Starting phenix.real_space_refine on Thu Jun 5 18:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgc_32483/06_2025/7wgc_32483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgc_32483/06_2025/7wgc_32483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgc_32483/06_2025/7wgc_32483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgc_32483/06_2025/7wgc_32483.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgc_32483/06_2025/7wgc_32483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgc_32483/06_2025/7wgc_32483.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.069 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 4178 2.51 5 N 1081 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6527 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: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} 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: "C" 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: 4.22, per 1000 atoms: 0.65 Number of scatterers: 6527 At special positions: 0 Unit cell: (81.32, 87.74, 120.91, 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 1231 8.00 N 1081 7.00 C 4178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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 C1301 " - " ASN C 343 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 803.3 milliseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 53.8% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.035A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.921A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.128A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.776A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.763A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.526A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.911A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 263 through 268 removed outlier: 4.225A pdb=" N GLY A 268 " --> pdb=" O HIS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.418A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.502A pdb=" N PHE A 327 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 331 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 4.065A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.709A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.548A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 532 removed outlier: 3.732A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.141A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.869A 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 'C' and resid 339 through 343 removed outlier: 3.518A pdb=" N PHE C 342 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.595A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.566A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.604A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 294 hydrogen bonds defined for protein. 831 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: 1.50 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2090 1.35 - 1.47: 1743 1.47 - 1.59: 2820 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6711 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.63e+00 ... (remaining 6706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 8930 1.90 - 3.81: 158 3.81 - 5.71: 21 5.71 - 7.61: 8 7.61 - 9.52: 3 Bond angle restraints: 9120 Sorted by residual: angle pdb=" C ASN C 331 " pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 121.70 130.63 -8.93 1.80e+00 3.09e-01 2.46e+01 angle pdb=" C LEU C 518 " pdb=" N HIS C 519 " pdb=" CA HIS C 519 " ideal model delta sigma weight residual 122.46 116.19 6.27 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C TRP A 461 " pdb=" N MET A 462 " pdb=" CA MET A 462 " ideal model delta sigma weight residual 121.58 114.86 6.72 1.95e+00 2.63e-01 1.19e+01 angle pdb=" CA MET A 462 " pdb=" CB MET A 462 " pdb=" CG MET A 462 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 angle pdb=" CB MET A 462 " pdb=" CG MET A 462 " pdb=" SD MET A 462 " ideal model delta sigma weight residual 112.70 121.69 -8.99 3.00e+00 1.11e-01 8.99e+00 ... (remaining 9115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3570 17.63 - 35.25: 375 35.25 - 52.88: 66 52.88 - 70.51: 16 70.51 - 88.13: 9 Dihedral angle restraints: 4036 sinusoidal: 1699 harmonic: 2337 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -154.56 68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.56 67.44 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 147.52 32.48 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 851 0.063 - 0.127: 107 0.127 - 0.190: 8 0.190 - 0.254: 2 0.254 - 0.317: 1 Chirality restraints: 969 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ARG C 355 " pdb=" N ARG C 355 " pdb=" C