Starting phenix.real_space_refine on Thu Jul 2 04:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2026/7fdh_31543.cif" } resolution = 3.72 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4150 2.51 5 N 1069 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.33, per 1000 atoms: 0.36 Number of scatterers: 6488 At special positions: 0 Unit cell: (122.72, 78, 76.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1232 8.00 N 1069 7.00 C 4150 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 NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 392.4 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 57.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.872A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.565A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.609A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.560A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.779A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.812A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.756A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (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 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.588A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.974A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.846A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.962A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.211A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.963A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.970A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.808A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.955A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.531A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 Processing helix chain 'E' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.960A 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 352 removed outlier: 5.692A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 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 474 320 hydrogen bonds defined for protein. 893 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: 0.87 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2079 1.35 - 1.47: 1767 1.47 - 1.59: 2768 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6672 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C5 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 6667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8902 2.20 - 4.39: 150 4.39 - 6.59: 15 6.59 - 8.79: 3 8.79 - 10.98: 1 Bond angle restraints: 9071 Sorted by residual: angle pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " ideal model delta sigma weight residual 114.40 125.38 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" N CYS A 141 " pdb=" CA CYS A 141 " pdb=" C CYS A 141 " ideal model delta sigma weight residual 108.96 115.21 -6.25 1.49e+00 4.50e-01 1.76e+01 angle pdb=" N CYS E 379 " pdb=" CA CYS E 379 " pdb=" C CYS E 379 " ideal model delta sigma weight residual 108.60 114.00 -5.40 1.46e+00 4.69e-01 1.37e+01 angle pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 114.40 121.73 -7.33 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS A 133 " pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " ideal model delta sigma weight residual 114.40 121.68 -7.28 2.30e+00 1.89e-01 1.00e+01 ... (remaining 9066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3459 17.59 - 35.19: 345 35.19 - 52.78: 66 52.78 - 70.37: 12 70.37 - 87.96: 10 Dihedral angle restraints: 3892 sinusoidal: 1567 harmonic: 2325 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 11.10 81.90 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+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 51.66 41.34 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 3889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 862 0.078 - 0.156: 97 0.156 - 0.234: 1 0.234 - 0.312: 1 0.312 - 0.390: 1 Chirality restraints: 962 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA CYS A 141 " pdb=" N CYS A 141 " pdb=" C CYS A 141 " pdb=" CB CYS A 141 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASN E 343 " pdb=" N ASN E 343 " pdb=" C ASN E 343 " pdb=" CB ASN E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 959 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 146 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 33 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ASN