Starting phenix.real_space_refine on Sat May 10 15:31:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrl_37779/05_2025/8wrl_37779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrl_37779/05_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_37779/05_2025/8wrl_37779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrl_37779/05_2025/8wrl_37779.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrl_37779/05_2025/8wrl_37779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrl_37779/05_2025/8wrl_37779.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.23, per 1000 atoms: 0.65 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: 1.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.72 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: 1.80 Time building geometry restraints manager: 1.78 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: 0.800 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (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 TRP 0.010 0.001 TRP A 594 HIS 0.013 0.001 HIS A 373 PHE 0.009 0.001 PHE A 32 TYR 0.030 0.002 TYR A 243 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 1.35417 ( 15) hydrogen bonds : bond 0.13046 ( 301) hydrogen bonds : angle 5.41717 ( 843) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.66505 ( 12) covalent geometry : bond 0.00433 ( 6656) covalent geometry : angle 0.69921 ( 9046) *********************** 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 : 0.758 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: 0.1861 time to fit residues: 22.2772 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 : 0.766 ------------------------------------------------------------------------------- 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 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 overall best weight: 1.0302 ------------------------------------------------------------------------------- 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 = 0.196984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149773 restraints weight = 6717.097| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.12 r_work: 0.3237 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0929 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= 0.145 Angle : 0.542 8.028 9073 Z= 0.273 Chirality : 0.042 0.182 959 Planarity : 0.004 0.038 1166 Dihedral : 8.575 59.333 965 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 21.76 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.31), residues: 786 helix: 0.93 (0.28), residues: 377 sheet: -0.45 (0.79), residues: 35 loop : -0.86 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.005 0.001 HIS A 378 PHE 0.012 0.001 PHE A 32 TYR 0.015 0.001 TYR A 41 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 5) link_NAG-ASN : angle 1.50883 ( 15) hydrogen bonds : bond 0.04251 ( 301) hydrogen bonds : angle 4.27950 ( 843) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.54628 ( 12) covalent geometry : bond 0.00334 ( 6656) covalent geometry : angle 0.53903 ( 9046) *********************** 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.722 Fit side-chains REVERT: A 35 GLU cc_start: 0.8040 (tp30) cc_final: 0.7825 (tp30) REVERT: A 87 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 299 ASP cc_start: 0.6980 (m-30) cc_final: 0.6604 (m-30) REVERT: A 544 ILE cc_start: 0.5874 (OUTLIER) cc_final: 0.5519 (mt) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 0.1743 time to fit residues: 23.0915 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 544 ILE Chi-restraints excluded: chain A residue 547 SER 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 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 62 optimal weight: 0.0010 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.199879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152397 restraints weight = 6825.838| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.08 r_work: 0.3291 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1191 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= 0.105 Angle : 0.500 6.226 9073 Z= 0.248 Chirality : 0.040 0.242 959 Planarity : 0.003 0.030 1166 Dihedral : 5.630 57.571 963 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.88 % Allowed : 21.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 786 helix: 1.09 (0.28), residues: 385 sheet: -0.14 (0.79), residues: 35 loop : -0.94 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 34 PHE 0.007 0.001 PHE A 523 TYR 0.011 0.001 TYR A 41 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 5) link_NAG-ASN : angle 1.87733 ( 15) hydrogen bonds : bond 0.03790 ( 301) hydrogen bonds : angle 4.02035 ( 843) SS BOND : bond 0.00088 ( 6) SS BOND : angle 0.53687 ( 12) covalent geometry : bond 0.00226 ( 6656) covalent geometry : angle 0.49420 ( 9046) *********************** 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 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.670 Fit side-chains REVERT: A 35 GLU cc_start: 0.8017 (tp30) cc_final: 0.7752 (tp30) REVERT: A 87 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 297 MET cc_start: 0.6956 (tpp) cc_final: 0.6738 (mmt) REVERT: A 299 ASP cc_start: 0.7059 (m-30) cc_final: 0.6731 (m-30) REVERT: A 398 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: A 544 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5457 (mt) outliers start: 20 outliers final: 11 residues processed: 101 average time/residue: 0.1609 time to fit residues: 22.4377 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 32 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.195558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.147873 restraints weight = 6913.713| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.28 r_work: 0.3245 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1274 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= 0.164 Angle : 0.535 5.461 9073 Z= 0.270 Chirality : 0.042 0.211 959 Planarity : 0.004 0.029 1166 Dihedral : 5.285 48.295 963 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.03 % Allowed : 20.89 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 786 helix: 1.19 (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 TRP 0.009 0.001 TRP A 566 HIS 0.004 0.001 HIS A 34 PHE 0.010 0.001 PHE A 523 TYR 0.014 0.002 TYR B 453 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 5) link_NAG-ASN : angle 1.95153 ( 15) hydrogen bonds : bond 0.04292 ( 301) hydrogen bonds : angle 4.09512 ( 843) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.46059 ( 12) covalent geometry : bond 0.00380 ( 6656) covalent geometry : angle 0.52917 ( 9046) *********************** 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 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.665 Fit side-chains REVERT: A 35 GLU cc_start: 0.8059 (tp30) cc_final: 0.7708 (tp30) REVERT: A 87 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 299 ASP cc_start: 0.7073 (m-30) cc_final: 0.6756 (m-30) REVERT: A 398 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 544 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5586 (mt) outliers start: 28 outliers final: 16 residues processed: 104 average time/residue: 0.1488 time to fit residues: 21.8917 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 283 VAL Chi-restraints excluded: chain A residue 291 ILE 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 64 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 2.4162 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.190817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145885 restraints weight = 6827.586| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.11 r_work: 0.3141 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6667 Z= 0.260 Angle : 0.614 6.437 9073 Z= 0.317 Chirality : 0.045 0.251 959 Planarity : 0.004 0.030 1166 Dihedral : 5.463 47.929 963 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.76 % Allowed : 20.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.31), residues: 786 helix: 0.79 (0.27), residues: 383 sheet: -0.94 (0.70), residues: 45 loop : -0.83 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 566 HIS 0.006 0.001 HIS A 34 PHE 0.014 0.002 PHE A 32 TYR 0.032 0.002 TYR A 237 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 5) link_NAG-ASN : angle 2.17965 ( 15) hydrogen bonds : bond 0.05149 ( 301) hydrogen bonds : angle 4.44317 ( 843) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.42348 ( 12) covalent geometry : bond 0.00616 ( 6656) covalent geometry : angle 0.60845 ( 9046) *********************** 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: 33 poor density : 81 time to evaluate : 0.651 Fit side-chains REVERT: A 35 GLU cc_start: 0.8283 (tp30) cc_final: 0.8051 (tp30) REVERT: A 87 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 150 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6973 (pp20) REVERT: A 237 TYR cc_start: 0.6885 (t80) cc_final: 0.6678 (t80) REVERT: A 299 ASP cc_start: 0.7138 (m-30) cc_final: 0.6819 (m-30) REVERT: A 398 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: A 455 MET cc_start: 0.7469 (ttp) cc_final: 0.7256 (ttp) REVERT: A 544 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5952 (mt) REVERT: B 378 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7865 (mmtm) REVERT: B 472 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7998 (tt) outliers start: 33 outliers final: 21 residues processed: 105 average time/residue: 0.1328 time to fit residues: 20.3635 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 473 TRP 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 415 THR 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 51 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.195383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.149880 restraints weight = 6758.757| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.97 r_work: 0.3201 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6667 Z= 0.114 Angle : 0.506 6.721 9073 Z= 0.257 Chirality : 0.041 0.223 959 Planarity : 0.003 0.030 1166 Dihedral : 4.827 45.174 963 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.32 % Allowed : 20.32 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.31), residues: 786 helix: 1.18 (0.28), residues: 377 sheet: -0.77 (0.68), residues: 45 loop : -0.80 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 271 HIS 0.003 0.001 HIS A 493 PHE 0.010 0.001 PHE A 327 TYR 0.028 0.001 TYR A 237 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 5) link_NAG-ASN : angle 1.70672 ( 15) hydrogen bonds : bond 0.04018 ( 301) hydrogen bonds : angle 4.05879 ( 843) SS BOND : bond 0.00078 ( 6) SS BOND : angle 0.47741 ( 12) covalent geometry : bond 0.00251 ( 6656) covalent