Starting phenix.real_space_refine on Mon Mar 11 00:02:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnk_34167/03_2024/8gnk_34167_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnk_34167/03_2024/8gnk_34167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnk_34167/03_2024/8gnk_34167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnk_34167/03_2024/8gnk_34167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnk_34167/03_2024/8gnk_34167_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnk_34167/03_2024/8gnk_34167_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.030 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 43 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 4100 2.51 5 N 940 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4177 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 23, 'TRANS': 501} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "A" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 261 Unusual residues: {' CL': 1, ' NA': 1, 'ABU': 1, 'CLR': 6, 'NAG': 2, 'PTY': 1} Classifications: {'undetermined': 12, 'water': 6} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.28, per 1000 atoms: 0.69 Number of scatterers: 6164 At special positions: 0 Unit cell: (79.776, 85.593, 110.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 43 16.00 P 1 15.00 Na 1 11.00 O 1078 8.00 N 940 7.00 C 4100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 601 " - " ASN A 184 " " NAG A 602 " - " ASN A 176 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 5 sheets defined 49.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 81 through 92 Proline residue: A 85 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.159A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 154 removed outlier: 3.687A pdb=" N LYS A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY A 124 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 132 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 136 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 137 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 140 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 141 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 143 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 212 through 230 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 242 through 259 removed outlier: 4.125A pdb=" N TYR A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.783A pdb=" N VAL A 259 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.586A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 349 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 378 through 411 removed outlier: 3.525A pdb=" N THR A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 439 removed outlier: 4.455A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.760A pdb=" N MET A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 504 through 518 Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.956A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.849A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 3.886A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.466A pdb=" N LYS L 104 " --> pdb=" O MET L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= C, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.853A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.630A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.086A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 711 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: 1.61 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 905 1.32 - 1.45: 1892 1.45 - 1.57: 3479 1.57 - 1.70: 2 1.70 - 1.82: 68 Bond restraints: 6346 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CA SER A 378 " pdb=" CB SER A 378 " ideal model delta sigma weight residual 1.534 1.492 0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C LYS A 448 " pdb=" O LYS A 448 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.26e-02 6.30e+03 1.08e+01 bond pdb=" C PRO A 376 " pdb=" O PRO A 376 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" CA LYS A 76 " pdb=" C LYS A 76 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.27e-02 6.20e+03 9.60e+00 ... (remaining 6341 not shown) Histogram of bond angle deviations from ideal: 92.78 - 101.03: 24 101.03 - 109.28: 508 109.28 - 117.53: 4128 117.53 - 125.77: 3856 125.77 - 134.02: 133 Bond angle restraints: 8649 Sorted by residual: angle pdb=" N ASN A 66 " pdb=" CA ASN A 66 " pdb=" C ASN A 66 " ideal model delta sigma weight residual 113.43 106.23 7.20 1.26e+00 6.30e-01 3.27e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 113.78 104.99 8.79 1.62e+00 3.81e-01 2.94e+01 angle pdb=" N SER A 295 " pdb=" CA SER A 295 " pdb=" C SER A 295 " ideal model delta sigma weight residual 112.45 106.28 6.17 1.39e+00 5.18e-01 1.97e+01 angle pdb=" N LEU A 64 " pdb=" CA LEU A 64 " pdb=" C LEU A 64 " ideal model delta sigma weight residual 113.21 108.41 4.80 1.15e+00 7.56e-01 1.74e+01 angle pdb=" N LYS A 117 " pdb=" CA LYS A 117 " pdb=" C LYS A 117 " ideal model delta sigma weight residual 113.23 108.11 5.12 1.24e+00 6.50e-01 1.70e+01 ... (remaining 8644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 3615 23.10 - 46.21: 294 46.21 - 69.31: 37 69.31 - 92.41: 1 92.41 - 115.52: 3 Dihedral angle restraints: 3950 sinusoidal: 1793 harmonic: 2157 Sorted by residual: dihedral pdb=" N CYS A 173 " pdb=" C CYS A 173 " pdb=" CA CYS A 173 " pdb=" CB CYS A 173 " ideal model delta harmonic sigma weight residual 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C CYS A 173 " pdb=" N CYS A 173 " pdb=" CA CYS A 173 " pdb=" CB CYS A 173 " ideal model delta harmonic sigma weight residual -122.60 -134.45 11.85 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -50.38 -35.62 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 899 0.085 - 0.169: 59 0.169 - 0.254: 4 0.254 - 0.338: 1 0.338 - 0.423: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA CYS A 173 " pdb=" N CYS A 173 " pdb=" C CYS A 173 " pdb=" CB CYS A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ASN A 66 " pdb=" N ASN A 66 " pdb=" C ASN A 66 " pdb=" CB ASN A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 961 