Starting phenix.real_space_refine on Fri Aug 22 17:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrl_37779/08_2025/8wrl_37779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrl_37779/08_2025/8wrl_37779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrl_37779/08_2025/8wrl_37779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrl_37779/08_2025/8wrl_37779.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrl_37779/08_2025/8wrl_37779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrl_37779/08_2025/8wrl_37779.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.083 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 4143 2.51 5 N 1070 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6472 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 13, 'TRANS': 182} 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.27, per 1000 atoms: 0.20 Number of scatterers: 6472 At special positions: 0 Unit cell: (74.336, 89.688, 117.968, 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 1222 8.00 N 1070 7.00 C 4143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 B 601 " - " ASN B 343 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 330.4 milliseconds Enol-peptide restraints added in 8.3 microseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 52.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.514A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.090A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.289A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.564A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix removed outlier: 4.002A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) 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 281 removed outlier: 3.718A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.765A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.529A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 376 through 385 removed outlier: 3.566A 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 398 through 413 removed outlier: 4.600A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.821A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.601A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.025A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.917A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.723A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.594A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) 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: 6.042A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.809A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.446A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 301 hydrogen bonds defined for protein. 843 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: 0.97 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1177 1.33 - 1.45: 1839 1.45 - 1.57: 3582 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6656 Sorted by residual: bond pdb=" CG HIS A 378 " pdb=" CD2 HIS A 378 " ideal model delta sigma weight residual 1.354 1.318 0.036 1.10e-02 8.26e+03 1.05e+01 bond pdb=" N THR A 371 " pdb=" CA THR A 371 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 7.00e+00 bond pdb=" CA ALA A 372 " pdb=" CB ALA A 372 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.68e-02 3.54e+03 6.84e+00 bond pdb=" CG HIS A 373 " pdb=" CD2 HIS A 373 " ideal model delta sigma weight residual 1.354 1.326 0.028 1.10e-02 8.26e+03 6.49e+00 bond pdb=" N GLU A 375 " pdb=" CA GLU A 375 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.41e+00 ... (remaining 6651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 8925 2.58 - 5.15: 96 5.15 - 7.73: 21 7.73 - 10.31: 2 10.31 - 12.88: 2 Bond angle restraints: 9046 Sorted by residual: angle pdb=" N MET A 376 " pdb=" CA MET A 376 " pdb=" C MET A 376 " ideal model delta sigma weight residual 114.31 101.82 12.49 1.29e+00 6.01e-01 9.37e+01 angle pdb=" C HIS A 378 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 121.02 108.14 12.88 1.51e+00 4.39e-01 7.28e+01 angle pdb=" CA HIS A 373 " pdb=" CB HIS A 373 " pdb=" CG HIS A 373 " ideal model delta sigma weight residual 113.80 121.23 -7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" N GLU A 375 " pdb=" CA GLU A 375 " pdb=" C GLU A 375 " ideal model delta sigma weight residual 112.88 104.91 7.97 1.29e+00 6.01e-01 3.82e+01 angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 118.66 -4.86 1.00e+00 1.00e+00 2.36e+01 ... (remaining 9041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 3448 21.10 - 42.19: 432 42.19 - 63.29: 82 63.29 - 84.39: 17 84.39 - 105.49: 18 Dihedral angle restraints: 3997 sinusoidal: 1677 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 22.41 70.59 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -45.95 -40.05 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA TRP A 349 " pdb=" C TRP A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 724 0.046 - 0.091: 171 0.091 - 0.137: 56 0.137 - 0.182: 6 0.182 - 0.227: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA GLU