Starting phenix.real_space_refine on Fri Aug 22 17:43:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc2_37090/08_2025/8kc2_37090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc2_37090/08_2025/8kc2_37090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kc2_37090/08_2025/8kc2_37090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc2_37090/08_2025/8kc2_37090.map" model { file = "/net/cci-nas-00/data/ceres_data/8kc2_37090/08_2025/8kc2_37090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc2_37090/08_2025/8kc2_37090.cif" } resolution = 2.6 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= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4135 2.51 5 N 1074 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6471 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1560 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} 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: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 0.24 Number of scatterers: 6471 At special positions: 0 Unit cell: (97.68, 76.56, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1225 8.00 N 1074 7.00 C 4135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 82 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 289.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 51.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.963A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.540A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.523A pdb=" N VAL A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.552A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 192 removed outlier: 3.570A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.003A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 248 removed outlier: 3.572A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.676A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.556A pdb=" N ILE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.813A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.844A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.000A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.518A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.501A pdb=" N GLU A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.381A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.622A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.844A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.566A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.241A pdb=" N ARG E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.560A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.908A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.558A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 261 hydrogen bonds defined for protein. 744 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: 0.61 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2077 1.35 - 1.47: 1713 1.47 - 1.59: 2803 1.59 - 1.72: 0 1.72 - 1.84: 56 Bond restraints: 6649 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.25e+01 bond pdb=" CE1 HIS A 378 " pdb=" NE2 HIS A 378 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CE1 HIS A 373 " pdb=" NE2 HIS A 373 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 ... (remaining 6644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8748 2.00 - 3.99: 240 3.99 - 5.99: 41 5.99 - 7.99: 4 7.99 - 9.99: 2 Bond angle restraints: 9035 Sorted by residual: angle pdb=" C ALA A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta sigma weight residual 120.49 130.48 -9.99 1.42e+00 4.96e-01 4.95e+01 angle pdb=" C MET A 383 " pdb=" N ALA A 384 " pdb=" CA ALA A 384 " ideal model delta sigma weight residual 120.29 110.38 9.91 1.42e+00 4.96e-01 4.87e+01 angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 119.25 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N PHE A 400 " pdb=" CA PHE A 400 " pdb=" C PHE A 400 " ideal model delta sigma weight residual 114.04 108.07 5.97 1.24e+00 6.50e-01 2.32e+01 ... (remaining 9030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.24: 3745 24.24 - 48.48: 200 48.48 - 72.72: 33 72.72 - 96.96: 6 96.96 - 121.20: 3 Dihedral angle restraints: 3987 sinusoidal: 1666 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -175.16 89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CA ASN E 360 " pdb=" C ASN E 360 " pdb=" N CYS E 361 " pdb=" CA CYS E 361 