Starting phenix.real_space_refine on Mon May 6 21:07:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqi_37746/05_2024/8wqi_37746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqi_37746/05_2024/8wqi_37746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqi_37746/05_2024/8wqi_37746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqi_37746/05_2024/8wqi_37746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqi_37746/05_2024/8wqi_37746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqi_37746/05_2024/8wqi_37746.pdb" } resolution = 3.5 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= 0.023 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 29 5.16 5 C 3186 2.51 5 N 909 2.21 5 O 950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 5074 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 145 Classifications: {'peptide': 17} Modifications used: {'COO': 1} Link IDs: {'TRANS': 16} Chain breaks: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.65 Number of scatterers: 5074 At special positions: 0 Unit cell: (109.88, 101.68, 78.72, 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 29 16.00 O 950 8.00 N 909 7.00 C 3186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 62.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'D' and resid 4 through 14 removed outlier: 4.278A pdb=" N VAL D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 28 through 37 Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.791A pdb=" N ILE D 52 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.902A pdb=" N VAL D 62 " --> pdb=" O HIS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.604A pdb=" N VAL D 104 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.636A pdb=" N VAL D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.501A pdb=" N ILE D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 189 through 198 removed outlier: 3.694A pdb=" N PHE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.547A pdb=" N VAL D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.545A pdb=" N SER D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.676A pdb=" N VAL D 235 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.722A pdb=" N SER D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 251 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.780A pdb=" N HIS D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 320 through 337 removed outlier: 3.668A pdb=" N HIS D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.317A pdb=" N ILE D 347 " --> pdb=" O VAL D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 376 removed outlier: 3.515A pdb=" N CYS D 363 " --> pdb=" O GLU D 359 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.921A pdb=" N ASN D 399 " --> pdb=" O MET D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 427 Processing helix chain 'D' and resid 432 through 456 Processing helix chain 'D' and resid 460 through 478 removed outlier: 3.661A pdb=" N LEU D 474 " --> pdb=" O GLN D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 534 through 541 removed outlier: 3.569A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN D 541 " --> pdb=" O HIS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 575 through 580 removed outlier: 3.993A pdb=" N SER D 580 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 592 removed outlier: 3.607A pdb=" N LEU D 588 " --> pdb=" O VAL D 584 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 589 " --> pdb=" O SER D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 608 Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.952A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'G' and resid -21 through -14 removed outlier: 3.742A pdb=" N LYS G -16 " --> pdb=" O HIS G -19 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS G -14 " --> pdb=" O HIS G -17 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 666 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: 1.19 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1734 1.34 - 1.46: 933 1.46 - 1.58: 2457 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 5165 Sorted by residual: bond pdb=" CB ILE D 555 " pdb=" CG2 ILE D 555 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" CB VAL D 391 " pdb=" CG2 VAL D 391 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.32e-01 bond pdb=" CB VAL D 540 " pdb=" CG1 VAL D 540 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.03e-01 bond pdb=" CB THR D 569 " pdb=" CG2 THR D 569 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CE LYS D 293 " pdb=" NZ LYS D 293 " ideal model delta sigma weight residual 1.489 1.466 0.023 3.00e-02 1.11e+03 5.86e-01 ... (remaining 5160 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.08: 108 107.08 - 113.82: 3000 113.82 - 120.56: 2026 120.56 - 127.30: 1814 127.30 - 134.04: 51 Bond angle restraints: 6999 Sorted by residual: angle pdb=" CA LEU D 50 " pdb=" CB LEU D 50 " pdb=" CG LEU D 50 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA GLN D 285 " pdb=" CB GLN D 285 " pdb=" CG GLN D 285 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 angle pdb=" C ASN D 155 " pdb=" N THR D 156 " pdb=" CA THR D 156 " ideal model delta sigma weight residual 120.82 125.22 -4.40 1.47e+00 4.63e-01 8.95e+00 angle pdb=" N ASN D 399 " pdb=" CA ASN D 399 " pdb=" C ASN D 399 " ideal model delta sigma weight residual 114.16 110.57 3.59 1.48e+00 4.57e-01 5.90e+00 angle pdb=" C GLN D 285 " pdb=" CA GLN D 285 " pdb=" CB GLN D 285 " ideal model delta sigma weight residual 111.42 114.31 -2.89 1.31e+00 5.83e-01 4.86e+00 ... (remaining 6994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 2678 15.80 - 31.60: 346 31.60 - 47.39: 76 47.39 - 63.19: 11 63.19 - 78.99: 3 Dihedral angle restraints: 3114 sinusoidal: 1228 harmonic: 1886 Sorted by residual: dihedral pdb=" CA ASN D 399 " pdb=" C ASN D 399 " pdb=" N GLU D 400 " pdb=" CA GLU D 400 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU D 50 " pdb=" C LEU D 50 " pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA THR D 551 " pdb=" C THR D 551 " pdb=" N LEU D 552 " pdb=" CA LEU D 552 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 587 0.042 - 0.084: 177 0.084 - 0.126: 34 0.126 - 0.168: 4 0.168 - 0.210: 1 Chirality restraints: 803 Sorted by residual: chirality pdb=" CG LEU D 50 " pdb=" CB LEU D 50 " pdb=" CD1 LEU D 50 " pdb=" CD2 LEU D 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE D 610 " pdb=" CA ILE D 610 " pdb=" CG1 ILE D 610 " pdb=" CG2 ILE D 610 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CB VAL D 71 " pdb=" CA VAL D 71 " pdb=" CG1 VAL D 71 " pdb=" CG2 VAL D 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 800 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 616 " 0.042 5.00e-02 4.00e+02 6.44e-02 6.65e+00 pdb=" N PRO D 617 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 617 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 617 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 123 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO D 124 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 404 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO D 405 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 405 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 405 " 0.027 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 300 2.73 - 3.27: 5332 3.27 - 3.82: 8581 3.82 - 4.36: 10027 4.36 - 4.90: 16903 Nonbonded interactions: 41143 Sorted by model distance: nonbonded pdb=" OD2 ASP D 548 " pdb=" OG1 THR D 551 " model vdw 2.188 2.440 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 354 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR D 449 " pdb=" O PRO D 497 " model vdw 2.236 2.440 nonbonded pdb=" O ASP G -20 " pdb=" ND1 HIS G -17 " model vdw 2.300 2.520 nonbonded pdb=" O ASP D 87 " pdb=" OG1 THR D 118 " model vdw 2.315 2.440 ... (remaining 41138 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: 5.880 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: 27.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.140 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 5165 Z= 0.218 Angle : 0.620 13.589 6999 Z= 0.325 Chirality : 0.040 0.210 803 Planarity : 0.005 0.064 909 Dihedral : 14.513 78.990 1892 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.75 (0.32), residues: 638 helix: -0.58 (0.25), residues: 389 sheet: None (None), residues: 0 loop : -1.99 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 367 HIS 0.005 0.001 HIS D 476 PHE 0.011 0.001 PHE D 388 TYR 0.015 0.001 TYR D 472 ARG 0.006 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.496 Fit side-chains REVERT: D 153 TYR cc_start: 0.6567 (m-80) cc_final: 0.5894 (m-10) REVERT: D 163 TYR cc_start: 0.8603 (t80) cc_final: 0.8109 (t80) REVERT: D 318 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7047 (ttt-90) REVERT: D 616 ILE cc_start: 0.9110 (tt) cc_final: 0.8845 (mm) REVERT: D 619 THR cc_start: 0.8598 (t) cc_final: 0.8255 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2224 time to fit residues: 31.7290 Evaluate side-chains 72 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN D 176 GLN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5165 Z= 0.290 Angle : 0.604 7.221 6999 Z= 0.319 Chirality : 0.040 0.136 803 Planarity : 0.005 0.069 909 Dihedral : 4.558 22.995 700 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 2.37 % Allowed : 11.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.27 (0.33), residues: 638 helix: -0.16 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 209 HIS 0.009 0.001 HIS D 166 PHE 0.009 0.001 PHE D 549 TYR 0.025 0.002 TYR D 472 ARG 0.005 0.001 ARG D 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: D 153 TYR cc_start: 0.6758 (m-80) cc_final: 0.5803 (m-10) REVERT: D 163 TYR cc_start: 0.8662 (t80) cc_final: 0.8288 (t80) REVERT: D 317 ILE cc_start: 0.7913 (mt) cc_final: 0.7638 (mt) REVERT: D 318 ARG cc_start: 0.7605 (ttp-110) cc_final: 0.7299 (ttt-90) REVERT: D 399 ASN cc_start: 0.8252 (t0) cc_final: 0.8021 (t0) REVERT: D 423 ASN cc_start: 0.7838 (m-40) cc_final: 0.7212 (t0) REVERT: D 544 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8216 (ptp90) outliers start: 13 outliers final: 7 residues processed: 84 average time/residue: 0.2100 time to fit residues: 22.5373 Evaluate side-chains 70 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN G -19 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5165 Z= 0.221 Angle : 0.578 7.682 6999 Z= 0.305 Chirality : 0.038 0.123 803 Planarity : 0.005 0.068 909 Dihedral : 4.456 22.957 700 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.19 % Allowed : 15.69 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.06 (0.33), residues: 638 helix: 0.05 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -1.91 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 209 HIS 0.005 0.001 HIS D 166 PHE 0.010 0.001 PHE D 284 TYR 0.020 0.001 TYR D 472 ARG 0.006 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.572 Fit side-chains REVERT: D 153 TYR cc_start: 0.6675 (m-80) cc_final: 0.5582 (m-10) REVERT: D 163 TYR cc_start: 0.8680 (t80) cc_final: 0.8263 (t80) REVERT: D 290 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6047 (mm) REVERT: D 318 ARG cc_start: 0.7628 (ttp-110) cc_final: 0.7316 (ttt-90) REVERT: D 399 ASN cc_start: 0.8224 (t0) cc_final: 0.7966 (t0) REVERT: D 423 ASN cc_start: 0.7865 (m-40) cc_final: 0.7273 (t0) REVERT: D 544 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8228 (ptp90) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.1845 time to fit residues: 19.1422 Evaluate side-chains 71 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 0.0570 chunk 54 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5165 Z= 0.180 Angle : 0.561 7.354 6999 Z= 0.294 Chirality : 0.037 0.124 803 Planarity : 0.004 0.066 909 Dihedral : 4.377 22.356 700 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.01 % Allowed : 18.25 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.82 (0.34), residues: 638 helix: 0.22 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.006 0.001 PHE D 284 TYR 0.017 0.001 TYR D 472 ARG 0.006 0.000 ARG D 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.597 Fit side-chains REVERT: D 69 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.4534 (p90) REVERT: D 163 TYR cc_start: 0.8717 (t80) cc_final: 0.8312 (t80) REVERT: D 290 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5793 (mm) REVERT: D 318 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7322 (ttt-90) REVERT: D 399 ASN cc_start: 0.8162 (t0) cc_final: 0.7913 (t0) REVERT: D 423 ASN cc_start: 0.7794 (m-40) cc_final: 0.7208 (t0) REVERT: D 543 ASN cc_start: 0.8135 (t0) cc_final: 0.7851 (m-40) REVERT: D 544 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8234 (ptp90) REVERT: D 606 ARG cc_start: 0.8374 (tpt-90) cc_final: 0.8086 (mmm-85) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.1943 time to fit residues: 21.3584 Evaluate side-chains 72 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5165 Z= 0.251 