A 375 " pdb=" N GLU A 375 " pdb=" C GLU A 375 " pdb=" CB GLU A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR A 122 " pdb=" CA THR A 122 " pdb=" OG1 THR A 122 " pdb=" CG2 THR A 122 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA MET A 376 " pdb=" N MET A 376 " pdb=" C MET A 376 " pdb=" CB MET A 376 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 956 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 370 " -0.019 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C LEU A 370 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 370 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 371 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " 0.052 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO B 479 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 378 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C HIS A 378 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS A 378 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 379 " 0.015 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 22 2.40 - 3.02: 3617 3.02 - 3.65: 9842 3.65 - 4.27: 14297 4.27 - 4.90: 24817 Nonbonded interactions: 52595 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O LYS A 441 " model vdw 1.771 3.040 nonbonded pdb=" CB PRO A 346 " pdb=" SD MET A 360 " model vdw 1.931 3.800 nonbonded pdb=" O ALA A 372 " pdb=" CG MET A 376 " model vdw 2.076 3.440 nonbonded pdb=" CD1 ILE A 358 " pdb=" SD MET A 376 " model vdw 2.152 3.820 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.229 3.040 ... (remaining 52590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 0.065 6667 Z= 0.216 Angle : 0.701 12.884 9073 Z= 0.410 Chirality : 0.045 0.227 959 Planarity : 0.005 0.076 1166 Dihedral : 19.509 105.486 2489 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.58 % Allowed : 23.34 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.30), residues: 786 helix: 0.69 (0.27), residues: 365 sheet: -0.64 (0.76), residues: 35 loop : -0.96 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.030 0.002 TYR A 243 PHE 0.009 0.001 PHE A 32 TRP 0.010 0.001 TRP A 594 HIS 0.013 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6656) covalent geometry : angle 0.69921 ( 9046) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.66505 ( 12) hydrogen bonds : bond 0.13046 ( 301) hydrogen bonds : angle 5.41717 ( 843) link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 1.35417 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.232 Fit side-chains REVERT: A 442 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7571 (mm-40) REVERT: A 483 GLU cc_start: 0.7827 (mp0) cc_final: 0.7485 (mp0) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.0642 time to fit residues: 7.7010 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 468 ILE 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: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.197363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.149780 restraints weight = 6832.175| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.20 r_work: 0.3262 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6667 Z= 0.134 Angle : 0.532 8.095 9073 Z= 0.267 Chirality : 0.042 0.190 959 Planarity : 0.004 0.038 1166 Dihedral : 8.701 60.267 965 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.59 % Allowed : 21.90 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.31), residues: 786 helix: 0.96 (0.28), residues: 377 sheet: -0.40 (0.78), residues: 35 loop : -0.85 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.014 0.001 TYR A 41 PHE 0.010 0.001 PHE A 32 TRP 0.007 0.001 TRP B 436 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6656) covalent geometry : angle 0.52953 ( 9046) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.57366 ( 12) hydrogen bonds : bond 0.04215 ( 301) hydrogen bonds : angle 4.26703 ( 843) link_NAG-ASN : bond 0.00383 ( 5) link_NAG-ASN : angle 1.44725 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.197 Fit side-chains REVERT: A 35 GLU cc_start: 0.7991 (tp30) cc_final: 0.7768 (tp30) REVERT: A 87 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7122 (tm-30) REVERT: A 201 ASP cc_start: 0.7991 (t0) cc_final: 0.7764 (t0) REVERT: A 299 ASP cc_start: 0.6940 (m-30) cc_final: 0.6561 (m-30) REVERT: A 483 GLU cc_start: 0.7897 (mp0) cc_final: 0.7484 (mp0) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 0.0636 time to fit residues: 8.6888 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.199272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.151599 restraints weight = 6813.117| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.10 r_work: 0.3285 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6667 Z= 0.103 Angle : 0.496 6.098 9073 Z= 0.246 Chirality : 0.040 0.247 959 Planarity : 0.003 0.030 1166 Dihedral : 5.605 56.928 963 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.17 % Allowed : 21.90 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.31), residues: 786 helix: 1.12 (0.28), residues: 385 sheet: -0.13 (0.79), residues: 35 loop : -0.93 