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 46.79 46.21 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 3984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 715 0.049 - 0.098: 175 0.098 - 0.147: 58 0.147 - 0.196: 3 0.196 - 0.245: 1 Chirality restraints: 952 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA HIS A 378 " pdb=" N HIS A 378 " pdb=" C HIS A 378 " pdb=" CB HIS A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA MET A 383 " pdb=" N MET A 383 " pdb=" C MET A 383 " pdb=" CB MET A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 949 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 518 " 0.402 9.50e-02 1.11e+02 1.80e-01 1.99e+01 pdb=" NE ARG A 518 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 518 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 389 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 415 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.025 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 17 2.44 - 3.06: 3972 3.06 - 3.67: 9148 3.67 - 4.29: 13433 4.29 - 4.90: 23562 Nonbonded interactions: 50132 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 1.829 2.230 nonbonded pdb=" O VAL E 445 " pdb=" OG SER E 446 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD2 ASP A 509 " model vdw 2.248 3.040 nonbonded pdb=" NZ LYS E 378 " pdb=" OH TYR E 380 " model vdw 2.285 3.120 nonbonded pdb=" OE2 GLU A 57 " pdb=" O6 NAG A 702 " model vdw 2.289 3.040 ... (remaining 50127 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: 10.940 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.020 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.006 0.273 6662 Z= 0.281 Angle : 0.769 9.987 9061 Z= 0.469 Chirality : 0.048 0.245 952 Planarity : 0.007 0.180 1170 Dihedral : 14.838 121.200 2478 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 0.87 % Allowed : 1.31 % Favored : 97.82 % 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 aren not related in a simple way. whole: -0.90 (0.30), residues: 786 helix: 0.37 (0.28), residues: 380 sheet: 1.20 (0.89), residues: 35 loop : -1.85 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.019 0.002 TYR A 521 PHE 0.024 0.002 PHE A 400 TRP 0.019 0.002 TRP A 473 HIS 0.010 0.002 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6649) covalent geometry : angle 0.75248 ( 9035) SS BOND : bond 0.00574 ( 7) SS BOND : angle 2.43349 ( 14) hydrogen bonds : bond 0.16728 ( 261) hydrogen bonds : angle 5.97924 ( 744) metal coordination : bond 0.20136 ( 2) link_BETA1-4 : bond 0.00339 ( 1) link_BETA1-4 : angle 0.97418 ( 3) link_NAG-ASN : bond 0.00731 ( 3) link_NAG-ASN : angle 4.08540 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.177 Fit side-chains REVERT: A 206 ASP cc_start: 0.7217 (t70) cc_final: 0.6895 (t0) REVERT: A 341 LYS cc_start: 0.8243 (pttp) cc_final: 0.7999 (pttp) REVERT: E 401 VAL cc_start: 0.8681 (p) cc_final: 0.8454 (t) outliers start: 6 outliers final: 3 residues processed: 175 average time/residue: 0.5627 time to fit residues: 102.6834 Evaluate side-chains 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain E residue 394 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.0040 chunk 74 optimal weight: 0.0980 overall best weight: 0.0908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 89 GLN A 299 ASN A 578 ASN A 601 ASN E 460 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108705 restraints weight = 9321.330| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.69 r_work: 0.3400 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6662 Z= 0.117 Angle : 0.578 9.841 9061 Z= 0.298 Chirality : 0.042 0.247 952 Planarity : 0.004 0.049 1170 Dihedral : 9.042 105.105 957 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 2.76 % Allowed : 11.19 % Favored : 86.05 % 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 aren not related in a simple way. whole: -0.47 (0.31), residues: 786 helix: 0.85 (0.29), residues: 373 sheet: 0.81 (0.88), residues: 36 loop : -1.68 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.018 0.001 TYR A 385 PHE 0.008 0.001 PHE E 377 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6649) covalent geometry : angle 0.56065 ( 9035) SS BOND : bond 0.00502 ( 7) SS BOND : angle 1.27484 ( 14) hydrogen bonds : bond 0.05202 ( 261) hydrogen bonds : angle 4.43272 ( 744) metal coordination : bond 0.00226 ( 2) link_BETA1-4 : bond 0.00451 ( 1) link_BETA1-4 : angle 1.18885 ( 3) link_NAG-ASN : bond 0.01329 ( 3) link_NAG-ASN : angle 4.20155 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.234 Fit side-chains REVERT: A 34 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: A 206 ASP cc_start: 0.7764 (t70) cc_final: 0.7504 (t0) REVERT: A 323 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8383 (tpt) REVERT: A 341 LYS cc_start: 0.8444 (pttp) cc_final: 0.8193 (pttp) REVERT: A 597 GLU cc_start: 0.8220 (tp30) cc_final: 0.7922 (tm-30) REVERT: A 608 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8305 (m) REVERT: E 460 ASN cc_start: 0.7967 (m-40) cc_final: 0.7450 (m110) outliers start: 19 outliers final: 4 residues processed: 161 average time/residue: 0.5129 time to fit residues: 86.3361 Evaluate side-chains 152 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 408 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.0970 chunk 67 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.0000 chunk 21 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 overall best weight: 0.0916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 493 HIS A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109068 restraints weight = 9210.166| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.69 r_work: 0.3410 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6662 Z= 0.103 Angle : 0.551 11.515 9061 Z= 0.278 Chirality : 0.042 0.332 952 Planarity : 0.004 0.049 1170 Dihedral : 7.803 94.496 955 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.62 % Allowed : 13.23 % Favored : 84.16 % 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 aren not related in a simple way. whole: -0.23 (0.31), residues: 786 helix: 1.14 (0.29), residues: 372 sheet: 0.93 (0.92), residues: 36 loop : -1.66 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.029 0.001 TYR A 521 PHE 0.008 0.001 PHE A 32 TRP 0.016 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6649) covalent geometry : angle 0.52950 ( 9035) SS BOND : bond 0.00428 ( 7) SS BOND : angle 0.98514 ( 14) hydrogen bonds : bond 0.04452 ( 261) hydrogen bonds : angle 4.19935 ( 744) metal coordination : bond 0.00114 ( 2) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 1.34462 ( 3) link_NAG-ASN : bond 0.00847 ( 3) link_NAG-ASN : angle 4.66890 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7739 (t70) cc_final: 0.7438 (t0) REVERT: A 323 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8288 (mmp) REVERT: A 341 LYS cc_start: 0.8426 (pttp) cc_final: 0.8183 (pttp) REVERT: A 597 GLU cc_start: 0.8238 (tp30) cc_final: 0.7938 (tm-30) REVERT: E 460 ASN cc_start: 0.7887 (m-40) cc_final: 0.7306 (m110) outliers start: 18 outliers final: 7 residues processed: 159 average time/residue: 0.5454 time to fit residues: 90.8840 Evaluate side-chains 152 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 98 GLN A 401 HIS A 578 ASN A 601 ASN E 394 ASN E 417 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.112764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103418 restraints weight = 9132.359| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.65 r_work: 0.3335 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6662 Z= 0.193 Angle : 0.633 8.471 9061 Z= 0.326 Chirality : 0.045 0.171 952 Planarity : 0.004 0.053 1170 Dihedral : 5.774 47.583 952 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.65 % Allowed : 13.08 % Favored : 82.27 % 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 aren not related in a simple way. whole: -0.40 (0.31), residues: 786 helix: 1.03 (0.28), residues: 377 sheet: 1.05 (0.92), residues: 36 loop : -1.84 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.034 0.002 TYR A 521 PHE 0.012 0.002 PHE A 588 TRP 0.017 0.002 TRP A 473 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 6649) covalent geometry : angle 0.62279 ( 9035) SS BOND : bond 0.00574 ( 7) SS BOND : angle 1.48503 ( 14) hydrogen bonds : bond 0.06061 ( 261) hydrogen bonds : angle 4.23451 ( 744) metal coordination : bond 0.00306 ( 2) link_BETA1-4 : bond 0.00577 ( 1) link_BETA1-4 : angle 1.80250 ( 3) link_NAG-ASN : bond 0.01045 ( 3) link_NAG-ASN : angle 3.02054 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.251 Fit side-chains REVERT: A 95 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8189 (mtt90) REVERT: A 190 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8018 (tmt) REVERT: A 206 ASP cc_start: 0.7859 (t70) cc_final: 0.7579 (t0) REVERT: A 