Angle : 0.604 9.409 6999 Z= 0.312 Chirality : 0.038 0.120 803 Planarity : 0.005 0.066 909 Dihedral : 4.421 22.977 700 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 3.10 % Allowed : 18.80 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.97 (0.34), residues: 638 helix: 0.13 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G -2 HIS 0.008 0.001 HIS D 100 PHE 0.007 0.001 PHE D 623 TYR 0.025 0.002 TYR D 472 ARG 0.005 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.272 Fit side-chains REVERT: D 69 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.4494 (p90) REVERT: D 163 TYR cc_start: 0.8745 (t80) cc_final: 0.8352 (t80) REVERT: D 290 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5784 (mm) REVERT: D 318 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7428 (ttt-90) REVERT: D 399 ASN cc_start: 0.8183 (t0) cc_final: 0.7921 (t0) REVERT: D 423 ASN cc_start: 0.7855 (m-40) cc_final: 0.7281 (t0) REVERT: D 544 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8311 (ptp90) REVERT: D 606 ARG cc_start: 0.8414 (tpt-90) cc_final: 0.8114 (mmm-85) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.2403 time to fit residues: 26.2156 Evaluate side-chains 76 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 511 ASN Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5165 Z= 0.271 Angle : 0.604 10.206 6999 Z= 0.313 Chirality : 0.038 0.122 803 Planarity : 0.005 0.065 909 Dihedral : 4.487 23.246 700 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.10 % Allowed : 21.72 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.01 (0.34), residues: 638 helix: 0.10 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G -2 HIS 0.007 0.001 HIS D 100 PHE 0.008 0.001 PHE D 623 TYR 0.024 0.002 TYR D 472 ARG 0.004 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.597 Fit side-chains REVERT: D 69 TYR cc_start: 0.5892 (OUTLIER) cc_final: 0.4415 (p90) REVERT: D 163 TYR cc_start: 0.8768 (t80) cc_final: 0.8398 (t80) REVERT: D 290 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.5790 (mm) REVERT: D 399 ASN cc_start: 0.8217 (t0) cc_final: 0.7936 (t0) REVERT: D 423 ASN cc_start: 0.7892 (m-40) cc_final: 0.7366 (t0) REVERT: D 557 ILE cc_start: 0.8728 (tt) cc_final: 0.8512 (tt) outliers start: 17 outliers final: 10 residues processed: 87 average time/residue: 0.1776 time to fit residues: 20.0727 Evaluate side-chains 78 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 511 ASN Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 51 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5165 Z= 0.164 Angle : 0.580 11.295 6999 Z= 0.299 Chirality : 0.037 0.132 803 Planarity : 0.004 0.064 909 Dihedral : 4.359 22.080 700 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.19 % Allowed : 22.99 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.66 (0.34), residues: 638 helix: 0.39 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G -2 HIS 0.005 0.001 HIS D 166 PHE 0.005 0.001 PHE D 549 TYR 0.021 0.001 TYR D 472 ARG 0.003 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.566 Fit side-chains REVERT: D 36 LEU cc_start: 0.6410 (mp) cc_final: 0.6036 (mp) REVERT: D 69 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.4455 (p90) REVERT: D 146 ASN cc_start: 0.7433 (m-40) cc_final: 0.7199 (m-40) REVERT: D 163 TYR cc_start: 0.8780 (t80) cc_final: 0.8432 (t80) REVERT: D 290 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5425 (mm) REVERT: D 342 ASP cc_start: 0.7553 (t70) cc_final: 0.7054 (t0) REVERT: D 423 ASN cc_start: 0.7858 (m-40) cc_final: 0.7271 (t0) REVERT: D 482 ARG cc_start: 0.8747 (ptm160) cc_final: 0.8391 (mtm110) REVERT: D 606 ARG cc_start: 0.8366 (tpt-90) cc_final: 0.8072 (mmm-85) outliers start: 12 outliers final: 5 residues processed: 80 average time/residue: 0.1781 time to fit residues: 18.7065 Evaluate side-chains 72 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 58 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5165 Z= 0.187 Angle : 0.587 11.887 6999 Z= 0.301 Chirality : 0.037 0.135 803 Planarity : 0.004 0.065 909 Dihedral : 4.283 22.220 700 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.37 % Allowed : 22.99 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.58 (0.34), residues: 638 helix: 0.47 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G -2 HIS 0.008 0.001 HIS D 166 PHE 0.005 