Starting phenix.real_space_refine on Sat May 10 16:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc2_37090/05_2025/8kc2_37090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc2_37090/05_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_37090/05_2025/8kc2_37090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc2_37090/05_2025/8kc2_37090.map" model { file = "/net/cci-nas-00/data/ceres_data/8kc2_37090/05_2025/8kc2_37090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc2_37090/05_2025/8kc2_37090.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.57, per 1000 atoms: 1.32 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: 1.63 Conformation dependent library (CDL) restraints added in 834.4 milliseconds 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: 0.62 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: 1.53 Time building geometry restraints manager: 0.89 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: 33.270 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.730 Find NCS groups from input model: 0.070 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP A 473 HIS 0.010 0.002 HIS A 378 PHE 0.024 0.002 PHE A 400 TYR 0.019 0.002 TYR A 521 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 3) link_NAG-ASN : angle 4.08540 ( 9) link_BETA1-4 : bond 0.00339 ( 1) link_BETA1-4 : angle 0.97418 ( 3) hydrogen bonds : bond 0.16728 ( 261) hydrogen bonds : angle 5.97924 ( 744) metal coordination : bond 0.20136 ( 2) SS BOND : bond 0.00574 ( 7) SS BOND : angle 2.43349 ( 14) covalent geometry : bond 0.00457 ( 6649) covalent geometry : angle 0.75248 ( 9035) *********************** 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 : 0.737 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: 1.3534 time to fit residues: 247.7016 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 : 0.712 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0000 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.0040 chunk 70 optimal weight: 0.9980 overall best weight: 0.1396 ------------------------------------------------------------------------------- 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 493 HIS A 578 ASN A 601 ASN E 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107918 restraints weight = 9193.195| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.68 r_work: 0.3389 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6662 Z= 0.119 Angle : 0.585 9.355 9061 Z= 0.302 Chirality : 0.043 0.270 952 Planarity : 0.004 0.049 1170 Dihedral : 9.013 105.469 957 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.27 % Rotamer: Outliers : 2.76 % Allowed : 11.48 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.31), residues: 786 helix: 0.84 (0.28), residues: 373 sheet: 0.89 (0.89), residues: 36 loop : -1.69 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.008 0.001 PHE E 374 TYR 0.021 0.001 TYR A 385 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00893 ( 3) link_NAG-ASN : angle 4.09466 ( 9) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 1.26837 ( 3) hydrogen bonds : bond 0.05231 ( 261) hydrogen bonds : angle 4.39630 ( 744) metal coordination : bond 0.00414 ( 2) SS BOND : bond 0.00505 ( 7) SS BOND : angle 1.35628 ( 14) covalent geometry : bond 0.00261 ( 6649) covalent geometry : angle 0.56859 ( 9035) *********************** 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 172 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.764 Fit side-chains REVERT: A 34 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7148 (tp40) REVERT: A 206 ASP cc_start: 0.7778 (t70) cc_final: 0.7506 (t0) REVERT: A 323 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: A 341 LYS cc_start: 0.8445 (pttp) cc_final: 0.8192 (pttp) REVERT: A 597 GLU cc_start: 0.8217 (tp30) cc_final: 0.7915 (tm-30) REVERT: A 608 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8314 (m) outliers start: 19 outliers final: 6 residues processed: 160 average time/residue: 1.2176 time to fit residues: 203.7777 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 : 0.667 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain E residue 335 LEU 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 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.0870 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.2314 ------------------------------------------------------------------------------- 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 ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105869 restraints weight = 9286.642| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.66 r_work: 0.3379 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6662 Z= 0.135 Angle : 0.592 11.093 9061 Z= 0.302 Chirality : 0.043 0.303 952 Planarity : 