323 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8339 (mmp) REVERT: A 334 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 341 LYS cc_start: 0.8400 (pttp) cc_final: 0.8171 (pttp) REVERT: A 350 ASP cc_start: 0.8124 (t0) cc_final: 0.7922 (t70) REVERT: A 597 GLU cc_start: 0.8184 (tp30) cc_final: 0.7903 (tm-30) REVERT: E 401 VAL cc_start: 0.8703 (p) cc_final: 0.8415 (t) outliers start: 32 outliers final: 12 residues processed: 171 average time/residue: 0.5344 time to fit residues: 95.6590 Evaluate side-chains 165 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 401 HIS A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104074 restraints weight = 9226.680| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.68 r_work: 0.3331 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6662 Z= 0.163 Angle : 0.619 9.972 9061 Z= 0.316 Chirality : 0.044 0.172 952 Planarity : 0.004 0.054 1170 Dihedral : 5.794 46.835 952 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.63 % Allowed : 14.39 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.31), residues: 786 helix: 1.07 (0.28), residues: 377 sheet: 0.85 (0.91), residues: 36 loop : -1.78 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.024 0.002 TYR A 521 PHE 0.010 0.001 PHE A 28 TRP 0.017 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6649) covalent geometry : angle 0.59471 ( 9035) SS BOND : bond 0.00662 ( 7) SS BOND : angle 1.62949 ( 14) hydrogen bonds : bond 0.05766 ( 261) hydrogen bonds : angle 4.21288 ( 744) metal coordination : bond 0.00196 ( 2) link_BETA1-4 : bond 0.00500 ( 1) link_BETA1-4 : angle 1.75600 ( 3) link_NAG-ASN : bond 0.01161 ( 3) link_NAG-ASN : angle 5.01493 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8207 (mtt90) REVERT: A 190 MET cc_start: 0.8300 (tmt) cc_final: 0.8014 (tmt) REVERT: A 206 ASP cc_start: 0.7850 (t70) cc_final: 0.7597 (t0) REVERT: A 323 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8291 (mmp) REVERT: A 334 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 350 ASP cc_start: 0.8198 (t0) cc_final: 0.7985 (t70) REVERT: A 536 ASP cc_start: 0.8112 (p0) cc_final: 0.7799 (p0) REVERT: A 581 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7983 (t) REVERT: A 597 GLU cc_start: 0.8188 (tp30) cc_final: 0.7916 (tm-30) REVERT: E 401 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8404 (t) outliers start: 25 outliers final: 12 residues processed: 163 average time/residue: 0.5438 time to fit residues: 92.7169 Evaluate side-chains 171 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 0.0070 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.113492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104132 restraints weight = 9180.077| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.66 r_work: 0.3333 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6662 Z= 0.146 Angle : 0.597 10.792 9061 Z= 0.306 Chirality : 0.043 0.173 952 Planarity : 0.004 0.055 1170 Dihedral : 5.096 46.362 952 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.63 % Allowed : 15.55 % Favored : 80.81 % 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 aren not related in a simple way. whole: -0.24 (0.31), residues: 786 helix: 1.16 (0.28), residues: 377 sheet: 0.85 (0.92), residues: 36 loop : -1.73 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.020 0.001 TYR A 521 PHE 0.009 0.001 PHE A 28 TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6649) covalent geometry : angle 0.57244 ( 9035) SS BOND : bond 0.00577 ( 7) SS BOND : angle 1.41762 ( 14) hydrogen bonds : bond 0.05438 ( 261) hydrogen bonds : angle 4.11559 ( 744) metal coordination : bond 0.00172 ( 2) link_BETA1-4 : bond 0.00331 ( 1) link_BETA1-4 : angle 1.63569 ( 3) link_NAG-ASN : bond 0.01050 ( 3) link_NAG-ASN : angle 5.04703 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7863 (t70) cc_final: 0.7576 (t0) REVERT: A 323 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8263 (mmp) REVERT: A 334 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 350 ASP cc_start: 0.8168 (t0) cc_final: 0.7943 (t0) REVERT: A 514 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7637 (ptp90) REVERT: A 536 ASP cc_start: 0.8070 (p0) cc_final: 0.7773 (p0) REVERT: A 581 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 597 GLU cc_start: 0.8188 (tp30) cc_final: 0.7909 (tm-30) REVERT: E 401 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8374 (t) REVERT: E 442 ASP cc_start: 0.8523 (m-30) cc_final: 0.8317 (m-30) outliers start: 25 outliers final: 6 residues processed: 161 average time/residue: 0.5256 time to fit residues: 88.3805 Evaluate side-chains 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 0.0370 chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 401 HIS A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104058 restraints weight = 9127.051| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.65 r_work: 0.3333 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6662 Z= 0.143 Angle : 0.593 10.955 9061 Z= 0.305 Chirality : 0.043 0.172 952 Planarity : 0.004 0.055 1170 Dihedral : 4.865 46.267 952 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.76 % Allowed : 16.86 % Favored : 80.38 % 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 aren not related in a simple way. whole: -0.16 (0.31), residues: 786 helix: 1.29 (0.28), residues: 369 sheet: 0.86 (0.90), residues: 36 loop : -1.70 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.035 0.001 TYR A 521 PHE 0.009 0.001 PHE A 28 TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6649) covalent geometry : angle 0.56992 ( 9035) SS BOND : bond 0.00548 ( 7) SS BOND : angle 1.32904 ( 14) hydrogen bonds : bond 0.05438 ( 261) hydrogen bonds : angle 4.09440 ( 744) metal coordination : bond 0.00170 ( 2) link_BETA1-4 : bond 0.00449 ( 1) link_BETA1-4 : angle 1.56105 ( 3) link_NAG-ASN : bond 0.01027 ( 3) link_NAG-ASN : angle 4.92733 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7884 (t70) cc_final: 0.7601 (t0) REVERT: A 323 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8270 (mmp) REVERT: A 334 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8322 (p) REVERT: A 514 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7654 (ptp90) REVERT: A 536 ASP cc_start: 0.8067 (p0) cc_final: 0.7779 (p0) REVERT: A 581 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7979 (t) REVERT: A 597 GLU cc_start: 0.8197 (tp30) cc_final: 0.7926 (tm-30) REVERT: E 401 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8371 (t) outliers start: 19 outliers final: 10 residues processed: 156 average time/residue: 0.5696 time to fit residues: 92.8732 Evaluate side-chains 160 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 0.1980 chunk 16 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 3 optimal weight: 0.0370 chunk 75 optimal weight: 0.2980 chunk 68 optimal weight: 0.0010 overall best weight: 0.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107232 restraints weight = 9255.364| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.67 r_work: 0.3384 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6662 Z= 0.104 Angle : 0.548 11.202 9061 Z= 0.281 Chirality : 0.041 0.191 952 Planarity : 0.004 0.054 1170 Dihedral : 4.549 45.111 952 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.62 % Allowed : 17.44 % Favored : 79.94 % 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 aren not related in a simple way. whole: -0.03 (0.31), residues: 786 helix: 1.44 (0.28), residues: 368 sheet: 0.92 (0.92), residues: 36 loop : -1.66 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 95 TYR 0.031 0.001 TYR A 521 PHE 0.006 0.001 PHE A 28 TRP 0.019 0.001 TRP A 163 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6649) covalent geometry : angle 0.52514 ( 9035) SS BOND : bond 0.00448 ( 7) SS BOND : angle 1.00319 ( 14) hydrogen bonds : bond 0.04252 ( 261) hydrogen bonds : angle 4.00834 ( 744) metal coordination : bond 0.00067 ( 2) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 1.28712 ( 3) link_NAG-ASN : bond 0.01028 ( 3) link_NAG-ASN : angle 4.79978 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7861 (t70) cc_final: 0.7523 (t0) REVERT: A 334 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (p) REVERT: A 536 ASP cc_start: 0.7994 (p0) cc_final: 0.7718 (p0) REVERT: A 597 GLU cc_start: 0.8214 (tp30) cc_final: 0.7957 (tm-30) REVERT: E 401 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8200 (t) outliers start: 18 outliers final: 9 residues processed: 151 average time/residue: 0.5282 time to fit residues: 83.4433 Evaluate side-chains 151 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.1980 chunk 47 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 18 optimal weight: 0.0170 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104908 restraints weight = 