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.011 0.001 TYR A 41 PHE 0.009 0.001 PHE A 369 TRP 0.006 0.001 TRP A 165 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6656) covalent geometry : angle 0.49034 ( 9046) SS BOND : bond 0.00089 ( 6) SS BOND : angle 0.53696 ( 12) hydrogen bonds : bond 0.03755 ( 301) hydrogen bonds : angle 3.99474 ( 843) link_NAG-ASN : bond 0.00381 ( 5) link_NAG-ASN : angle 1.87648 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.217 Fit side-chains REVERT: A 35 GLU cc_start: 0.8059 (tp30) cc_final: 0.7794 (tp30) REVERT: A 87 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 201 ASP cc_start: 0.7935 (t70) cc_final: 0.7691 (t0) REVERT: A 297 MET cc_start: 0.6997 (tpp) cc_final: 0.6758 (mmt) REVERT: A 299 ASP cc_start: 0.7045 (m-30) cc_final: 0.6730 (m-30) REVERT: A 398 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: A 544 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5444 (mt) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.0598 time to fit residues: 8.8868 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.193708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146242 restraints weight = 6962.123| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.32 r_work: 0.3209 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6667 Z= 0.183 Angle : 0.554 5.431 9073 Z= 0.281 Chirality : 0.042 0.213 959 Planarity : 0.004 0.029 1166 Dihedral : 5.317 47.566 963 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.89 % Allowed : 21.47 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.31), residues: 786 helix: 1.14 (0.28), residues: 377 sheet: -0.34 (0.80), residues: 35 loop : -0.85 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.017 0.002 TYR A 381 PHE 0.012 0.001 PHE A 32 TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6656) covalent geometry : angle 0.54847 ( 9046) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.43705 ( 12) hydrogen bonds : bond 0.04468 ( 301) hydrogen bonds : angle 4.13802 ( 843) link_NAG-ASN : bond 0.00321 ( 5) link_NAG-ASN : angle 1.99440 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.195 Fit side-chains REVERT: A 35 GLU cc_start: 0.8048 (tp30) cc_final: 0.7725 (tp30) REVERT: A 87 GLU cc_start: 0.7619 (tm-30) cc_final: 0.6998 (tm-30) REVERT: A 299 ASP cc_start: 0.7077 (m-30) cc_final: 0.6773 (m-30) REVERT: A 398 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: A 483 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7856 (mm-30) REVERT: A 544 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5602 (mt) outliers start: 27 outliers final: 16 residues processed: 102 average time/residue: 0.0609 time to fit residues: 8.7646 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.195557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133999 restraints weight = 6947.829| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.40 r_work: 0.3307 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6667 Z= 0.143 Angle : 0.514 5.330 9073 Z= 0.261 Chirality : 0.041 0.218 959 Planarity : 0.003 0.030 1166 Dihedral : 4.989 46.233 963 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.32 % Allowed : 20.89 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.31), residues: 786 helix: 1.25 (0.28), residues: 377 sheet: -0.60 (0.71), residues: 45 loop : -0.79 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.037 0.002 TYR A 237 PHE 0.009 0.001 PHE A 32 TRP 0.019 0.001 TRP A 271 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6656) covalent geometry : angle 0.50908 ( 9046) SS BOND : bond 0.00102 ( 6) SS BOND : angle 0.45264 ( 12) hydrogen bonds : bond 0.04235 ( 301) hydrogen bonds : angle 4.05188 ( 843) link_NAG-ASN : bond 0.00326 ( 5) link_NAG-ASN : angle 1.83030 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.175 Fit side-chains REVERT: A 35 GLU cc_start: 0.8084 (tp30) cc_final: 0.7774 (tp30) REVERT: A 87 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 97 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7796 (mt) REVERT: A 150 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6946 (pp20) REVERT: A 237 TYR cc_start: 0.6799 (t80) cc_final: 0.6571 (t80) REVERT: A 299 ASP cc_start: 0.7107 (m-30) cc_final: 0.6804 (m-30) REVERT: A 398 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: A 544 ILE cc_start: 0.6029 (OUTLIER) cc_final: 0.5683 (mt) REVERT: B 472 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7630 (tt) outliers start: 30 outliers final: 15 residues processed: 105 average time/residue: 0.0502 time to fit residues: 7.8230 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.196799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148992 restraints weight = 6888.164| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.26 r_work: 0.3238 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6667 Z= 0.130 Angle : 0.511 5.338 9073 Z= 0.260 Chirality : 0.041 0.216 959 Planarity : 0.003 0.029 1166 Dihedral : 4.748 43.875 963 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.18 % Allowed : 21.33 