0.004 0.052 1170 Dihedral : 7.738 92.603 955 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.91 % Allowed : 13.37 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.31), residues: 786 helix: 1.02 (0.28), residues: 377 sheet: 1.07 (0.92), residues: 36 loop : -1.82 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 32 TYR 0.031 0.002 TYR A 521 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01233 ( 3) link_NAG-ASN : angle 4.68532 ( 9) link_BETA1-4 : bond 0.00489 ( 1) link_BETA1-4 : angle 1.51392 ( 3) hydrogen bonds : bond 0.05380 ( 261) hydrogen bonds : angle 4.23190 ( 744) metal coordination : bond 0.00153 ( 2) SS BOND : bond 0.00511 ( 7) SS BOND : angle 1.25467 ( 14) covalent geometry : bond 0.00308 ( 6649) covalent geometry : angle 0.57167 ( 9035) *********************** 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 180 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7343 (tttp) REVERT: A 95 ARG cc_start: 0.8395 (mtt90) cc_final: 0.8163 (mtt90) REVERT: A 206 ASP cc_start: 0.7789 (t70) cc_final: 0.7540 (t0) REVERT: A 323 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8324 (mmp) REVERT: A 341 LYS cc_start: 0.8409 (pttp) cc_final: 0.8180 (pttp) REVERT: A 597 GLU cc_start: 0.8188 (tp30) cc_final: 0.7888 (tm-30) outliers start: 20 outliers final: 9 residues processed: 168 average time/residue: 1.2621 time to fit residues: 222.0743 Evaluate side-chains 162 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 408 ARG 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 71 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 0.0040 chunk 17 optimal weight: 0.0020 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 overall best weight: 0.0536 ------------------------------------------------------------------------------- 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 E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108297 restraints weight = 9326.015| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.71 r_work: 0.3397 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1902 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= 0.102 Angle : 0.544 10.423 9061 Z= 0.275 Chirality : 0.041 0.165 952 Planarity : 0.004 0.051 1170 Dihedral : 5.740 50.411 952 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.05 % Allowed : 14.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.31), residues: 786 helix: 1.27 (0.29), residues: 366 sheet: 1.03 (0.94), residues: 36 loop : -1.66 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.002 0.000 HIS A 241 PHE 0.007 0.001 PHE A 32 TYR 0.039 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 3) link_NAG-ASN : angle 2.76307 ( 9) link_BETA1-4 : bond 0.00620 ( 1) link_BETA1-4 : angle 1.59393 ( 3) hydrogen bonds : bond 0.04186 ( 261) hydrogen bonds : angle 4.13068 ( 744) metal coordination : bond 0.00079 ( 2) SS BOND : bond 0.00405 ( 7) SS BOND : angle 0.94622 ( 14) covalent geometry : bond 0.00217 ( 6649) covalent geometry : angle 0.53586 ( 9035) *********************** 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 168 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7782 (t70) cc_final: 0.7533 (t0) REVERT: A 341 LYS cc_start: 0.8428 (pttp) cc_final: 0.8193 (pttp) REVERT: A 597 GLU cc_start: 0.8242 (tp30) cc_final: 0.7957 (tm-30) REVERT: E 442 ASP cc_start: 0.8419 (m-30) cc_final: 0.8189 (m-30) REVERT: E 460 ASN cc_start: 0.8046 (m-40) cc_final: 0.7567 (m110) outliers start: 21 outliers final: 6 residues processed: 160 average time/residue: 1.2006 time to fit residues: 201.3524 Evaluate side-chains 152 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 1 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 3 optimal weight: 0.0470 chunk 8 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 0.1416 ------------------------------------------------------------------------------- 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 E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107272 restraints weight = 9176.244| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.66 r_work: 0.3386 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1982 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= 0.110 Angle : 0.560 9.594 9061 Z= 0.282 Chirality : 0.042 0.177 952 Planarity : 0.004 0.051 1170 Dihedral : 5.604 45.937 952 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.91 % Allowed : 15.41 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.31), residues: 786 helix: 1.33 (0.29), residues: 368 sheet: 0.91 (0.94), residues: 36 loop : -1.69 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 32 TYR 0.021 0.001 TYR A 521 ARG 0.004 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 3) link_NAG-ASN : angle 4.16906 ( 9) link_BETA1-4 : bond 0.00478 ( 1) link_BETA1-4 : angle 1.60229 ( 3) hydrogen bonds : bond 0.04457 ( 261) hydrogen bonds : angle 4.04310 ( 744) metal coordination : bond 0.00083 ( 2) SS BOND : bond 0.00492 ( 7) SS BOND : angle 1.23229 ( 14) covalent geometry : bond 0.00245 ( 6649) covalent geometry : angle 0.54221 ( 9035) *********************** 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 165 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7324 (ttpp) cc_final: 0.6810 (tttm) REVERT: A 35 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: A 206 ASP cc_start: 0.7799 (t70) cc_final: 0.7570 (t0) REVERT: A 597 GLU cc_start: 0.8217 (tp30) cc_final: 0.7946 (tm-30) REVERT: E 401 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8257 (t) REVERT: E 442 ASP cc_start: 0.8420 (m-30) cc_final: 0.8196 (m-30) REVERT: E 460 ASN cc_start: 0.8095 (m-40) cc_final: 0.7598 (m110) outliers start: 20 outliers final: 10 residues processed: 158 average time/residue: 1.1667 time to fit residues: 193.4475 Evaluate side-chains 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 334 THR 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 394 ASN Chi-restraints excluded: chain E residue 401 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 21 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 70 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 578 ASN A 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103398 restraints weight = 9133.353| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.65 r_work: 0.3340 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6662 Z= 0.157 Angle : 0.603 9.656 9061 Z= 0.310 Chirality : 0.044 0.172 952 Planarity : 0.004 0.053 1170 Dihedral : 5.173 46.855 952 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.91 % Allowed : 15.55 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 786 helix: 1.32 (0.29), residues: 368 sheet: 0.65 (0.89), residues: 36 loop : -1.74 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 32 TYR 0.035 0.002 TYR A 521 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00776 ( 3) link_NAG-ASN : angle 4.04556 ( 9) link_BETA1-4 : bond 0.00468 ( 1) link_BETA1-4 : angle 1.68226 ( 3) hydrogen bonds : bond 0.05448 ( 261) hydrogen bonds : angle 4.09595 ( 744) metal coordination : bond 0.00179 ( 2) SS BOND : bond 0.00562 ( 7) SS BOND : angle 1.40321 ( 14) covalent geometry : bond 0.00372 ( 6649) covalent geometry : angle 0.58672 ( 9035) *********************** 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 174 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7437 (ttpp) cc_final: 0.6945 (tttt) REVERT: A 35 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: A 206 ASP cc_start: 0.7832 (t70) cc_final: 0.7573 (t0) REVERT: A 597 GLU cc_start: 0.8184 (tp30) cc_final: 0.7907 (tm-30) REVERT: E 401 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8391 (t) REVERT: E 403 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.7499 (ttm-80) outliers start: 20 outliers final: 11 residues processed: 159 average time/residue: 1.2491 time to fit residues: 208.0137 Evaluate side-chains 161 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 305 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 600 LYS 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 483 VAL Chi-restraints excluded: chain E residue 514 SER 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 3 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 0.0870 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 58 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.1316 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106519 restraints weight = 9147.828| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.68 r_work: 0.3372 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6662 Z= 0.108 Angle : 0.539 7.174 9061 Z= 0.278 Chirality : 0.041 0.168 952 Planarity : 0.004 0.052 1170 Dihedral : 4.820 45.624 952 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.05 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.31), residues: 786 helix: 1.40 (0.28), residues: 368 sheet: 0.68 (0.90), residues: 36 loop : -1.69 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 32 TYR 0.023 0.001 TYR A 521 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 3) link_NAG-ASN : angle 3.16230 ( 9) link_BETA1-4 : bond 0.00426 ( 1) link_BETA1-4 : angle 1.42227 ( 3) hydrogen bonds : bond 0.04500 ( 261) hydrogen bonds : angle 4.05910 ( 744) metal coordination : bond 0.00063 ( 2) SS BOND : bond 0.00442 ( 7) SS BOND : angle 1.06713 ( 14) covalent geometry : bond 0.00236 ( 6649) covalent geometry : angle 0.52776 ( 9035) *********************** 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 166 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7242 (ttpp) cc_final: 0.6951 (ptmm) REVERT: A 35 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 206 ASP cc_start: 0.7830 (t70) cc_final: 0.7531 (t0) REVERT: A 536 ASP cc_start: 0.7997 (p0) cc_final: 0.7729 (p0) REVERT: A 597 GLU cc_start: 0.8213 (tp30) cc_final: 0.7946 (tm-30) REVERT: E 401 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8263 (t) REVERT: E 403 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7481 (ttm-80) REVERT: E 442 ASP cc_start: 0.8447 (m-30) cc_final: 0.8225 (m-30) REVERT: E 500 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8571 (p) outliers start: 21 outliers final: 11 residues processed: 153 average time/residue: 1.2221 time to fit residues: 195.6230 Evaluate side-chains 155 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 305 GLU 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 A residue 531 GLN Chi-restraints excluded: chain A residue 600 LYS 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 500 THR Chi-restraints excluded: chain E residue 514 SER 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 45 optimal weight: 0.0970 chunk 20 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 0.4980 chunk 77 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 19 optimal weight: 0.0030 overall best weight: 0.1186 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.116254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106838 restraints weight = 9147.991| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.67 r_work: 0.3378 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6662 Z= 0.107 Angle : 0.551 7.657 9061 Z= 0.281 Chirality : 0.042 0.236 952 Planarity : 0.004 0.052 1170 Dihedral : 4.681 45.528 952 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.33 % Allowed : 18.02 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 786 helix: 1.45 (0.28), residues: 368 sheet: 0.70 (0.91), residues: 36 loop : -1.64 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.003 0.000 HIS A 241 PHE 0.008 0.001 PHE A 32 TYR 0.029 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 3) link_NAG-ASN : angle 2.71687 ( 9) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 1.37521 ( 3) hydrogen bonds : bond 0.04388 ( 261) hydrogen bonds : angle 4.00264 ( 744) metal coordination : bond 0.00085 ( 2) SS BOND : bond 0.00425 ( 7) SS BOND : angle 1.02049 ( 14) covalent geometry : bond 0.00238 ( 6649) covalent geometry : angle 0.54350 ( 9035) *********************** 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 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7181 (ttpp) cc_final: 0.6897 (ptmm) REVERT: A 35 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: A 206 ASP cc_start: 0.7839 (t70) cc_final: 0.7535 (t0) REVERT: A 597 GLU cc_start: 0.8203 (tp30) cc_final: 0.7949 (tm-30) REVERT: E 401 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8253 (t) REVERT: E 403 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7466 (ttm-80) REVERT: E 460 ASN cc_start: 0.8177 (m-40) cc_final: 0.7716 (m110) REVERT: E 500 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8556 (p) outliers start: 16 outliers final: 9 residues processed: 150 average time/residue: 1.2471 time to fit residues: 195.8740 Evaluate side-chains 151 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 305 GLU 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 360 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER 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 37 optimal weight: 0.0370 chunk 18 optimal weight: 0.0030 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.2246 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.114584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105152 restraints weight = 9281.295| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.69 r_work: 0.3351 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6662 Z= 0.130 Angle : 0.568 9.056 9061 Z= 0.293 Chirality : 0.043 0.256 952 Planarity : 0.004 0.052 1170 Dihedral : 4.671 45.794 952 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.33 % Allowed : 17.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.31), residues: 786 helix: 1.47 (0.28), residues: 368 sheet: 0.65 (0.90), residues: 36 loop : -1.67 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 32 TYR 0.034 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01428 ( 3) link_NAG-ASN : angle 4.28544 ( 9) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 1.38460 ( 3) hydrogen bonds : bond 0.04856 ( 261) hydrogen bonds : angle 4.01123 ( 744) metal coordination : bond 0.00127 ( 2) SS BOND : bond 0.00459 ( 7) SS BOND : angle 1.14694 ( 14) covalent geometry : bond 0.00297 ( 6649) covalent geometry : angle 0.55018 ( 9035) *********************** 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 159 