A 33 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN A 33 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS A 34 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 583 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.024 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 196 2.70 - 3.25: 6959 3.25 - 3.80: 10455 3.80 - 4.35: 13483 4.35 - 4.90: 22150 Nonbonded interactions: 53243 Sorted by model distance: nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.145 3.040 nonbonded pdb=" O VAL E 367 " pdb=" OG SER E 371 " model vdw 2.147 3.040 nonbonded pdb=" NE2 GLN A 221 " pdb=" OD1 ASP A 225 " model vdw 2.213 3.120 nonbonded pdb=" OG SER A 511 " pdb=" NH2 ARG A 514 " model vdw 2.224 3.120 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.236 3.040 ... (remaining 53238 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.880 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6684 Z= 0.206 Angle : 0.751 10.983 9100 Z= 0.430 Chirality : 0.048 0.390 962 Planarity : 0.005 0.051 1170 Dihedral : 14.578 87.964 2381 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.29 % Allowed : 2.88 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.25), residues: 788 helix: -1.53 (0.22), residues: 377 sheet: -0.84 (0.69), residues: 50 loop : -2.49 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 169 TYR 0.021 0.002 TYR E 453 PHE 0.015 0.002 PHE A 314 TRP 0.024 0.002 TRP A 473 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 ( 6672) covalent geometry : angle 0.73489 / 0.43 ( 9071) SS BOND : bond 0.00425 / 0.29 ( 7) SS BOND : angle 3.24811 / 1.85 ( 14) hydrogen bonds : bond 0.14443 / 8.83 ( 320) hydrogen bonds : angle 6.54927 / 4.79 ( 893) link_NAG-ASN : bond 0.00866 / 0.61 ( 5) link_NAG-ASN : angle 2.30054 / 1.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8102 (m-40) cc_final: 0.7867 (t0) REVERT: A 98 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7860 (tp-100) REVERT: A 123 MET cc_start: 0.7787 (mtm) cc_final: 0.7464 (mtt) REVERT: A 165 TRP cc_start: 0.7254 (t60) cc_final: 0.5965 (t60) REVERT: A 455 MET cc_start: 0.8600 (tmm) cc_final: 0.8285 (tmm) REVERT: A 478 TRP cc_start: 0.7962 (m100) cc_final: 0.7587 (m100) REVERT: A 497 TYR cc_start: 0.7564 (m-80) cc_final: 0.6574 (m-80) REVERT: A 505 HIS cc_start: 0.7573 (m90) cc_final: 0.7157 (m-70) REVERT: E 366 SER cc_start: 0.8329 (m) cc_final: 0.8047 (p) REVERT: E 396 TYR cc_start: 0.7613 (m-80) cc_final: 0.6939 (m-10) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.0917 time to fit residues: 14.9181 Evaluate side-chains 84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN A 221 GLN A 239 HIS A 290 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN E 334 ASN E 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082197 restraints weight = 13710.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084885 restraints weight = 7271.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086638 restraints weight = 4941.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087575 restraints weight = 3917.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088256 restraints weight = 3452.342| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6684 Z= 0.178 Angle : 0.675 9.683 9100 Z= 0.344 Chirality : 0.047 0.312 962 Planarity : 0.005 0.066 1170 Dihedral : 4.857 22.329 863 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.29 % Allowed : 11.37 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.28), residues: 788 helix: 0.00 (0.25), residues: 388 sheet: -0.33 (0.72), residues: 51 loop : -1.38 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 219 TYR 0.021 0.002 TYR A 183 PHE 0.012 0.001 PHE E 392 TRP 0.017 0.002 TRP A 473 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6672) covalent geometry : angle 0.66922 / 0.34 ( 9071) SS BOND : bond 0.00816 / 0.56 ( 7) SS BOND : angle 1.79615 / 0.90 ( 14) hydrogen bonds : bond 0.05292 / 3.56 ( 320) hydrogen bonds : angle 5.10107 / 3.74 ( 893) link_NAG-ASN : bond 0.00698 / 0.49 ( 5) link_NAG-ASN : angle 1.61869 / 0.98 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8137 (m-40) cc_final: 0.7867 (t0) REVERT: A 114 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8359 (ptpp) REVERT: A 123 MET cc_start: 0.7969 (mtm) cc_final: 0.7736 (mtt) REVERT: A 165 TRP cc_start: 0.7233 (t60) cc_final: 0.6398 (t60) REVERT: A 222 LEU cc_start: 0.8579 (tp) cc_final: 0.8375 (tp) REVERT: A 455 MET cc_start: 0.8589 (tmm) cc_final: 0.8306 (tmm) REVERT: A 497 TYR cc_start: 0.7861 (m-80) cc_final: 0.6675 (m-80) REVERT: A 505 HIS cc_start: 0.7575 (m90) cc_final: 0.7173 (m-70) REVERT: A 557 MET cc_start: 0.9206 (tmm) cc_final: 0.8749 (tmm) REVERT: E 340 GLU cc_start: 0.7849 (pt0) cc_final: 0.7524 (mm-30) REVERT: E 392 PHE cc_start: 0.8463 (m-80) cc_final: 0.8180 (m-10) REVERT: E 424 LYS cc_start: 0.7797 (tptt) cc_final: 0.7525 (tppt) REVERT: E 450 ASN cc_start: 0.8451 (m110) cc_final: 0.8173 (t0) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.0815 time to fit residues: 11.2544 Evaluate side-chains 86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS B ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084732 restraints weight = 25732.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089272 restraints weight = 10218.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090446 restraints weight = 5095.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090788 restraints weight = 4170.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091156 restraints weight = 3821.566| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6684 Z= 0.124 Angle : 0.614 8.904 9100 Z= 0.311 Chirality : 0.043 0.226 962 Planarity : 0.004 0.042 1170 Dihedral : 4.367 19.157 862 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.29 % Allowed : 11.94 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.29), residues: 788 helix: 0.76 (0.26), residues: 391 sheet: 0.07 (0.71), residues: 51 loop : -0.90 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 466 TYR 0.019 0.002 TYR A 183 PHE 0.011 0.001 PHE A 230 TRP 0.018 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6672) covalent geometry : angle 0.61067 / 0.31 ( 9071) SS BOND : bond 0.00450 / 0.28 ( 7) SS BOND : angle 1.10898 / 0.57 ( 14) hydrogen bonds : bond 0.04494 / 3.06 ( 320) hydrogen bonds : angle 4.62281 / 3.38 ( 893) link_NAG-ASN : bond 0.00521 / 0.36 ( 5) link_NAG-ASN : angle 1.46772 / 0.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8157 (m-40) cc_final: 0.7869 (t0) REVERT: A 123 MET cc_start: 0.7808 (mtm) cc_final: 0.7598 (mtt) REVERT: A 165 TRP cc_start: 0.7201 (t60) cc_final: 0.6595 (t60) REVERT: A 455 MET cc_start: 0.8387 (tmm) cc_final: 0.8133 (tmm) REVERT: A 481 LYS cc_start: 0.7581 (mttt) cc_final: 0.7299 (mttt) REVERT: A 489 GLU cc_start: 0.8774 (pm20) cc_final: 0.8562 (pm20) REVERT: A 497 TYR cc_start: 0.7927 (m-80) cc_final: 0.6689 (m-80) REVERT: A 505 HIS cc_start: 0.7541 (m90) cc_final: 0.7079 (m-70) REVERT: A 557 MET cc_start: 0.9160 (tmm) cc_final: 0.8713 (tmm) REVERT: E 340 GLU cc_start: 0.8082 (pt0) cc_final: 0.7405 (mm-30) REVERT: E 392 PHE cc_start: 0.8607 (m-80) cc_final: 0.8240 (m-10) REVERT: E 424 LYS cc_start: 0.7872 (tptt) cc_final: 0.7588 (tppt) outliers start: 8 outliers final: 4 residues processed: 113 average time/residue: 0.0821 time to fit residues: 12.3455 Evaluate side-chains 94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082229 restraints weight = 32061.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086315 restraints weight = 12057.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088991 restraints weight = 6686.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090724 restraints weight = 4648.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091689 restraints weight = 3739.469| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6684 Z= 0.134 Angle : 0.636 9.152 9100 Z= 0.314 Chirality : 0.044 0.208 962 Planarity : 0.004 0.037 1170 Dihedral : 4.286 18.461 862 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 13.09 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.30), residues: 788 helix: 1.08 (0.26), residues: 387 sheet: 0.42 (0.72), residues: 50 loop : -0.66 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 457 TYR 0.019 0.001 TYR A 183 PHE 0.016 0.001 PHE A 603 TRP 0.053 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6672) covalent geometry : angle 0.63208 / 0.31 ( 9071) SS BOND : bond 0.00637 / 0.44 ( 7) SS BOND : angle 1.40406 / 0.71 ( 14) hydrogen bonds : bond 0.04382 / 2.99 ( 320) hydrogen bonds : angle 4.48163 / 3.29 ( 893) link_NAG-ASN : bond 0.00509 / 0.35 ( 5) link_NAG-ASN : angle 1.37687 / 0.