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.31), residues: 786 helix: 1.17 (0.28), residues: 383 sheet: -0.30 (0.79), residues: 35 loop : -0.70 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.029 0.001 TYR A 237 PHE 0.008 0.001 PHE A 523 TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6656) covalent geometry : angle 0.50609 ( 9046) SS BOND : bond 0.00096 ( 6) SS BOND : angle 0.48355 ( 12) hydrogen bonds : bond 0.04040 ( 301) hydrogen bonds : angle 4.00464 ( 843) link_NAG-ASN : bond 0.00307 ( 5) link_NAG-ASN : angle 1.73551 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.227 Fit side-chains REVERT: A 35 GLU cc_start: 0.8012 (tp30) cc_final: 0.7666 (tp30) REVERT: A 87 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 150 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: A 201 ASP cc_start: 0.8167 (t70) cc_final: 0.7964 (t0) REVERT: A 297 MET cc_start: 0.6962 (tpp) cc_final: 0.6739 (mmt) REVERT: A 299 ASP cc_start: 0.7128 (m-30) cc_final: 0.6917 (m-30) REVERT: A 398 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 467 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: A 544 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5558 (mt) REVERT: A 589 GLU cc_start: 0.8327 (tp30) cc_final: 0.8119 (tp30) REVERT: B 471 GLU cc_start: 0.7691 (pt0) cc_final: 0.7464 (pt0) outliers start: 29 outliers final: 17 residues processed: 107 average time/residue: 0.0524 time to fit residues: 8.2714 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.197094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134957 restraints weight = 6840.421| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.57 r_work: 0.3300 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6667 Z= 0.127 Angle : 0.502 5.416 9073 Z= 0.256 Chirality : 0.041 0.218 959 Planarity : 0.003 0.029 1166 Dihedral : 4.608 42.670 963 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.89 % Allowed : 21.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.31), residues: 786 helix: 1.17 (0.28), residues: 384 sheet: -0.34 (0.78), residues: 35 loop : -0.69 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.023 0.001 TYR A 237 PHE 0.010 0.001 PHE A 523 TRP 0.014 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6656) covalent geometry : angle 0.49837 ( 9046) SS BOND : bond 0.00091 ( 6) SS BOND : angle 0.48522 ( 12) hydrogen bonds : bond 0.04004 ( 301) hydrogen bonds : angle 3.98875 ( 843) link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 1.61248 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.234 Fit side-chains REVERT: A 35 GLU cc_start: 0.8067 (tp30) cc_final: 0.7707 (tp30) REVERT: A 87 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7130 (tm-30) REVERT: A 150 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6990 (pp20) REVERT: A 297 MET cc_start: 0.6899 (tpp) cc_final: 0.6588 (tpp) REVERT: A 299 ASP cc_start: 0.7159 (m-30) cc_final: 0.6950 (m-30) REVERT: A 398 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: A 467 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: A 483 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7819 (mp0) REVERT: A 544 ILE cc_start: 0.6055 (OUTLIER) cc_final: 0.5705 (mt) REVERT: A 589 GLU cc_start: 0.8335 (tp30) cc_final: 0.8120 (tp30) REVERT: B 471 GLU cc_start: 0.7768 (pt0) cc_final: 0.7547 (pt0) outliers start: 27 outliers final: 21 residues processed: 101 average time/residue: 0.0604 time to fit residues: 8.8965 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.199264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151925 restraints weight = 6785.341| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.14 r_work: 0.3276 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6667 Z= 0.111 Angle : 0.489 5.524 9073 Z= 0.248 Chirality : 0.040 0.215 959 Planarity : 0.003 0.029 1166 Dihedral : 4.431 41.089 963 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.75 % Allowed : 21.33 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.31), residues: 786 helix: 1.30 (0.28), residues: 381 sheet: -0.21 (0.80), residues: 35 loop : -0.62 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 393 TYR 0.021 0.001 TYR A 237 PHE 0.008 0.001 PHE A 523 TRP 0.014 0.001 TRP A 168 HIS 0.003 0.000 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6656) covalent geometry : angle 0.48584 ( 9046) SS BOND : bond 0.00079 ( 6) SS BOND : angle 0.52568 ( 12) hydrogen bonds : bond 0.03816 ( 301) hydrogen bonds : angle 3.92380 ( 843) link_NAG-ASN : bond 0.00322 ( 5) link_NAG-ASN : angle 1.45823 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.176 Fit side-chains REVERT: A 35 GLU cc_start: 0.8035 (tp30) cc_final: 0.7686 (tp30) REVERT: A 87 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 150 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7013 (pp20) REVERT: A 398 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: A 467 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: A 483 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7778 (mp0) REVERT: A 544 ILE cc_start: 0.5930 (OUTLIER) cc_final: 0.5567 (mt) REVERT: B 471 GLU cc_start: 0.7659 (pt0) cc_final: 0.7395 (pt0) outliers start: 26 outliers final: 19 residues processed: 102 average time/residue: 0.0594 time to fit residues: 8.7515 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.0980 chunk 72 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.201807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.155448 restraints weight = 6885.445| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.03 r_work: 0.3308 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6667 Z= 0.108 Angle : 0.495 7.367 9073 Z= 0.250 Chirality : 0.040 0.215 959 Planarity : 0.003 0.029 1166 Dihedral : 4.343 39.817 963 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.75 % Allowed : 21.04 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.31), residues: 786 helix: 1.45 (0.28), residues: 375 sheet: -0.06 (0.81), residues: 35 loop : -0.72 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.019 0.001 TYR A 237 PHE 0.009 0.001 PHE A 523 TRP 0.014 0.001 TRP A 168 HIS 0.003 0.000 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6656) covalent geometry : angle 0.49231 ( 9046) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.55015 ( 12) hydrogen bonds : bond 0.03721 ( 301) hydrogen bonds : angle 3.91840 ( 843) link_NAG-ASN : bond 0.00328 ( 5) link_NAG-ASN : angle 1.39374 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.212 Fit side-chains REVERT: A 35 GLU cc_start: 0.7968 (tp30) cc_final: 0.7617 (tp30) REVERT: A 87 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 150 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7042 (pp20) REVERT: A 467 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6934 (mt-10) REVERT: A 483 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7747 (mp0) REVERT: A 544 ILE cc_start: 0.5896 (OUTLIER) cc_final: 0.5549 (mt) REVERT: B 471 GLU cc_start: 0.7605 (pt0) cc_final: 0.7375 (pt0) outliers start: 26 outliers final: 19 residues processed: 101 average time/residue: 0.0510 time to fit residues: 7.6173 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.197447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.150513 restraints weight = 6811.208| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.12 r_work: 0.3288 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6667 Z= 0.124 Angle : 0.518 7.041 9073 Z= 0.263 Chirality : 0.041 0.221 959 Planarity : 0.003 0.029 1166 Dihedral : 4.407 39.708 961 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.31 % Allowed : 21.90 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.31), residues: 786 helix: 1.34 (0.28), residues: 381 sheet: -0.64 (0.78), residues: 40 loop : -0.57 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.019 0.001 TYR A 237 PHE 0.029 0.001 PHE B 374 TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6656) covalent geometry : angle 0.51333 ( 9046) SS BOND : bond 0.00247 ( 6) SS BOND : angle 1.26067 ( 12) hydrogen bonds : bond 0.03823 ( 301) hydrogen bonds : angle 4.00548 ( 843) link_NAG-ASN : bond 0.00335 ( 5) link_NAG-ASN : angle 1.41265 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.216 Fit side-chains REVERT: A 35 GLU cc_start: 0.8018 (tp30) cc_final: 0.7643 (tp30) REVERT: A 87 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 150 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: A 467 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: A 483 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 527 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 544 ILE cc_start: 0.5921 (OUTLIER) cc_final: 0.5575 (mt) REVERT: B 378 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7216 (mmtm) REVERT: B 471 GLU cc_start: 0.7658 (pt0) cc_final: 0.7436 (pt0) outliers start: 23 outliers final: 18 residues processed: 100 average time/residue: 0.0502 time to fit residues: 7.4181 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 64 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.197935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150685 restraints weight = 6860.548| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.21 r_work: 0.3299 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6667 Z= 0.125 Angle : 0.515 7.011 9073 Z= 0.261 Chirality : 0.041 0.227 959 Planarity : 0.003 0.029 1166 Dihedral : 4.380 40.231 961 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.31 % Allowed : 21.90 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.31), residues: 786 helix: 1.37 (0.28), residues: 378 sheet: -0.52 (0.79), residues: 40 loop : -0.67 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.019 0.001 TYR A 237 PHE 0.030 0.001 PHE B 374 TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6656) covalent geometry : angle 0.51146 ( 9046) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.84580 ( 12) hydrogen bonds : bond 0.03856 ( 301) hydrogen bonds : angle 4.00056 ( 843) link_NAG-ASN : bond 0.00336 ( 5) link_NAG-ASN : angle 1.42866 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.40 seconds wall clock time: 26 minutes 32.58 seconds (1592.58 seconds total)