9238.411| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.67 r_work: 0.3362 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6662 Z= 0.136 Angle : 0.590 10.975 9061 Z= 0.305 Chirality : 0.043 0.197 952 Planarity : 0.004 0.054 1170 Dihedral : 4.555 45.732 952 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.18 % Allowed : 18.46 % Favored : 79.36 % 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 aren not related in a simple way. whole: -0.01 (0.31), residues: 786 helix: 1.51 (0.29), residues: 368 sheet: 0.76 (0.90), residues: 36 loop : -1.70 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.040 0.001 TYR A 521 PHE 0.008 0.001 PHE A 28 TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6649) covalent geometry : angle 0.56572 ( 9035) SS BOND : bond 0.00532 ( 7) SS BOND : angle 1.91331 ( 14) hydrogen bonds : bond 0.05055 ( 261) hydrogen bonds : angle 4.04588 ( 744) metal coordination : bond 0.00151 ( 2) link_BETA1-4 : bond 0.00479 ( 1) link_BETA1-4 : angle 1.41315 ( 3) link_NAG-ASN : bond 0.01067 ( 3) link_NAG-ASN : angle 4.78780 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7878 (t70) cc_final: 0.7582 (t0) REVERT: A 536 ASP cc_start: 0.8067 (p0) cc_final: 0.7780 (p0) REVERT: A 597 GLU cc_start: 0.8230 (tp30) cc_final: 0.7971 (tm-30) REVERT: E 401 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8339 (t) outliers start: 15 outliers final: 8 residues processed: 154 average time/residue: 0.5228 time to fit residues: 84.2710 Evaluate side-chains 153 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.0170 chunk 37 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103776 restraints weight = 9150.308| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.66 r_work: 0.3329 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6662 Z= 0.155 Angle : 0.613 10.693 9061 Z= 0.320 Chirality : 0.044 0.192 952 Planarity : 0.005 0.055 1170 Dihedral : 4.689 45.140 952 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.45 % Allowed : 19.33 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.31), residues: 786 helix: 1.48 (0.29), residues: 368 sheet: 0.53 (0.89), residues: 36 loop : -1.72 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.046 0.002 TYR A 521 PHE 0.009 0.001 PHE A 28 TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6649) covalent geometry : angle 0.59117 ( 9035) SS BOND : bond 0.00567 ( 7) SS BOND : angle 1.81382 ( 14) hydrogen bonds : bond 0.05521 ( 261) hydrogen bonds : angle 4.12206 ( 744) metal coordination : bond 0.00193 ( 2) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 1.37149 ( 3) link_NAG-ASN : bond 0.01098 ( 3) link_NAG-ASN : angle 4.71905 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7296 (mp0) REVERT: A 206 ASP cc_start: 0.7875 (t70) cc_final: 0.7594 (t0) REVERT: A 536 ASP cc_start: 0.8067 (p0) cc_final: 0.7786 (p0) REVERT: A 597 GLU cc_start: 0.8224 (tp30) cc_final: 0.7969 (tm-30) REVERT: E 401 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8399 (t) outliers start: 10 outliers final: 7 residues processed: 155 average time/residue: 0.5629 time to fit residues: 91.3343 Evaluate side-chains 155 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103352 restraints weight = 9105.407| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.65 r_work: 0.3320 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6662 Z= 0.166 Angle : 0.622 10.647 9061 Z= 0.325 Chirality : 0.045 0.220 952 Planarity : 0.005 0.055 1170 Dihedral : 4.749 45.921 952 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.31 % Allowed : 19.62 % Favored : 79.07 % 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 aren not related in a simple way. whole: -0.07 (0.31), residues: 786 helix: 1.44 (0.29), residues: 369 sheet: 0.52 (0.88), residues: 36 loop : -1.69 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.050 0.002 TYR A 521 PHE 0.010 0.001 PHE A 28 TRP 0.017 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6649) covalent geometry : angle 0.59955 ( 9035) SS BOND : bond 0.00567 ( 7) SS BOND : angle 1.79851 ( 14) hydrogen bonds : bond 0.05741 ( 261) hydrogen bonds : angle 4.16332 ( 744) metal coordination : bond 0.00193 ( 2) link_BETA1-4 : bond 0.00400 ( 1) link_BETA1-4 : angle 1.41304 ( 3) link_NAG-ASN : bond 0.01126 ( 3) link_NAG-ASN : angle 4.74026 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.08 seconds wall clock time: 47 minutes 33.10 seconds (2853.10 seconds total)