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8154 (m-40) cc_final: 0.7906 (t0) REVERT: A 161 ARG cc_start: 0.6826 (mtp85) cc_final: 0.6112 (mtp180) REVERT: A 165 TRP cc_start: 0.7240 (t60) cc_final: 0.6150 (t60) REVERT: A 455 MET cc_start: 0.8358 (tmm) cc_final: 0.8079 (tmm) REVERT: A 478 TRP cc_start: 0.7921 (m100) cc_final: 0.7546 (m100) REVERT: A 505 HIS cc_start: 0.7540 (m90) cc_final: 0.7051 (m-70) REVERT: E 340 GLU cc_start: 0.7860 (pt0) cc_final: 0.7337 (mm-30) outliers start: 9 outliers final: 9 residues processed: 100 average time/residue: 0.0732 time to fit residues: 9.7071 Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 0.0050 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081382 restraints weight = 25450.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084973 restraints weight = 10726.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087368 restraints weight = 6351.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088891 restraints weight = 4611.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089828 restraints weight = 3804.835| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6684 Z= 0.169 Angle : 0.645 9.048 9100 Z= 0.324 Chirality : 0.045 0.213 962 Planarity : 0.005 0.057 1170 Dihedral : 4.399 19.120 862 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 15.54 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.30), residues: 788 helix: 0.98 (0.26), residues: 387 sheet: 0.28 (0.72), residues: 51 loop : -0.49 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 357 TYR 0.019 0.002 TYR E 453 PHE 0.019 0.002 PHE A 327 TRP 0.036 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 6672) covalent geometry : angle 0.63971 / 0.32 ( 9071) SS BOND : bond 0.00334 / 0.20 ( 7) SS BOND : angle 1.50200 / 0.77 ( 14) hydrogen bonds : bond 0.04622 / 3.14 ( 320) hydrogen bonds : angle 4.57142 / 3.37 ( 893) link_NAG-ASN : bond 0.00672 / 0.46 ( 5) link_NAG-ASN : angle 1.57923 / 0.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8165 (m-40) cc_final: 0.7918 (t0) REVERT: A 455 MET cc_start: 0.8389 (tmm) cc_final: 0.7996 (tmm) REVERT: A 478 TRP cc_start: 0.8037 (m100) cc_final: 0.7594 (m100) REVERT: A 505 HIS cc_start: 0.7616 (m90) cc_final: 0.7134 (m-70) REVERT: A 557 MET cc_start: 0.9135 (tmm) cc_final: 0.8659 (tmm) REVERT: E 340 GLU cc_start: 0.7777 (pt0) cc_final: 0.7406 (mm-30) REVERT: E 392 PHE cc_start: 0.8254 (m-10) cc_final: 0.7982 (m-10) REVERT: E 507 PRO cc_start: 0.9344 (Cg_exo) cc_final: 0.9091 (Cg_endo) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.0841 time to fit residues: 11.6221 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.110661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084864 restraints weight = 15475.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087810 restraints weight = 7855.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089737 restraints weight = 5200.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090962 restraints weight = 4050.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091704 restraints weight = 3484.268| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6684 Z= 0.139 Angle : 0.633 9.502 9100 Z= 0.315 Chirality : 0.043 0.193 962 Planarity : 0.004 0.045 1170 Dihedral : 4.300 17.592 862 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 16.12 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.30), residues: 788 helix: 1.10 (0.26), residues: 387 sheet: 0.52 (0.73), residues: 50 loop : -0.34 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.019 0.002 TYR A 183 PHE 0.019 0.001 PHE A 327 TRP 0.029 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6672) covalent geometry : angle 0.62811 / 0.31 ( 9071) SS BOND : bond 0.00365 / 0.23 ( 7) SS BOND : angle 1.55281 / 0.81 ( 14) hydrogen bonds : bond 0.04331 / 2.94 ( 320) hydrogen bonds : angle 4.44358 / 3.27 ( 893) link_NAG-ASN : bond 0.00575 / 0.40 ( 5) link_NAG-ASN : angle 1.51931 / 0.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8161 (m-40) cc_final: 0.7903 (t0) REVERT: A 249 MET cc_start: 0.7892 (mmm) cc_final: 0.7674 (mmm) REVERT: A 455 MET cc_start: 0.8258 (tmm) cc_final: 0.7850 (tmm) REVERT: A 505 HIS cc_start: 0.7597 (m90) cc_final: 0.7105 (m-70) REVERT: A 557 MET cc_start: 0.9109 (tmm) cc_final: 0.8629 (tmm) REVERT: E 340 GLU cc_start: 0.7784 (pt0) cc_final: 0.7368 (mm-30) REVERT: E 357 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7192 (ttm-80) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.0804 time to fit residues: 10.8922 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083836 restraints weight = 13769.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086512 restraints weight = 7455.