.001 PHE C 523 TRP 0.010 0.001 TRP C 478 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7495) covalent geometry : angle 0.55014 (10162) SS BOND : bond 0.00567 ( 4) SS BOND : angle 1.16656 ( 8) hydrogen bonds : bond 0.04420 ( 337) hydrogen bonds : angle 4.51671 ( 981) link_ALPHA1-2 : bond 0.01145 ( 1) link_ALPHA1-2 : angle 3.14810 ( 3) link_ALPHA1-3 : bond 0.00971 ( 1) link_ALPHA1-3 : angle 1.29810 ( 3) link_ALPHA1-6 : bond 0.00093 ( 1) link_ALPHA1-6 : angle 1.89249 ( 3) link_BETA1-4 : bond 0.00896 ( 5) link_BETA1-4 : angle 3.24213 ( 15) link_NAG-ASN : bond 0.00565 ( 6) link_NAG-ASN : angle 3.51951 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.214 Fit side-chains REVERT: D 347 SER cc_start: 0.7796 (p) cc_final: 0.7592 (p) REVERT: D 380 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: C 343 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7603 (m) REVERT: C 597 GLU cc_start: 0.7993 (tp30) cc_final: 0.7447 (tp30) REVERT: C 600 ARG cc_start: 0.7681 (mmm-85) cc_final: 0.7261 (mtm-85) REVERT: C 668 GLU cc_start: 0.7398 (pm20) cc_final: 0.6955 (pm20) outliers start: 18 outliers final: 10 residues processed: 172 average time/residue: 0.5316 time to fit residues: 96.2586 Evaluate side-chains 172 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 72 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN C 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.135549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114257 restraints weight = 9174.462| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.73 r_work: 0.3440 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7513 Z= 0.154 Angle : 0.606 9.646 10212 Z= 0.293 Chirality : 0.044 0.345 1096 Planarity : 0.004 0.051 1291 Dihedral : 7.682 88.193 1252 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.06 % Allowed : 23.32 % Favored : 74.61 % 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: 0.85 (0.28), residues: 862 helix: 1.24 (0.25), residues: 448 sheet: 0.73 (0.62), residues: 66 loop : -0.27 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 697 TYR 0.019 0.002 TYR C 385 PHE 0.018 0.001 PHE C 523 TRP 0.011 0.001 TRP C 163 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7495) covalent geometry : angle 0.57279 (10162) SS BOND : bond 0.00590 ( 4) SS BOND : angle 1.20066 ( 8) hydrogen bonds : bond 0.04560 ( 337) hydrogen bonds : angle 4.54244 ( 981) link_ALPHA1-2 : bond 0.01134 ( 1) link_ALPHA1-2 : angle 3.20574 ( 3) link_ALPHA1-3 : bond 0.00941 ( 1) link_ALPHA1-3 : angle 1.26619 ( 3) link_ALPHA1-6 : bond 0.00046 ( 1) link_ALPHA1-6 : angle 1.89361 ( 3) link_BETA1-4 : bond 0.00840 ( 5) link_BETA1-4 : angle 3.23318 ( 15) link_NAG-ASN : bond 0.00337 ( 6) link_NAG-ASN : angle 3.38140 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.296 Fit side-chains REVERT: D 347 SER cc_start: 0.7799 (p) cc_final: 0.7590 (p) REVERT: C 343 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7593 (m) REVERT: C 597 GLU cc_start: 0.7970 (tp30) cc_final: 0.7414 (tp30) REVERT: C 600 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7246 (mtm-85) REVERT: C 621 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.7659 (ttp-170) REVERT: C 668 GLU cc_start: 0.7406 (pm20) cc_final: 0.6960 (pm20) REVERT: C 701 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7224 (mt-10) outliers start: 16 outliers final: 11 residues processed: 169 average time/residue: 0.5827 time to fit residues: 103.5080 Evaluate side-chains 172 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 29 optimal weight: 0.0040 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN C 82 ASN C 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114842 