geometry : angle 0.50177 ( 9046) *********************** 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 119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.717 Fit side-chains REVERT: A 35 GLU cc_start: 0.8096 (tp30) cc_final: 0.7854 (tp30) REVERT: A 87 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 150 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: A 297 MET cc_start: 0.7238 (tpp) cc_final: 0.6915 (tpp) REVERT: A 299 ASP cc_start: 0.7209 (m-30) cc_final: 0.6899 (m-30) REVERT: A 398 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: A 467 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: A 483 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7856 (mp0) REVERT: A 544 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5709 (mt) REVERT: B 471 GLU cc_start: 0.7770 (pt0) cc_final: 0.7563 (pt0) outliers start: 30 outliers final: 16 residues processed: 112 average time/residue: 0.1420 time to fit residues: 22.8725 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 489 TYR 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 71 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.195673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148003 restraints weight = 6748.057| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.18 r_work: 0.3254 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6667 Z= 0.138 Angle : 0.523 6.631 9073 Z= 0.267 Chirality : 0.042 0.230 959 Planarity : 0.003 0.029 1166 Dihedral : 4.787 43.235 963 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.89 % Allowed : 21.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 786 helix: 1.14 (0.28), residues: 383 sheet: -0.75 (0.70), residues: 45 loop : -0.74 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE A 523 TYR 0.024 0.001 TYR A 237 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 5) link_NAG-ASN : angle 1.66019 ( 15) hydrogen bonds : bond 0.04144 ( 301) hydrogen bonds : angle 4.06031 ( 843) SS BOND : bond 0.00227 ( 6) SS BOND : angle 1.06739 ( 12) covalent geometry : bond 0.00316 ( 6656) covalent geometry : angle 0.51748 ( 9046) *********************** 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 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.647 Fit side-chains REVERT: A 35 GLU cc_start: 0.7992 (tp30) cc_final: 0.7660 (tp30) REVERT: A 87 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 150 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: A 297 MET cc_start: 0.6962 (tpp) cc_final: 0.6599 (tpp) REVERT: A 299 ASP cc_start: 0.7177 (m-30) cc_final: 0.6961 (m-30) REVERT: A 398 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: A 467 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: A 483 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7802 (mp0) REVERT: A 544 ILE cc_start: 0.5908 (OUTLIER) cc_final: 0.5559 (mt) REVERT: B 471 GLU cc_start: 0.7646 (pt0) cc_final: 0.7418 (pt0) outliers start: 27 outliers final: 20 residues processed: 104 average time/residue: 0.1354 time to fit residues: 20.5460 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 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 379 CYS 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 14 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.197574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148973 restraints weight = 6764.197| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.96 r_work: 0.3284 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1623 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= 0.111 Angle : 0.495 6.183 9073 Z= 0.253 Chirality : 0.041 0.220 959 Planarity : 0.003 0.029 1166 Dihedral : 4.570 41.781 963 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.89 % Allowed : 21.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.31), residues: 786 helix: 1.21 (0.28), residues: 384 sheet: -0.63 (0.71), residues: 45 loop : -0.68 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE A 327 TYR 0.022 0.001 TYR A 237 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 5) link_NAG-ASN : angle 1.46665 ( 15) hydrogen bonds : bond 0.03843 ( 301) hydrogen bonds : angle 3.95609 ( 843) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.80908 ( 12) covalent geometry : bond 0.00246 ( 6656) covalent geometry : angle 0.49148 ( 9046) *********************** 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 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.716 Fit side-chains REVERT: A 35 GLU cc_start: 0.7896 (tp30) cc_final: 0.7570 (tp30) REVERT: A 87 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7139 (tm-30) REVERT: A 299 ASP cc_start: 0.7209 (m-30) cc_final: 0.6996 (m-30) REVERT: A 398 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: A 467 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: A 483 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7788 (mp0) REVERT: A 544 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5505 (mt) REVERT: B 357 ARG cc_start: 0.5664 (OUTLIER) cc_final: 0.5328 (ptp-110) REVERT: B 471 GLU cc_start: 0.7545 (pt0) cc_final: 0.7311 (pt0) outliers start: 27 outliers final: 18 residues processed: 104 average time/residue: 0.1376 time to fit residues: 20.7929 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 357 ARG 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 25 