ARG C 355 " pdb=" CB ARG C 355 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE C 332 " pdb=" CA ILE C 332 " pdb=" CG1 ILE C 332 " pdb=" CG2 ILE C 332 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 966 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO C 479 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 384 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO C 521 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.017 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 382 2.73 - 3.27: 6821 3.27 - 3.82: 10569 3.82 - 4.36: 11942 4.36 - 4.90: 20366 Nonbonded interactions: 50080 Sorted by model distance: nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.191 3.040 nonbonded pdb=" OG SER A 155 " pdb=" OD1 ASP A 157 " model vdw 2.204 3.040 nonbonded pdb=" N SER A 19 " pdb=" OD1 ASN C 477 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR C 500 " model vdw 2.224 3.040 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.232 3.040 ... (remaining 50075 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.140 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 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 : 0.003 0.041 6723 Z= 0.148 Angle : 0.644 9.517 9149 Z= 0.331 Chirality : 0.044 0.317 969 Planarity : 0.004 0.044 1175 Dihedral : 14.721 88.132 2513 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.30), residues: 791 helix: 0.77 (0.27), residues: 384 sheet: 0.51 (0.65), residues: 48 loop : -1.06 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.002 0.001 HIS A 239 PHE 0.017 0.001 PHE C 400 TYR 0.009 0.001 TYR C 495 ARG 0.010 0.001 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 5) link_NAG-ASN : angle 2.73336 ( 15) hydrogen bonds : bond 0.14036 ( 294) hydrogen bonds : angle 4.88236 ( 831) SS BOND : bond 0.00174 ( 7) SS BOND : angle 0.86538 ( 14) covalent geometry : bond 0.00313 ( 6711) covalent geometry : angle 0.63478 ( 9120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.776 Fit side-chains REVERT: C 455 LEU cc_start: 0.8402 (tp) cc_final: 0.8190 (tp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1744 time to fit residues: 20.7884 Evaluate side-chains 68 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.211780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.203053 restraints weight = 13203.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.203176 restraints weight = 8052.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.203152 restraints weight = 8033.371| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6723 Z= 0.141 Angle : 0.611 9.238 9149 Z= 0.313 Chirality : 0.044 0.355 969 Planarity : 0.004 0.043 1175 Dihedral : 5.803 39.875 969 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.71 % Allowed : 7.85 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.13 % 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: -0.08 (0.30), residues: 791 helix: 0.73 (0.27), residues: 384 sheet: 0.70 (0.64), residues: 51 loop : -1.01 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS A 373 PHE 0.029 0.002 PHE A 438 TYR 0.013 0.001 TYR A 516 ARG 0.005 0.000 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 5) link_NAG-ASN : angle 2.82061 ( 15) hydrogen bonds : bond 0.04718 ( 294) hydrogen bonds : angle 4.26102 ( 831) SS BOND : bond 0.00159 ( 7) SS BOND : angle 0.74553 ( 14) covalent geometry : bond 0.00317 ( 6711) covalent geometry : angle 0.59999 ( 9120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.578 Fit side-chains REVERT: A 454 TYR cc_start: 0.7723 (t80) cc_final: 0.7126 (t80) REVERT: C 406 GLU cc_start: 0.7285 (mp0) cc_final: 0.6865 (mp0) REVERT: C 448 ASN cc_start: 0.7738 (t0) cc_final: 0.7420 (t0) REVERT: C 455 LEU cc_start: 0.8311 (tp) cc_final: 0.8103 (tp) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.1635 time to fit residues: 17.5457 Evaluate side-chains 73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 581 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.211835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.203689 restraints weight = 13938.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.203780 restraints weight = 8666.