0.001 PHE D 623 TYR 0.021 0.001 TYR D 472 ARG 0.006 0.000 ARG D 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.651 Fit side-chains REVERT: D 36 LEU cc_start: 0.6355 (mp) cc_final: 0.6142 (mp) REVERT: D 69 TYR cc_start: 0.5796 (OUTLIER) cc_final: 0.4504 (p90) REVERT: D 146 ASN cc_start: 0.7474 (m-40) cc_final: 0.7248 (m-40) REVERT: D 163 TYR cc_start: 0.8793 (t80) cc_final: 0.8459 (t80) REVERT: D 290 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5359 (mm) REVERT: D 342 ASP cc_start: 0.7573 (t70) cc_final: 0.7110 (t0) REVERT: D 423 ASN cc_start: 0.7795 (m-40) cc_final: 0.7260 (t0) REVERT: D 482 ARG cc_start: 0.8780 (ptm160) cc_final: 0.8423 (ptm160) REVERT: D 606 ARG cc_start: 0.8388 (tpt-90) cc_final: 0.8145 (mmm-85) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.1886 time to fit residues: 19.0949 Evaluate side-chains 70 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 577 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5165 Z= 0.252 Angle : 0.627 11.971 6999 Z= 0.320 Chirality : 0.038 0.133 803 Planarity : 0.005 0.064 909 Dihedral : 4.382 23.129 700 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.55 % Allowed : 22.99 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.74 (0.34), residues: 638 helix: 0.35 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G -2 HIS 0.007 0.001 HIS D 166 PHE 0.007 0.001 PHE D 623 TYR 0.022 0.002 TYR D 472 ARG 0.005 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.566 Fit side-chains REVERT: D 69 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.4423 (p90) REVERT: D 163 TYR cc_start: 0.8815 (t80) cc_final: 0.8477 (t80) REVERT: D 200 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7172 (mt) REVERT: D 290 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5482 (mm) REVERT: D 342 ASP cc_start: 0.7684 (t70) cc_final: 0.7199 (t0) REVERT: D 399 ASN cc_start: 0.8188 (t0) cc_final: 0.7924 (t0) REVERT: D 423 ASN cc_start: 0.7839 (m-40) cc_final: 0.7363 (t0) REVERT: D 482 ARG cc_start: 0.8821 (ptm160) cc_final: 0.8447 (ptm160) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.1612 time to fit residues: 17.1918 Evaluate side-chains 77 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5165 Z= 0.202 Angle : 0.606 12.644 6999 Z= 0.309 Chirality : 0.037 0.120 803 Planarity : 0.004 0.063 909 Dihedral : 4.354 22.631 700 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.19 % Allowed : 23.91 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.63 (0.34), residues: 638 helix: 0.44 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G -2 HIS 0.007 0.001 HIS D 166 PHE 0.006 0.001 PHE D 623 TYR 0.021 0.001 TYR D 472 ARG 0.005 0.000 ARG D 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.539 Fit side-chains REVERT: D 69 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.4474 (p90) REVERT: D 163 TYR cc_start: 0.8795 (t80) cc_final: 0.8462 (t80) REVERT: D 200 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7196 (mt) REVERT: D 290 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5427 (mm) REVERT: D 342 ASP cc_start: 0.7604 (t70) cc_final: 0.7143 (t0) REVERT: D 423 ASN cc_start: 0.7822 (m-40) cc_final: 0.7348 (t0) REVERT: D 482 ARG cc_start: 0.8804 (ptm160) cc_final: 0.8455 (ptm160) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1585 time to fit residues: 15.9381 Evaluate side-chains 74 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.185657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.156948 restraints weight = 6286.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156515 restraints weight = 6155.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157846 restraints weight = 5023.006| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5165 Z= 0.262 Angle : 0.643 11.934 6999 Z= 0.324 Chirality : 0.039 0.126 803 Planarity : 0.005 0.064 909 Dihedral : 4.410 23.213 700 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 2.37 % Allowed : 24.27 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.75 (0.34), residues: 638 helix: 0.36 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.93 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.007 0.001 PHE D 623 TYR 0.022 0.002 TYR D 472 ARG 0.003 0.000 ARG D 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.07 seconds wall clock time: 36 minutes 22.42 seconds (2182.42 seconds total)