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.194329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146720 restraints weight = 6907.331| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.12 r_work: 0.3198 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6667 Z= 0.184 Angle : 0.546 5.748 9073 Z= 0.281 Chirality : 0.043 0.239 959 Planarity : 0.004 0.030 1166 Dihedral : 4.822 43.693 961 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.31), residues: 786 helix: 1.10 (0.28), residues: 383 sheet: -0.77 (0.70), residues: 45 loop : -0.69 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.005 0.001 HIS A 34 PHE 0.009 0.001 PHE A 523 TYR 0.023 0.002 TYR A 237 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 1.64834 ( 15) hydrogen bonds : bond 0.04393 ( 301) hydrogen bonds : angle 4.10094 ( 843) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.75261 ( 12) covalent geometry : bond 0.00431 ( 6656) covalent geometry : angle 0.54149 ( 9046) *********************** 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 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.726 Fit side-chains REVERT: A 35 GLU cc_start: 0.8058 (tp30) cc_final: 0.7731 (tp30) REVERT: A 87 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 150 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: A 299 ASP cc_start: 0.7199 (m-30) cc_final: 0.6990 (m-30) REVERT: A 398 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: A 467 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: A 483 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 544 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5711 (mt) REVERT: B 357 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5428 (ptp-110) REVERT: B 471 GLU cc_start: 0.7821 (pt0) cc_final: 0.7586 (pt0) outliers start: 27 outliers final: 20 residues processed: 105 average time/residue: 0.1405 time to fit residues: 21.3348 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 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 357 ARG Chi-restraints excluded: chain B residue 379 CYS 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 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 13 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.196670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.149407 restraints weight = 6833.493| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.15 r_work: 0.3256 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6667 Z= 0.119 Angle : 0.506 5.766 9073 Z= 0.258 Chirality : 0.041 0.229 959 Planarity : 0.003 0.029 1166 Dihedral : 4.597 42.281 961 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.60 % Allowed : 21.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.31), residues: 786 helix: 1.19 (0.28), residues: 384 sheet: -0.67 (0.71), residues: 45 loop : -0.66 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.003 0.000 HIS A 493 PHE 0.009 0.001 PHE A 523 TYR 0.021 0.001 TYR A 237 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 5) link_NAG-ASN : angle 1.49009 ( 15) hydrogen bonds : bond 0.03968 ( 301) hydrogen bonds : angle 4.00335 ( 843) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.72180 ( 12) covalent geometry : bond 0.00266 ( 6656) covalent geometry : angle 0.50193 ( 9046) ********************** 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 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.671 Fit side-chains REVERT: A 35 GLU cc_start: 0.7958 (tp30) cc_final: 0.7616 (tp30) REVERT: A 87 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 150 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: A 299 ASP cc_start: 0.7217 (m-30) cc_final: 0.7008 (m-30) REVERT: A 398 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: A 467 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: A 483 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7769 (mp0) REVERT: A 544 ILE cc_start: 0.5883 (OUTLIER) cc_final: 0.5533 (mt) REVERT: B 471 GLU cc_start: 0.7733 (pt0) cc_final: 0.7481 (pt0) outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 0.1258 time to fit residues: 19.3595 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 379 CYS 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: 1.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 0.0170 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.197374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.150059 restraints weight = 6905.543| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.19 r_work: 0.3242 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6667 Z= 0.125 Angle : 0.511 5.786 9073 Z= 0.261 Chirality : 0.041 0.228 959 Planarity : 0.004 0.033 1166 Dihedral : 4.529 41.443 961 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.89 % Allowed : 21.90 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 786 helix: 1.24 (0.28), residues: 381 sheet: -0.40 (0.79), residues: 35 loop : -0.66 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.009 0.001 PHE A 327 TYR 0.020 0.001 TYR A 237 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 1.45253 ( 15) hydrogen bonds : bond 0.03963 ( 301) hydrogen bonds : angle 3.98820 ( 843) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.68156 ( 12) covalent geometry : bond 0.00284 ( 6656) covalent geometry : angle 0.50762 ( 9046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.61 seconds wall clock time: 57 minutes 3.78 seconds (3423.78 seconds total)