Starting phenix.real_space_refine on Fri Dec 27 20:14:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgc_32483/12_2024/7wgc_32483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgc_32483/12_2024/7wgc_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_32483/12_2024/7wgc_32483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgc_32483/12_2024/7wgc_32483.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgc_32483/12_2024/7wgc_32483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgc_32483/12_2024/7wgc_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-5532/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: 5.55, per 1000 atoms: 0.85 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: 1.61 Conformation dependent library (CDL) restraints added in 891.7 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: 0.64 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: 1.82 Time building geometry restraints manager: 1.87 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: 3.890 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.660 Find NCS groups from input model: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- 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 6711 Z= 0.200 Angle : 0.635 9.517 9120 Z= 0.329 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 *********************** 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 : 0.814 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: 0.1988 time to fit residues: 23.6169 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 : 0.782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 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 6711 Z= 0.199 Angle : 0.600 8.764 9120 Z= 0.311 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 *********************** 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 : 0.597 Fit side-chains REVERT: A 454 TYR cc_start: 0.7707 (t80) cc_final: 0.7114 (t80) REVERT: C 406 GLU cc_start: 0.7166 (mp0) cc_final: 0.6802 (mp0) REVERT: C 448 ASN cc_start: 0.7687 (t0) cc_final: 0.7389 (t0) REVERT: C 455 LEU cc_start: 0.8325 (tp) cc_final: 0.8116 (tp) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.1744 time to fit residues: 18.4666 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 : 0.800 ------------------------------------------------------------------------------- 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 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6711 Z= 0.168 Angle : 0.564 8.515 9120 Z= 0.290 Chirality : 0.043 0.349 969 Planarity : 0.003 0.041 1175 Dihedral : 5.463 37.727 969 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.57 % Allowed : 12.55 % Favored : 86.88 % 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: 0.76 (0.65), residues: 51 loop : -0.96 (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 *********************** 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 77 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.734 Fit side-chains REVERT: A 190 MET cc_start: 0.7246 (tpt) cc_final: 0.6938 (tpt) REVERT: A 408 MET cc_start: 0.8075 (mpp) cc_final: 0.7805 (mpp) REVERT: A 454 TYR cc_start: 0.7732 (t80) cc_final: 0.6989 (t80) REVERT: C 448 ASN cc_start: 0.7681 (t0) cc_final: 0.7376 (t0) REVERT: C 455 LEU cc_start: 0.8334 (tp) cc_final: 0.8117 (tp) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1998 time to fit residues: 20.0715 Evaluate side-chains 71 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 37 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6711 Z= 0.170 Angle : 0.561 8.708 9120 Z= 0.289 Chirality : 0.043 0.348 969 Planarity : 0.003 0.041 1175 Dihedral : 5.364 37.037 969 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.14 % Allowed : 13.41 % Favored : 85.45 % 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: 0.16 (0.30), residues: 791 helix: 0.99 (0.28), residues: 375 sheet: 0.78 (0.67), residues: 51 loop : -0.91 (0.33), residues: 365 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 0.030 0.001 PHE A 438 TYR 0.011 0.001 TYR A 516 ARG 0.003 0.000 ARG C 493 *********************** 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 78 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.835 Fit side-chains REVERT: A 123 MET cc_start: 0.4351 (mmt) cc_final: 0.4115 (mmp) REVERT: A 190 MET cc_start: 0.7109 (tpt) cc_final: 0.6835 (tpt) REVERT: A 454 TYR cc_start: 0.7780 (t80) cc_final: 0.7032 (t80) REVERT: C 448 ASN cc_start: 0.7693 (t0) cc_final: 0.7384 (t0) REVERT: C 455 LEU cc_start: 0.8308 (tp) cc_final: 0.8077 (tp) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.1794 time to fit residues: 18.2109 Evaluate side-chains 73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6711 Z= 0.192 Angle : 0.586 9.928 9120 Z= 0.297 Chirality : 0.043 0.344 969 Planarity : 0.003 0.041 1175 Dihedral : 5.532 38.641 969 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.00 % Allowed : 13.84 % Favored : 84.17 % 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: 0.98 (0.28), residues: 375 sheet: 0.26 (0.67), residues: 56 loop : -0.91 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.003 0.001 HIS C 519 PHE 0.029 0.002 PHE A 438 TYR 0.015 0.001 TYR C 369 ARG 0.004 0.000 ARG C 355 *********************** 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 84 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.740 Fit side-chains REVERT: A 190 MET cc_start: 0.7103 (tpt) cc_final: 0.6794 (tpt) REVERT: A 454 TYR cc_start: 0.7771 (t80) cc_final: 0.7049 (t80) REVERT: C 448 ASN cc_start: 0.7733 (t0) cc_final: 0.7387 (t0) REVERT: C 455 LEU cc_start: 0.8249 (tp) cc_final: 0.8019 (tp) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.1686 time to fit residues: 18.7116 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 : 0.805 ------------------------------------------------------------------------------- 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 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 503 LEU 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 18 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6711 Z= 0.220 Angle : 0.618 10.965 9120 Z= 0.313 Chirality : 0.044 0.348 969 Planarity : 0.004 0.043 1175 Dihedral : 5.714 41.423 969 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.00 % Allowed : 14.69 % 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: 0.00 (0.30), residues: 791 helix: 0.90 (0.28), residues: 374 sheet: 0.16 (0.66), residues: 56 loop : -0.96 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.003 0.001 HIS C 519 PHE 0.020 0.001 PHE A 327 TYR 0.012 0.001 TYR C 369 ARG 0.004 0.000 ARG C 355 *********************** 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 82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.772 Fit side-chains REVERT: A 190 MET cc_start: 0.7133 (tpt) cc_final: 0.6885 (tpt) REVERT: A 454 TYR cc_start: 0.7669 (t80) cc_final: 0.7013 (t80) REVERT: C 448 ASN cc_start: 0.7538 (t0) cc_final: 0.7248 (t0) REVERT: C 455 LEU cc_start: 0.8232 (tp) cc_final: 0.8010 (tp) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.1676 time to fit residues: 17.9311 Evaluate side-chains 74 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 503 LEU 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 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.0030 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6711 Z= 0.271 Angle : 0.658 9.849 9120 Z= 0.338 Chirality : 0.045 0.354 969 Planarity : 0.004 0.045 1175 Dihedral : 6.151 45.167 969 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.85 % Allowed : 15.26 % Favored : 82.88 % 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: -0.19 (0.30), residues: 791 helix: 0.70 (0.27), residues: 381 sheet: 0.42 (0.68), residues: 51 loop : -1.08 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS A 373 PHE 0.032 0.002 PHE A 438 TYR 0.013 0.001 TYR C 453 ARG 0.005 0.000 ARG C 355 *********************** 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 82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.800 Fit side-chains REVERT: A 190 MET cc_start: 0.7221 (tpt) cc_final: 0.6999 (tpt) REVERT: A 454 TYR cc_start: 0.7851 (t80) cc_final: 0.7031 (t80) REVERT: C 448 ASN cc_start: 0.7628 (t0) cc_final: 0.7303 (t0) REVERT: C 455 LEU cc_start: 0.8198 (tp) cc_final: 0.7947 (tp) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.1735 time to fit residues: 18.4716 Evaluate side-chains 75 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 503 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 418 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** 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** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 6711 Z= 0.363 Angle : 0.757 12.849 9120 Z= 0.387 Chirality : 0.049 0.370 969 Planarity : 0.005 0.050 1175 Dihedral : 6.776 50.066 969 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.28 % Allowed : 15.83 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % Twisted Proline : 2.56 % Twisted General : 0.40 % 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: -0.56 (0.30), residues: 791 helix: 0.38 (0.27), residues: 388 sheet: 0.32 (0.65), residues: 48 loop : -1.29 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 373 PHE 0.031 0.002 PHE A 438 TYR 0.017 0.002 TYR C 453 ARG 0.006 0.001 ARG C 355 *********************** 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 79 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.795 Fit side-chains REVERT: A 190 MET cc_start: 0.7191 (tpt) cc_final: 0.6984 (tpt) REVERT: A 454 TYR cc_start: 0.7958 (t80) cc_final: 0.7088 (t80) REVERT: C 448 ASN cc_start: 0.7702 (t0) cc_final: 0.7383 (t0) REVERT: C 455 LEU cc_start: 0.8205 (tp) cc_final: 0.7960 (tp) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.1756 time to fit residues: 18.2300 Evaluate side-chains 72 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 503 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 67 optimal weight: 0.0000 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- 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** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6711 Z= 0.159 Angle : 0.591 7.766 9120 Z= 0.301 Chirality : 0.043 0.357 969 Planarity : 0.004 0.049 1175 Dihedral : 5.441 39.059 969 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.14 % Allowed : 17.55 % Favored : 81.31 % 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: -0.10 (0.30), residues: 791 helix: 0.81 (0.28), residues: 375 sheet: 0.01 (0.67), residues: 53 loop : -0.99 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.002 0.001 HIS A 540 PHE 0.030 0.002 PHE A 438 TYR 0.011 0.001 TYR C 369 ARG 0.004 0.000 ARG C 355 *********************** 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: 8 poor density : 74 time to evaluate : 0.930 Fit side-chains REVERT: A 454 TYR cc_start: 0.7665 (t80) cc_final: 0.6866 (t80) REVERT: C 448 ASN cc_start: 0.7535 (t0) cc_final: 0.7252 (t0) REVERT: C 455 LEU cc_start: 0.8185 (tp) cc_final: 0.7965 (tp) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1694 time to fit residues: 18.9111 Evaluate side-chains 74 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 0.0370 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 overall best weight: 0.2470 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6711 Z= 0.160 Angle : 0.606 9.117 9120 Z= 0.303 Chirality : 0.042 0.354 969 Planarity : 0.004 0.045 1175 Dihedral : 5.013 36.900 969 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.86 % Allowed : 17.97 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.13 % 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: -0.00 (0.30), residues: 791 helix: 0.80 (0.28), residues: 377 sheet: 0.16 (0.69), residues: 53 loop : -0.85 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 594 HIS 0.002 0.000 HIS A 540 PHE 0.032 0.002 PHE A 438 TYR 0.016 0.001 TYR C 369 ARG 0.003 0.000 ARG C 355 ********************** 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 79 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.209 Fit side-chains REVERT: A 454 TYR cc_start: 0.7729 (t80) cc_final: 0.6947 (t80) REVERT: C 406 GLU cc_start: 0.7388 (mp0) cc_final: 0.7008 (pm20) REVERT: C 448 ASN cc_start: 0.7429 (t0) cc_final: 0.7150 (t0) REVERT: C 455 LEU cc_start: 0.8266 (tp) cc_final: 0.8042 (tp) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.2640 time to fit residues: 30.6438 Evaluate side-chains 75 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 330 ASN ** 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 = 0.4592 r_free = 0.4592 target = 0.212623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.203795 restraints weight = 13728.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.203922 restraints weight = 8734.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.203910 restraints weight = 8471.699| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6711 Z= 0.171 Angle : 0.610 7.948 9120 Z= 0.305 Chirality : 0.043 0.352 969 Planarity : 0.004 0.045 1175 Dihedral : 5.175 37.004 969 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.00 % Allowed : 17.97 % Favored : 81.03 % 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: -0.00 (0.30), residues: 791 helix: 0.73 (0.27), residues: 389 sheet: 0.31 (0.68), residues: 54 loop : -0.83 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 594 HIS 0.002 0.001 HIS A 265 PHE 0.033 0.001 PHE A 438 TYR 0.015 0.001 TYR C 369 ARG 0.003 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.93 seconds wall clock time: 31 minutes 29.37 seconds (1889.37 seconds total)