restraints weight = 9242.192| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.75 r_work: 0.3447 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7513 Z= 0.129 Angle : 0.593 9.500 10212 Z= 0.286 Chirality : 0.043 0.331 1096 Planarity : 0.004 0.046 1291 Dihedral : 7.447 84.513 1249 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.55 % Allowed : 23.97 % Favored : 74.48 % 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: 0.91 (0.28), residues: 862 helix: 1.29 (0.25), residues: 449 sheet: 0.67 (0.62), residues: 66 loop : -0.23 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 697 TYR 0.019 0.001 TYR C 385 PHE 0.017 0.001 PHE D 374 TRP 0.011 0.001 TRP C 163 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7495) covalent geometry : angle 0.55755 (10162) SS BOND : bond 0.00548 ( 4) SS BOND : angle 1.09327 ( 8) hydrogen bonds : bond 0.04305 ( 337) hydrogen bonds : angle 4.52133 ( 981) link_ALPHA1-2 : bond 0.01245 ( 1) link_ALPHA1-2 : angle 3.26493 ( 3) link_ALPHA1-3 : bond 0.00951 ( 1) link_ALPHA1-3 : angle 1.28564 ( 3) link_ALPHA1-6 : bond 0.00134 ( 1) link_ALPHA1-6 : angle 1.85134 ( 3) link_BETA1-4 : bond 0.00899 ( 5) link_BETA1-4 : angle 3.21084 ( 15) link_NAG-ASN : bond 0.00590 ( 6) link_NAG-ASN : angle 3.47858 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.304 Fit side-chains REVERT: D 347 SER cc_start: 0.7808 (p) cc_final: 0.7602 (p) REVERT: C 343 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7570 (m) REVERT: C 597 GLU cc_start: 0.7981 (tp30) cc_final: 0.7441 (tp30) REVERT: C 600 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7266 (mtm-85) REVERT: C 621 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7633 (ttp-170) REVERT: C 668 GLU cc_start: 0.7405 (pm20) cc_final: 0.6966 (pm20) REVERT: C 701 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7202 (mt-10) outliers start: 12 outliers final: 9 residues processed: 164 average time/residue: 0.6451 time to fit residues: 111.2717 Evaluate side-chains 170 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 354 TYR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 4 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 GLN C 82 ASN ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115205 restraints weight = 9216.055| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.73 r_work: 0.3453 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7513 Z= 0.129 Angle : 0.596 9.456 10212 Z= 0.286 Chirality : 0.043 0.329 1096 Planarity : 0.004 0.044 1291 Dihedral : 7.261 79.712 1249 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.42 % Allowed : 24.23 % Favored : 74.36 % 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: 0.91 (0.29), residues: 862 helix: 1.29 (0.25), residues: 449 sheet: 0.71 (0.62), residues: 66 loop : -0.23 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 697 TYR 0.017 0.001 TYR C 385 PHE 0.016 0.001 PHE D 374 TRP 0.010 0.001 TRP C 163 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7495) covalent geometry : angle 0.56365 (10162) SS BOND : bond 0.00548 ( 4) SS BOND : angle 1.09007 ( 8) hydrogen bonds : bond 0.04269 ( 337) hydrogen bonds : angle 4.51813 ( 981) link_ALPHA1-2 : bond 0.01339 ( 1) link_ALPHA1-2 : angle 3.35495 ( 3) link_ALPHA1-3 : bond 0.00955 ( 1) link_ALPHA1-3 : angle 1.29835 ( 3) link_ALPHA1-6 : bond 0.00145 ( 1) link_ALPHA1-6 : angle 1.83260 ( 3) link_BETA1-4 : bond 0.00887 ( 5) link_BETA1-4 : angle 3.17296 ( 15) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 3.28730 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.32 seconds wall clock time: 63 minutes 46.47 seconds (3826.47 seconds total)