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 162 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C LYS A 162 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS A 162 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 163 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 57 " 0.010 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C CYS A 57 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS A 57 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 58 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 95 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO L 96 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.030 5.00e-02 4.00e+02 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1439 2.78 - 3.31: 5637 3.31 - 3.84: 10043 3.84 - 4.37: 12044 4.37 - 4.90: 21055 Nonbonded interactions: 50218 Sorted by model distance: nonbonded pdb=" OH TYR L 95 " pdb=" OE2 GLU H 50 " model vdw 2.252 2.440 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.258 2.440 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.288 2.440 nonbonded pdb=" O PHE A 450 " pdb=" OG SER A 454 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR A 523 " pdb=" O TYR A 527 " model vdw 2.310 2.440 ... (remaining 50213 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.210 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.060 Find NCS groups from input model: 0.160 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6346 Z= 0.267 Angle : 0.670 8.791 8649 Z= 0.414 Chirality : 0.046 0.423 964 Planarity : 0.004 0.053 1021 Dihedral : 15.250 115.518 2575 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.47 % Allowed : 23.82 % Favored : 75.71 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 745 helix: 0.97 (0.28), residues: 374 sheet: 0.49 (0.56), residues: 108 loop : -0.85 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.001 0.000 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.016 0.001 TYR A 554 ARG 0.008 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.682 Fit side-chains REVERT: A 318 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7654 (ttt-90) outliers start: 3 outliers final: 3 residues processed: 79 average time/residue: 0.2271 time to fit residues: 22.9169 Evaluate side-chains 76 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6346 Z= 0.169 Angle : 0.507 9.773 8649 Z= 0.257 Chirality : 0.040 0.169 964 Planarity : 0.005 0.053 1021 Dihedral : 8.361 88.158 1299 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.05 % Allowed : 23.19 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.32), residues: 745 helix: 1.11 (0.27), residues: 378 sheet: 0.37 (0.57), residues: 102 loop : -0.67 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.001 0.000 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.014 0.001 TYR L 95 ARG 0.005 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.704 Fit side-chains REVERT: A 183 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6644 (t) REVERT: A 227 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7192 (t80) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 0.2156 time to fit residues: 23.8175 Evaluate side-chains 83 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6346 Z= 0.193 Angle : 0.508 11.429 8649 Z= 0.254 Chirality : 0.039 0.161 964 Planarity : 0.004 0.053 1021 Dihedral : 7.561 65.740 1296 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.31 % Allowed : 23.19 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.32), residues: 745 helix: 1.13 (0.27), residues: 378 sheet: 0.26 (0.56), residues: 101 loop : -0.72 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.015 0.001 PHE A 339 TYR 0.016 0.001 TYR L 95 ARG 0.006 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.694 Fit side-chains REVERT: A 183 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6739 (p) REVERT: A 227 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7161 (t80) REVERT: A 391 MET cc_start: 0.7570 (mmt) cc_final: 0.7322 (mmt) REVERT: A 566 ARG cc_start: 0.7378 (tpp80) cc_final: 0.7157 (tpp80) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 0.2017 time to fit residues: 24.6521 Evaluate side-chains 94 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 0.0170 chunk 58 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6346 Z= 0.170 Angle : 0.468 5.699 8649 Z= 0.238 Chirality : 0.038 0.158 964 Planarity : 0.004 0.053 1021 Dihedral : 6.848 58.323 1296 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.42 % Allowed : 21.77 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.32), residues: 745 helix: 1.23 (0.27), residues: 378 sheet: 0.27 (0.55), residues: 101 loop : -0.69 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.014 0.001 TYR L 95 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.706 Fit side-chains REVERT: A 227 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 350 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8091 (mttm) REVERT: A 391 MET cc_start: 0.7583 (mmt) cc_final: 0.7339 (mmt) outliers start: 28 outliers final: 18 residues processed: 101 average time/residue: 0.1995 time to fit residues: 26.2628 Evaluate side-chains 98 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6346 Z= 0.223 Angle : 0.495 5.732 8649 Z= 0.253 Chirality : 0.040 0.177 964 Planarity : 0.004 0.055 1021 Dihedral : 6.939 58.484 1296 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.42 % Allowed : 21.45 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.32), residues: 745 helix: 1.18 (0.27), residues: 379 sheet: 0.24 (0.56), residues: 101 loop : -0.82 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 HIS 0.003 0.001 HIS H 80 PHE 0.016 0.001 PHE A 339 TYR 0.015 0.001 TYR L 95 ARG 0.006 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 0.517 Fit side-chains REVERT: A 183 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6524 (p) REVERT: A 227 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7117 (t80) REVERT: A 350 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8136 (mttm) REVERT: A 391 MET cc_start: 0.7652 (mmt) cc_final: 0.7436 (mmt) outliers start: 28 outliers final: 22 residues processed: 97 average time/residue: 0.1964 time to fit residues: 24.9311 Evaluate