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6934 (ptmm) REVERT: A 35 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 206 ASP cc_start: 0.7861 (t70) cc_final: 0.7582 (t0) REVERT: A 536 ASP cc_start: 0.8015 (p0) cc_final: 0.7743 (p0) REVERT: A 597 GLU cc_start: 0.8223 (tp30) cc_final: 0.7960 (tm-30) REVERT: E 401 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8339 (t) REVERT: E 403 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7919 (ttm170) REVERT: E 442 ASP cc_start: 0.8462 (m-30) cc_final: 0.8239 (m-30) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 1.1617 time to fit residues: 184.0733 Evaluate side-chains 154 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 305 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 514 SER 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 45 optimal weight: 0.0170 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 13 optimal weight: 0.0870 chunk 73 optimal weight: 0.0570 chunk 32 optimal weight: 0.4980 overall best weight: 0.0892 ------------------------------------------------------------------------------- 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 ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107792 restraints weight = 9342.665| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.70 r_work: 0.3390 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6662 Z= 0.102 Angle : 0.540 9.975 9061 Z= 0.277 Chirality : 0.041 0.215 952 Planarity : 0.004 0.052 1170 Dihedral : 4.456 45.147 952 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.03 % Allowed : 18.46 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 786 helix: 1.60 (0.29), residues: 366 sheet: 0.68 (0.91), residues: 36 loop : -1.53 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.002 0.000 HIS A 241 PHE 0.007 0.001 PHE A 32 TYR 0.032 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01144 ( 3) link_NAG-ASN : angle 4.48421 ( 9) link_BETA1-4 : bond 0.00530 ( 1) link_BETA1-4 : angle 1.25385 ( 3) hydrogen bonds : bond 0.04074 ( 261) hydrogen bonds : angle 3.97310 ( 744) metal coordination : bond 0.00071 ( 2) SS BOND : bond 0.00392 ( 7) SS BOND : angle 0.90342 ( 14) covalent geometry : bond 0.00218 ( 6649) covalent geometry : angle 0.52039 ( 9035) ********************** 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 154 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 206 ASP cc_start: 0.7848 (t70) cc_final: 0.7486 (t0) REVERT: A 514 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7664 (ptp90) REVERT: A 597 GLU cc_start: 0.8221 (tp30) cc_final: 0.7976 (tm-30) REVERT: E 401 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8160 (t) REVERT: E 403 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7882 (ttm170) REVERT: E 460 ASN cc_start: 0.8064 (m-40) cc_final: 0.7523 (m110) outliers start: 14 outliers final: 7 residues processed: 148 average time/residue: 1.2649 time to fit residues: 196.6800 Evaluate side-chains 148 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 233 ILE 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 E residue 336 CYS Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 514 SER 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 42 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 0.0980 chunk 23 optimal weight: 0.3980 chunk 74 optimal weight: 0.0000 chunk 40 optimal weight: 0.4980 chunk 76 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1302 ------------------------------------------------------------------------------- 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 ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106142 restraints weight = 9453.981| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.70 r_work: 0.3376 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6662 Z= 0.107 Angle : 0.543 10.430 9061 Z= 0.279 Chirality : 0.042 0.217 952 Planarity : 0.004 0.052 1170 Dihedral : 4.370 45.199 952 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.60 % Allowed : 18.90 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.31), residues: 786 helix: 1.59 (0.29), residues: 368 sheet: 0.68 (0.91), residues: 36 loop : -1.61 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 32 TYR 0.035 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01087 ( 3) link_NAG-ASN : angle 4.47612 ( 9) link_BETA1-4 : bond 0.00426 ( 1) link_BETA1-4 : angle 1.24792 ( 3) hydrogen bonds : bond 0.04302 ( 261) hydrogen bonds : angle 3.96665 ( 744) metal coordination : bond 0.00105 ( 2) SS BOND : bond 0.00400 ( 7) SS BOND : angle 0.98514 ( 14) covalent geometry : bond 0.00234 ( 6649) covalent geometry : angle 0.52274 ( 9035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6446.39 seconds wall clock time: 112 minutes 51.85 seconds (6771.85 seconds total)