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.203779 restraints weight = 7603.937| |-----------------------------------------------------------------------------| r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 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 : 0.003 0.042 6723 Z= 0.121 Angle : 0.578 9.136 9149 Z= 0.294 Chirality : 0.043 0.349 969 Planarity : 0.003 0.042 1175 Dihedral : 5.476 37.805 969 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.57 % Allowed : 12.70 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.13 % 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 (0.30), residues: 791 helix: 0.85 (0.28), residues: 381 sheet: 0.75 (0.65), residues: 51 loop : -0.97 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS A 345 PHE 0.029 0.001 PHE A 438 TYR 0.013 0.001 TYR C 369 ARG 0.004 0.000 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 5) link_NAG-ASN : angle 2.76742 ( 15) hydrogen bonds : bond 0.04298 ( 294) hydrogen bonds : angle 4.07805 ( 831) SS BOND : bond 0.00160 ( 7) SS BOND : angle 0.96274 ( 14) covalent geometry : bond 0.00266 ( 6711) covalent geometry : angle 0.56634 ( 9120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.650 Fit side-chains REVERT: A 190 MET cc_start: 0.7162 (tpt) cc_final: 0.6875 (tpt) REVERT: A 408 MET cc_start: 0.8228 (mpp) cc_final: 0.7903 (mpp) REVERT: A 454 TYR cc_start: 0.7751 (t80) cc_final: 0.7000 (t80) REVERT: C 448 ASN cc_start: 0.7733 (t0) cc_final: 0.7405 (t0) REVERT: C 455 LEU cc_start: 0.8299 (tp) cc_final: 0.8091 (tp) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.1809 time to fit residues: 18.1136 Evaluate side-chains 70 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4573 r_free = 0.4573 target = 0.209665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.202205 restraints weight = 13798.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.203114 restraints weight = 8964.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.202632 restraints weight = 6519.857| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6723 Z= 0.180 Angle : 0.664 13.518 9149 Z= 0.336 Chirality : 0.046 0.353 969 Planarity : 0.004 0.044 1175 Dihedral : 6.119 43.670 969 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.43 % Allowed : 13.55 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.27 % 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: -0.14 (0.30), residues: 791 helix: 0.75 (0.27), residues: 381 sheet: 0.67 (0.68), residues: 51 loop : -1.12 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.005 0.001 HIS C 519 PHE 0.030 0.002 PHE A 438 TYR 0.015 0.001 TYR C 453 ARG 0.005 0.001 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 5) link_NAG-ASN : angle 2.86350 ( 15) hydrogen bonds : bond 0.05028 ( 294) hydrogen bonds : angle 4.18617 ( 831) SS BOND : bond 0.00180 ( 7) SS BOND : angle 0.93460 ( 14) covalent geometry : bond 0.00413 ( 6711) covalent geometry : angle 0.65331 ( 9120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.745 Fit side-chains REVERT: A 454 TYR cc_start: 0.7835 (t80) cc_final: 0.7122 (t80) REVERT: C 448 ASN cc_start: 0.7613 (t0) cc_final: 0.7282 (t0) REVERT: C 455 LEU cc_start: 0.8159 (tp) cc_final: 0.7946 (tp) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1828 time to fit residues: 17.6689 Evaluate side-chains 68 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.0050 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.211038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.201948 restraints weight = 13606.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.202020 restraints weight = 8626.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.201986 restraints weight = 8564.733| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6723 Z= 0.130 Angle : 0.598 9.249 9149 Z= 0.302 Chirality : 0.044 0.353 969 Planarity : 0.003 0.044 1175 Dihedral : 5.643 40.110 969 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.43 % Allowed : 14.55 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.13 % 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: -0.04 (0.30), residues: 791 helix: 0.84 (0.28), residues: 381 sheet: 0.69 (0.68), residues: 51 loop : -1.06 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS A 535 PHE 0.025 0.001 PHE A 438 TYR 0.011 0.001 TYR A 516 ARG 0.004 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 5) link_NAG-ASN : angle 2.82224 ( 15) hydrogen bonds : bond 0.04395 ( 294) hydrogen bonds : angle 4.04211 ( 831) SS BOND : bond 0.00159 ( 7) SS BOND : angle 0.80859 ( 14) covalent geometry : bond 0.00291 ( 6711) covalent geometry : angle 0.58716 ( 9120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.777 Fit side-chains REVERT: A 190 MET cc_start: 0.7206 (tpt) cc_final: 0.6927 (tpt) REVERT: A 408 MET cc_start: 0.8250 (mpp) cc_final: 0.7985 (mpp) REVERT: A 454 TYR cc_start: 0.7805 (t80) cc_final: 0.7012 (t80) REVERT: C 448 ASN cc_start: 0.7584 (t0) cc_final: 0.7252 (t0) REVERT: C 455 LEU cc_start: 0.8230 (tp) cc_final: 0.8005 (tp) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.1811 time to fit residues: 19.9267 Evaluate side-chains 71 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4595 r_free = 0.4595 target = 0.212282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.203968 restraints weight = 13748.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.204038 restraints weight = 8809.