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088314 restraints weight = 5157.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089310 restraints weight = 4109.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090051 restraints weight = 3618.232| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6684 Z= 0.179 Angle : 0.672 9.356 9100 Z= 0.336 Chirality : 0.044 0.179 962 Planarity : 0.004 0.040 1170 Dihedral : 4.452 18.938 862 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.16 % Allowed : 17.27 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.30), residues: 788 helix: 0.99 (0.26), residues: 386 sheet: 0.50 (0.72), residues: 50 loop : -0.29 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.019 0.002 TYR E 453 PHE 0.020 0.002 PHE A 327 TRP 0.025 0.002 TRP A 477 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 6672) covalent geometry : angle 0.66621 / 0.33 ( 9071) SS BOND : bond 0.00478 / 0.31 ( 7) SS BOND : angle 1.75762 / 0.94 ( 14) hydrogen bonds : bond 0.04686 / 3.16 ( 320) hydrogen bonds : angle 4.59856 / 3.39 ( 893) link_NAG-ASN : bond 0.00707 / 0.50 ( 5) link_NAG-ASN : angle 1.66707 / 0.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8156 (m-40) cc_final: 0.7896 (t0) REVERT: A 505 HIS cc_start: 0.7579 (m90) cc_final: 0.7099 (m-70) REVERT: A 557 MET cc_start: 0.9105 (tmm) cc_final: 0.8632 (tmm) REVERT: E 340 GLU cc_start: 0.7717 (pt0) cc_final: 0.7389 (mm-30) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.0744 time to fit residues: 10.2748 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085166 restraints weight = 20669.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088280 restraints weight = 9325.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089173 restraints weight = 5636.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089671 restraints weight = 4564.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090458 restraints weight = 4331.299| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6684 Z= 0.158 Angle : 0.678 9.624 9100 Z= 0.339 Chirality : 0.044 0.174 962 Planarity : 0.004 0.048 1170 Dihedral : 4.397 17.640 862 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.16 % Allowed : 18.71 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.30), residues: 788 helix: 1.04 (0.26), residues: 384 sheet: 0.53 (0.71), residues: 50 loop : -0.14 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.019 0.002 TYR E 369 PHE 0.036 0.002 PHE E 392 TRP 0.026 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6672) covalent geometry : angle 0.67364 / 0.34 ( 9071) SS BOND : bond 0.00320 / 0.18 ( 7) SS BOND : angle 1.53693 / 0.80 ( 14) hydrogen bonds : bond 0.04529 / 3.04 ( 320) hydrogen bonds : angle 4.55208 / 3.34 ( 893) link_NAG-ASN : bond 0.00628 / 0.44 ( 5) link_NAG-ASN : angle 1.54756 / 0.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8190 (m-40) cc_final: 0.7909 (t0) REVERT: A 376 MET cc_start: 0.8893 (mmm) cc_final: 0.8654 (tpt) REVERT: A 505 HIS cc_start: 0.7611 (m90) cc_final: 0.7140 (m-70) REVERT: A 557 MET cc_start: 0.9069 (tmm) cc_final: 0.8615 (tmm) REVERT: A 572 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: E 340 GLU cc_start: 0.7867 (pt0) cc_final: 0.7433 (mm-30) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.0825 time to fit residues: 11.2607 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.112373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083792 restraints weight = 27581.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087657 restraints weight = 11211.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090190 restraints weight = 6491.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091832 restraints weight = 4643.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.092890 restraints weight = 3791.624| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6684 Z= 0.137 Angle : 0.679 9.625 9100 Z= 0.337 Chirality : 0.043 0.200 962 Planarity : 0.004 0.048 1170 Dihedral : 4.285 20.629 862 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.16 % Allowed : 18.56 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.30), residues: 788 helix: 1.09 (0.27), residues: 386 sheet: 0.51 (0.70), residues: 50 loop : -0.05 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.018 0.001 TYR A 183 PHE 0.019 0.002 PHE A 603 TRP 0.026 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6672) covalent geometry : angle 0.67420 / 0.34 ( 9071) SS BOND : bond 0.00442 / 0.28 ( 7) SS BOND : angle 1.68430 / 0.89 ( 14) hydrogen bonds : bond 0.04302 / 2.90 ( 320) hydrogen bonds : angle 4.48455 / 3.28 ( 893) link_NAG-ASN : bond 0.00533 / 0.37 ( 5) link_NAG-ASN : angle 1.54495 / 0.