side-chains 102 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6346 Z= 0.195 Angle : 0.485 5.782 8649 Z= 0.247 Chirality : 0.039 0.181 964 Planarity : 0.004 0.052 1021 Dihedral : 6.844 58.157 1296 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.73 % Allowed : 21.29 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.32), residues: 745 helix: 1.23 (0.27), residues: 379 sheet: 0.24 (0.56), residues: 101 loop : -0.76 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 230 HIS 0.003 0.001 HIS H 80 PHE 0.014 0.001 PHE A 339 TYR 0.015 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 0.719 Fit side-chains REVERT: A 183 THR cc_start: 0.7045 (OUTLIER) cc_final: 0.6536 (p) REVERT: A 227 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 350 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8113 (mttm) REVERT: A 391 MET cc_start: 0.7642 (mmt) cc_final: 0.7436 (mmt) REVERT: L 92 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7078 (m-80) outliers start: 30 outliers final: 21 residues processed: 105 average time/residue: 0.1900 time to fit residues: 26.3911 Evaluate side-chains 102 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6346 Z= 0.151 Angle : 0.463 5.697 8649 Z= 0.235 Chirality : 0.038 0.154 964 Planarity : 0.004 0.053 1021 Dihedral : 6.493 59.585 1296 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.26 % Allowed : 22.08 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.32), residues: 745 helix: 1.38 (0.28), residues: 378 sheet: 0.28 (0.56), residues: 101 loop : -0.70 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 230 HIS 0.001 0.000 HIS H 80 PHE 0.011 0.001 PHE A 339 TYR 0.011 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.748 Fit side-chains REVERT: A 183 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6554 (p) REVERT: A 227 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7136 (t80) REVERT: L 92 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7024 (m-80) outliers start: 27 outliers final: 19 residues processed: 100 average time/residue: 0.1870 time to fit residues: 24.8880 Evaluate side-chains 99 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 44 optimal weight: 0.0060 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6346 Z= 0.137 Angle : 0.461 5.822 8649 Z= 0.232 Chirality : 0.038 0.154 964 Planarity : 0.004 0.053 1021 Dihedral : 6.268 57.938 1296 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.79 % Allowed : 22.87 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.32), residues: 745 helix: 1.44 (0.28), residues: 378 sheet: 0.37 (0.54), residues: 107 loop : -0.68 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.002 0.000 HIS H 80 PHE 0.011 0.001 PHE A 339 TYR 0.011 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.686 Fit side-chains REVERT: A 174 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.6101 (m-80) REVERT: A 183 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 227 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7186 (t80) REVERT: L 92 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7002 (m-80) outliers start: 24 outliers final: 19 residues processed: 97 average time/residue: 0.1965 time to fit residues: 25.0526 Evaluate side-chains 99 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6346 Z= 0.184 Angle : 0.476 5.700 8649 Z= 0.242 Chirality : 0.039 0.160 964 Planarity : 0.004 0.053 1021 Dihedral : 6.330 57.124 1296 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.79 % Allowed : 22.56 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.32), residues: 745 helix: 1.39 (0.28), residues: 378 sheet: 0.23 (0.57), residues: 101 loop : -0.69 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 230 HIS 0.004 0.001 HIS H 80 PHE 0.014 0.001 PHE A 339 TYR 0.014 0.001 TYR L 95 ARG 0.007 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.684 Fit side-chains REVERT: A 183 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6606 (p) REVERT: A 227 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7120 (t80) REVERT: L 92 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7087 (m-80) outliers start: 24 outliers final: 21 residues processed: 95 average time/residue: 0.1894 time to fit residues: 24.0833 Evaluate side-chains 101 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 0.0770 chunk 6 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6346 Z= 0.115 Angle : 0.442 5.682 8649 Z= 0.224 Chirality : 0.037 0.152 964 Planarity : 0.004 0.053 1021 Dihedral : 5.975 58.506 1296 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.68 % Allowed : 23.50 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.32), residues: 745 helix: 1.58 (0.28), residues: 377 sheet: 0.29 (0.54), residues: 107 loop : -0.71 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 230 HIS 0.002 0.001 HIS H 80 PHE 0.009 0.001 PHE A 466 TYR 0.018 0.001 TYR A 554 ARG 0.007 0.000 ARG A 566 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.693 Fit side-chains REVERT: A 183 THR cc_start: 0.6796 (OUTLIER) cc_final: 0.6564 (p) REVERT: A 227 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7180 (t80) REVERT: A 566 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7262 (tpp80) outliers start: 17 outliers final: 14 residues processed: 93 average time/residue: 0.2083 time to fit residues: 25.8075 Evaluate side-chains 94 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107265 restraints weight = 7252.515| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.24 r_work: 0.3064 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6346 Z= 0.156 Angle : 0.459 5.677 8649 Z= 0.232 Chirality : 0.038 0.155 964 Planarity : 0.004 0.053 1021 Dihedral : 5.998 57.371 1296 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.15 % Allowed : 23.03 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.32), residues: 745 helix: 1.55 (0.28), residues: 377 sheet: 0.23 (0.54), residues: 107 loop : -0.73 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 230 HIS 0.003 0.001 HIS H 80 PHE 0.012 0.001 PHE A 339 TYR 0.017 0.001 TYR A 554 ARG 0.007 0.000 ARG A 566 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.27 seconds wall clock time: 33 minutes 57.04 seconds (2037.04 seconds total)