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.204021 restraints weight = 9064.681| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6723 Z= 0.118 Angle : 0.580 9.767 9149 Z= 0.292 Chirality : 0.043 0.350 969 Planarity : 0.003 0.043 1175 Dihedral : 5.360 38.492 969 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.14 % Allowed : 15.55 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.13 % 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: 0.06 (0.31), residues: 791 helix: 0.92 (0.28), residues: 380 sheet: 0.24 (0.66), residues: 56 loop : -0.94 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS C 519 PHE 0.025 0.001 PHE A 438 TYR 0.009 0.001 TYR A 516 ARG 0.004 0.000 ARG C 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 5) link_NAG-ASN : angle 2.75357 ( 15) hydrogen bonds : bond 0.04128 ( 294) hydrogen bonds : angle 3.97132 ( 831) SS BOND : bond 0.00151 ( 7) SS BOND : angle 0.64440 ( 14) covalent geometry : bond 0.00259 ( 6711) covalent geometry : angle 0.56965 ( 9120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.800 Fit side-chains REVERT: A 190 MET cc_start: 0.7066 (tpt) cc_final: 0.6865 (tpt) REVERT: A 408 MET cc_start: 0.8212 (mpp) cc_final: 0.7978 (mpp) REVERT: A 454 TYR cc_start: 0.7680 (t80) cc_final: 0.7034 (t80) REVERT: C 448 ASN cc_start: 0.7544 (t0) cc_final: 0.7235 (t0) REVERT: C 455 LEU cc_start: 0.8180 (tp) cc_final: 0.7965 (tp) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.1678 time to fit residues: 17.2198 Evaluate side-chains 70 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.211560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.202997 restraints weight = 13800.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.203045 restraints weight = 9082.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.203042 restraints weight = 8906.663| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6723 Z= 0.126 Angle : 0.594 9.169 9149 Z= 0.299 Chirality : 0.043 0.348 969 Planarity : 0.003 0.043 1175 Dihedral : 5.423 38.795 969 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.43 % Allowed : 16.26 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % 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: 0.05 (0.31), residues: 791 helix: 0.91 (0.28), residues: 381 sheet: 0.19 (0.66), residues: 56 loop : -0.93 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS C 519 PHE 0.029 0.001 PHE A 438 TYR 0.016 0.001 TYR C 351 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 5) link_NAG-ASN : angle 2.76537 ( 15) hydrogen bonds : bond 0.04193 ( 294) hydrogen bonds : angle 3.93916 ( 831) SS BOND : bond 0.00130 ( 7) SS BOND : angle 0.65848 ( 14) covalent geometry : bond 0.00283 ( 6711) covalent geometry : angle 0.58377 ( 9120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.946 Fit side-chains REVERT: A 454 TYR cc_start: 0.7811 (t80) cc_final: 0.6982 (t80) REVERT: C 448 ASN cc_start: 0.7559 (t0) cc_final: 0.7241 (t0) REVERT: C 455 LEU cc_start: 0.8220 (tp) cc_final: 0.8012 (tp) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.1642 time to fit residues: 17.6222 Evaluate side-chains 76 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.211096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.201787 restraints weight = 13507.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.201813 restraints weight = 8904.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.201818 restraints weight = 8866.908| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6723 Z= 0.134 Angle : 0.621 9.148 9149 Z= 0.312 Chirality : 0.043 0.351 969 Planarity : 0.004 0.043 1175 Dihedral : 5.485 38.888 969 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.14 % Allowed : 16.41 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % 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 (0.30), residues: 791 helix: 0.86 (0.28), residues: 381 sheet: 0.16 (0.66), residues: 56 loop : -0.89 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.003 0.001 HIS A 239 PHE 0.030 0.002 PHE A 438 TYR 0.015 0.001 TYR C 351 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 5) link_NAG-ASN : angle 2.78048 ( 15) hydrogen bonds : bond 0.04305 ( 294) hydrogen bonds : angle 3.97663 ( 831) SS BOND : bond 0.00132 ( 7) SS BOND : angle 0.67038 ( 14) covalent geometry : bond 0.00303 ( 6711) covalent geometry : angle 0.61120 ( 9120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.683 Fit side-chains REVERT: A 408 MET cc_start: 0.8244 (mpp) cc_final: 0.8012 (mpp) REVERT: A 454 TYR cc_start: 0.7815 (t80) cc_final: 0.6972 (t80) REVERT: C 448 ASN cc_start: 0.7595 (t0) cc_final: 0.7266 (t0) REVERT: C 455 LEU cc_start: 0.8208 (tp) cc_final: 0.7986 (tp) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.1573 time to fit residues: 17.7598 Evaluate side-chains 77 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0470 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.210950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.202238 restraints weight = 13801.