Starting phenix.real_space_refine on Mon Mar 11 01:30:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgc_32483/03_2024/7wgc_32483.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgc_32483/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgc_32483/03_2024/7wgc_32483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgc_32483/03_2024/7wgc_32483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgc_32483/03_2024/7wgc_32483.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgc_32483/03_2024/7wgc_32483.pdb" } 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 Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.05, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.63 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: 1.69 Time building geometry restraints manager: 2.76 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: 98.66 - 105.74: 156 105.74 - 112.82: 3429 112.82 - 119.90: 2369 119.90 - 126.99: 3063 126.99 - 134.07: 103 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 2.440 nonbonded pdb=" OG SER A 155 " pdb=" OD1 ASP A 157 " model vdw 2.204 2.440 nonbonded pdb=" N SER A 19 " pdb=" OD1 ASN C 477 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR C 500 " model vdw 2.224 2.440 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.232 2.440 ... (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 ========== 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: 2.570 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: 9.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.350 Find NCS groups from input model: 0.170 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.810 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: 0.1857 time to fit residues: 22.1554 Evaluate side-chains 68 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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: 0.6980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 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: 0.5541 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6711 Z= 0.227 Angle : 0.613 9.044 9120 Z= 0.314 Chirality : 0.044 0.359 969 Planarity : 0.004 0.045 1175 Dihedral : 6.153 50.084 969 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.86 % Allowed : 7.85 % Favored : 91.30 % 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: -0.07 (0.30), residues: 791 helix: 0.82 (0.27), residues: 382 sheet: 0.56 (0.63), residues: 51 loop : -1.08 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.003 0.001 HIS A 373 PHE 0.029 0.002 PHE A 438 TYR 0.013 0.001 TYR A 516 ARG 0.006 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 82 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8089 (mpp) cc_final: 0.7888 (mpp) REVERT: A 454 TYR cc_start: 0.7712 (t80) cc_final: 0.7112 (t80) REVERT: C 455 LEU cc_start: 0.8374 (tp) cc_final: 0.8122 (tp) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.1751 time to fit residues: 18.9281 Evaluate side-chains 73 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 498 CYS 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: 2.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 48 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** A 552 GLN A 556 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6711 Z= 0.175 Angle : 0.567 8.793 9120 Z= 0.289 Chirality : 0.043 0.355 969 Planarity : 0.003 0.043 1175 Dihedral : 5.732 48.951 969 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.14 % Allowed : 12.70 % Favored : 86.16 % 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: 0.93 (0.28), residues: 382 sheet: 0.54 (0.64), residues: 51 loop : -1.03 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.001 0.001 HIS A 265 PHE 0.029 0.001 PHE A 438 TYR 0.013 0.001 TYR C 369 ARG 0.005 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 81 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.767 Fit side-chains REVERT: A 454 TYR cc_start: 0.7763 (t80) cc_final: 0.6998 (t80) REVERT: A 471 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6158 (p0) REVERT: C 430 THR cc_start: 0.6256 (p) cc_final: 0.6022 (p) REVERT: C 455 LEU cc_start: 0.8377 (tp) cc_final: 0.8129 (tp) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.1890 time to fit residues: 20.3486 Evaluate side-chains 78 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 405 ASP 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6711 Z= 0.177 Angle : 0.560 8.986 9120 Z= 0.286 Chirality : 0.042 0.354 969 Planarity : 0.003 0.042 1175 Dihedral : 5.639 49.774 969 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.57 % Allowed : 14.12 % Favored : 84.31 % 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: 0.09 (0.30), residues: 791 helix: 0.97 (0.28), residues: 381 sheet: 0.56 (0.66), residues: 51 loop : -1.01 (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 C 519 PHE 0.029 0.001 PHE A 438 TYR 0.011 0.001 TYR A 516 ARG 0.004 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 82 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.873 Fit side-chains REVERT: A 190 MET cc_start: 0.7105 (tpt) cc_final: 0.6833 (tpt) REVERT: A 454 TYR cc_start: 0.7798 (t80) cc_final: 0.7046 (t80) REVERT: A 471 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6103 (p0) REVERT: C 455 LEU cc_start: 0.8340 (tp) cc_final: 0.8071 (tp) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.1849 time to fit residues: 19.8291 Evaluate side-chains 77 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN 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 471 ASP Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 405 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 19 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6711 Z= 0.148 Angle : 0.537 8.495 9120 Z= 0.273 Chirality : 0.042 0.353 969 Planarity : 0.003 0.041 1175 Dihedral : 5.311 46.903 969 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.28 % Allowed : 15.12 % Favored : 82.60 % 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: 0.17 (0.31), residues: 791 helix: 1.08 (0.28), residues: 381 sheet: 0.15 (0.67), residues: 53 loop : -0.95 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.000 HIS A 265 PHE 0.024 0.001 PHE A 438 TYR 0.014 0.001 TYR C 369 ARG 0.005 0.000 ARG C 493 *********************** 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 88 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.816 Fit side-chains REVERT: A 123 MET cc_start: 0.4351 (mmt) cc_final: 0.4103 (mmp) REVERT: A 454 TYR cc_start: 0.7759 (t80) cc_final: 0.6998 (t80) REVERT: A 471 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6058 (p0) REVERT: C 455 LEU cc_start: 0.8341 (tp) cc_final: 0.8081 (tp) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.1853 time to fit residues: 21.3744 Evaluate side-chains 77 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 471 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6711 Z= 0.156 Angle : 0.540 7.803 9120 Z= 0.274 Chirality : 0.042 0.352 969 Planarity : 0.003 0.040 1175 Dihedral : 5.232 45.843 969 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.71 % Allowed : 15.12 % Favored : 83.17 % 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: 0.20 (0.30), residues: 791 helix: 1.07 (0.28), residues: 380 sheet: 0.19 (0.67), residues: 53 loop : -0.87 (0.33), residues: 358 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 0.014 0.001 PHE C 400 TYR 0.012 0.001 TYR C 369 ARG 0.007 0.000 ARG C 493 *********************** 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 81 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.777 Fit side-chains REVERT: A 454 TYR cc_start: 0.7752 (t80) cc_final: 0.6995 (t80) REVERT: A 471 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6272 (p0) REVERT: C 455 LEU cc_start: 0.8341 (tp) cc_final: 0.8076 (tp) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.1697 time to fit residues: 18.2131 Evaluate side-chains 75 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 471 ASP 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 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- 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 250 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 6711 Z= 0.331 Angle : 0.711 12.577 9120 Z= 0.363 Chirality : 0.046 0.357 969 Planarity : 0.004 0.042 1175 Dihedral : 6.566 59.503 969 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 2.14 % Allowed : 15.69 % Favored : 82.17 % 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: 379 sheet: 0.48 (0.70), residues: 48 loop : -1.06 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.004 0.001 HIS A 373 PHE 0.032 0.002 PHE A 327 TYR 0.015 0.002 TYR C 453 ARG 0.009 0.001 ARG C 493 *********************** 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 fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.080 Fit side-chains REVERT: A 454 TYR cc_start: 0.7861 (t80) cc_final: 0.7194 (t80) REVERT: A 471 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6496 (p0) REVERT: C 455 LEU cc_start: 0.8330 (tp) cc_final: 0.8012 (tp) outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.2075 time to fit residues: 22.8543 Evaluate side-chains 73 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 ASN 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 471 ASP 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 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6711 Z= 0.212 Angle : 0.611 8.363 9120 Z= 0.311 Chirality : 0.044 0.369 969 Planarity : 0.004 0.046 1175 Dihedral : 6.072 58.367 969 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 2.00 % Allowed : 16.69 % Favored : 81.31 % 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: -0.10 (0.30), residues: 791 helix: 0.81 (0.27), residues: 376 sheet: -0.07 (0.66), residues: 53 loop : -0.97 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS C 519 PHE 0.032 0.002 PHE A 438 TYR 0.011 0.001 TYR C 369 ARG 0.009 0.001 ARG C 493 *********************** 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 84 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.743 Fit side-chains REVERT: A 454 TYR cc_start: 0.7814 (t80) cc_final: 0.6958 (t80) REVERT: A 471 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6396 (p0) REVERT: C 455 LEU cc_start: 0.8386 (tp) cc_final: 0.8082 (tp) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.1650 time to fit residues: 18.3318 Evaluate side-chains 80 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 ASN 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 471 ASP 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 517 LEU 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 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 0.1933 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= 0.198 Angle : 0.600 8.225 9120 Z= 0.304 Chirality : 0.043 0.365 969 Planarity : 0.004 0.046 1175 Dihedral : 5.919 57.781 969 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.85 % Allowed : 17.55 % Favored : 80.60 % 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: 0.02 (0.30), residues: 791 helix: 0.96 (0.28), residues: 374 sheet: -0.11 (0.66), residues: 53 loop : -0.94 (0.33), residues: 364 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 0.031 0.001 PHE A 438 TYR 0.016 0.001 TYR C 369 ARG 0.010 0.001 ARG C 493 *********************** 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 fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.787 Fit side-chains REVERT: A 454 TYR cc_start: 0.7770 (t80) cc_final: 0.6906 (t80) REVERT: A 471 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6398 (p0) REVERT: C 455 LEU cc_start: 0.8397 (tp) cc_final: 0.8083 (tp) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1682 time to fit residues: 18.3188 Evaluate side-chains 77 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 ASN 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 471 ASP 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: 0.0980 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6711 Z= 0.187 Angle : 0.602 8.149 9120 Z= 0.303 Chirality : 0.043 0.359 969 Planarity : 0.004 0.045 1175 Dihedral : 5.766 56.377 969 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.85 % Allowed : 18.12 % Favored : 80.03 % 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: 0.04 (0.30), residues: 791 helix: 0.94 (0.28), residues: 375 sheet: -0.09 (0.67), residues: 53 loop : -0.89 (0.33), residues: 363 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 0.033 0.002 PHE A 438 TYR 0.015 0.001 TYR C 369 ARG 0.010 0.001 ARG C 493 ********************** 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 80 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.808 Fit side-chains REVERT: A 454 TYR cc_start: 0.7786 (t80) cc_final: 0.6930 (t80) REVERT: A 471 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6371 (p0) REVERT: C 455 LEU cc_start: 0.8380 (tp) cc_final: 0.8074 (tp) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.1674 time to fit residues: 17.7705 Evaluate side-chains 77 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 ASN 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 471 ASP 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 17 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 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 477 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 = 0.4570 r_free = 0.4570 target = 0.210135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.201263 restraints weight = 13766.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.201310 restraints weight = 8604.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.201301 restraints weight = 9015.908| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.2058 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= 0.213 Angle : 0.618 8.401 9120 Z= 0.313 Chirality : 0.043 0.361 969 Planarity : 0.004 0.045 1175 Dihedral : 5.949 57.861 969 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.85 % Allowed : 18.12 % Favored : 80.03 % 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: 0.01 (0.30), residues: 791 helix: 0.93 (0.28), residues: 374 sheet: -0.08 (0.67), residues: 53 loop : -0.94 (0.33), residues: 364 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 0.034 0.002 PHE A 438 TYR 0.015 0.001 TYR C 369 ARG 0.010 0.001 ARG C 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.06 seconds wall clock time: 29 minutes 7.19 seconds (1747.19 seconds total)