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8168 (m-40) cc_final: 0.7937 (t0) REVERT: A 481 LYS cc_start: 0.7523 (mmmm) cc_final: 0.7211 (mmmt) REVERT: A 505 HIS cc_start: 0.7636 (m90) cc_final: 0.7160 (m-70) REVERT: A 557 MET cc_start: 0.9046 (tmm) cc_final: 0.8591 (tmm) REVERT: A 572 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: E 340 GLU cc_start: 0.7612 (pt0) cc_final: 0.7303 (mm-30) REVERT: E 469 SER cc_start: 0.8926 (t) cc_final: 0.8659 (p) REVERT: E 511 VAL cc_start: 0.9098 (t) cc_final: 0.8866 (p) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.0847 time to fit residues: 12.2959 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.113247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088435 restraints weight = 21109.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091332 restraints weight = 9458.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092460 restraints weight = 5917.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092809 restraints weight = 4738.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.093301 restraints weight = 4472.763| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6684 Z= 0.141 Angle : 0.683 9.882 9100 Z= 0.341 Chirality : 0.043 0.199 962 Planarity : 0.004 0.043 1170 Dihedral : 4.267 16.807 862 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.87 % Allowed : 18.85 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.31), residues: 788 helix: 1.10 (0.26), residues: 387 sheet: 0.48 (0.70), residues: 50 loop : 0.07 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 357 TYR 0.018 0.001 TYR A 183 PHE 0.019 0.001 PHE A 603 TRP 0.023 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6672) covalent geometry : angle 0.67894 / 0.34 ( 9071) SS BOND : bond 0.00325 / 0.18 ( 7) SS BOND : angle 1.62444 / 0.88 ( 14) hydrogen bonds : bond 0.04283 / 2.87 ( 320) hydrogen bonds : angle 4.46848 / 3.27 ( 893) link_NAG-ASN : bond 0.00539 / 0.38 ( 5) link_NAG-ASN : angle 1.42962 / 0.84 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8220 (m-40) cc_final: 0.7969 (t0) REVERT: A 497 TYR cc_start: 0.7910 (m-80) cc_final: 0.6406 (m-80) REVERT: A 505 HIS cc_start: 0.7501 (m90) cc_final: 0.7049 (m-70) REVERT: A 557 MET cc_start: 0.9028 (tmm) cc_final: 0.8609 (tmm) REVERT: A 572 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8274 (m-40) REVERT: E 340 GLU cc_start: 0.7697 (pt0) cc_final: 0.7341 (mm-30) REVERT: E 469 SER cc_start: 0.8925 (t) cc_final: 0.8678 (p) REVERT: E 511 VAL cc_start: 0.9096 (t) cc_final: 0.8882 (p) outliers start: 12 outliers final: 11 residues processed: 105 average time/residue: 0.0772 time to fit residues: 10.8844 Evaluate side-chains 106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.111797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086957 restraints weight = 19894.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089883 restraints weight = 9310.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091070 restraints weight = 5675.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091649 restraints weight = 4497.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091884 restraints weight = 4132.136| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6684 Z= 0.163 Angle : 0.704 8.729 9100 Z= 0.350 Chirality : 0.044 0.194 962 Planarity : 0.004 0.050 1170 Dihedral : 4.370 20.150 862 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 18.85 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.31), residues: 788 helix: 1.04 (0.27), residues: 389 sheet: 0.36 (0.69), residues: 50 loop : 0.02 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 357 TYR 0.018 0.001 TYR A 183 PHE 0.019 0.002 PHE A 603 TRP 0.025 0.002 TRP A 477 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6672) covalent geometry : angle 0.69896 / 0.35 ( 9071) SS BOND : bond 0.00352 / 0.20 ( 7) SS BOND : angle 1.60401 / 0.86 ( 14) hydrogen bonds : bond 0.04418 / 2.96 ( 320) hydrogen bonds : angle 4.51760 / 3.32 ( 893) link_NAG-ASN : bond 0.00641 / 0.45 ( 5) link_NAG-ASN : angle 1.59611 / 0.94 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.64 seconds wall clock time: 24 minutes 29.24 seconds (1469.24 seconds total)