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.202274 restraints weight = 9115.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.202270 restraints weight = 9004.306| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6723 Z= 0.144 Angle : 0.640 9.288 9149 Z= 0.321 Chirality : 0.044 0.358 969 Planarity : 0.004 0.043 1175 Dihedral : 5.600 40.720 969 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.85 % Allowed : 16.55 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % 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: -0.01 (0.30), residues: 791 helix: 0.81 (0.27), residues: 381 sheet: 0.04 (0.65), residues: 56 loop : -0.87 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.003 0.001 HIS A 239 PHE 0.031 0.002 PHE A 438 TYR 0.015 0.001 TYR C 351 ARG 0.004 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 5) link_NAG-ASN : angle 2.84635 ( 15) hydrogen bonds : bond 0.04462 ( 294) hydrogen bonds : angle 4.01184 ( 831) SS BOND : bond 0.00117 ( 7) SS BOND : angle 0.66129 ( 14) covalent geometry : bond 0.00325 ( 6711) covalent geometry : angle 0.63019 ( 9120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.738 Fit side-chains REVERT: A 408 MET cc_start: 0.8245 (mpp) cc_final: 0.7983 (mpp) REVERT: A 454 TYR cc_start: 0.7766 (t80) cc_final: 0.6970 (t80) REVERT: C 448 ASN cc_start: 0.7601 (t0) cc_final: 0.7277 (t0) REVERT: C 455 LEU cc_start: 0.8159 (tp) cc_final: 0.7955 (tp) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.1705 time to fit residues: 18.4071 Evaluate side-chains 76 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.0870 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.212296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.203436 restraints weight = 13863.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.203503 restraints weight = 8840.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.203482 restraints weight = 8772.339| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6723 Z= 0.121 Angle : 0.629 9.332 9149 Z= 0.312 Chirality : 0.043 0.360 969 Planarity : 0.003 0.043 1175 Dihedral : 5.301 38.400 969 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.28 % Allowed : 17.40 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 791 helix: 0.90 (0.28), residues: 375 sheet: 0.03 (0.64), residues: 56 loop : -0.79 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS A 239 PHE 0.033 0.002 PHE A 438 TYR 0.014 0.001 TYR C 351 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 5) link_NAG-ASN : angle 2.83575 ( 15) hydrogen bonds : bond 0.04102 ( 294) hydrogen bonds : angle 3.95140 ( 831) SS BOND : bond 0.00155 ( 7) SS BOND : angle 0.65690 ( 14) covalent geometry : bond 0.00266 ( 6711) covalent geometry : angle 0.61837 ( 9120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.685 Fit side-chains REVERT: A 408 MET cc_start: 0.8247 (mpp) cc_final: 0.7968 (mpp) REVERT: A 454 TYR cc_start: 0.7789 (t80) cc_final: 0.6958 (t80) REVERT: C 448 ASN cc_start: 0.7567 (t0) cc_final: 0.7239 (t0) REVERT: C 455 LEU cc_start: 0.8240 (tp) cc_final: 0.8020 (tp) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.1554 time to fit residues: 16.6464 Evaluate side-chains 75 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.211664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.202652 restraints weight = 13616.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.202681 restraints weight = 8892.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.202676 restraints weight = 8534.361| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6723 Z= 0.131 Angle : 0.632 9.327 9149 Z= 0.315 Chirality : 0.043 0.358 969 Planarity : 0.004 0.043 1175 Dihedral : 5.424 39.585 969 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.57 % Allowed : 16.98 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 791 helix: 0.91 (0.28), residues: 375 sheet: 0.04 (0.65), residues: 56 loop : -0.80 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS A 239 PHE 0.032 0.002 PHE A 438 TYR 0.015 0.001 TYR C 351 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 5) link_NAG-ASN : angle 2.83137 ( 15) hydrogen bonds : bond 0.04260 ( 294) hydrogen bonds : angle 3.97483 ( 831) SS BOND : bond 0.00129 ( 7) SS BOND : angle 0.66555 ( 14) covalent geometry : bond 0.00296 ( 6711) covalent geometry : angle 0.62186 ( 9120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.41 seconds wall clock time: 39 minutes 55.75 seconds (2395.75 seconds total)