Starting phenix.real_space_refine on Thu Mar 6 05:47:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqi_37746/03_2025/8wqi_37746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqi_37746/03_2025/8wqi_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/cci-nas-00/data/ceres_data/8wqi_37746/03_2025/8wqi_37746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqi_37746/03_2025/8wqi_37746.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqi_37746/03_2025/8wqi_37746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqi_37746/03_2025/8wqi_37746.cif" } 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.89, per 1000 atoms: 1.16 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 627.2 milliseconds 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: 0.48 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: 1.20 Time building geometry restraints manager: 1.40 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: 0.00 - 2.72: 6941 2.72 - 5.44: 52 5.44 - 8.15: 5 8.15 - 10.87: 0 10.87 - 13.59: 1 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 3.040 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 354 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR D 449 " pdb=" O PRO D 497 " model vdw 2.236 3.040 nonbonded pdb=" O ASP G -20 " pdb=" ND1 HIS G -17 " model vdw 2.300 3.120 nonbonded pdb=" O ASP D 87 " pdb=" OG1 THR D 118 " model vdw 2.315 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.585 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: 0.2195 time to fit residues: 31.4214 Evaluate side-chains 72 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.197125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167110 restraints weight = 6256.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167022 restraints weight = 6225.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.168526 restraints weight = 5375.525| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5165 Z= 0.324 Angle : 0.635 7.460 6999 Z= 0.335 Chirality : 0.041 0.123 803 Planarity : 0.005 0.070 909 Dihedral : 4.622 22.766 700 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 1.82 % Allowed : 11.68 % Favored : 86.50 % 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: -1.30 (0.33), residues: 638 helix: -0.15 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 209 HIS 0.008 0.001 HIS D 166 PHE 0.010 0.001 PHE D 549 TYR 0.025 0.002 TYR D 472 ARG 0.006 0.001 ARG D 387 *********************** 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 85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.402 Fit side-chains REVERT: D 153 TYR cc_start: 0.6494 (m-80) cc_final: 0.5524 (m-10) REVERT: D 163 TYR cc_start: 0.8597 (t80) cc_final: 0.8189 (t80) REVERT: D 318 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7433 (ttt-90) REVERT: D 399 ASN cc_start: 0.7961 (t0) cc_final: 0.7734 (t0) REVERT: D 423 ASN cc_start: 0.7828 (m-40) cc_final: 0.7293 (t0) REVERT: D 544 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.8017 (ptp90) REVERT: D 567 ASP cc_start: 0.8756 (t0) cc_final: 0.8521 (t0) outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 0.2480 time to fit residues: 26.0718 Evaluate side-chains 72 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 498 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 58 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS D 511 ASN G -19 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.199988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.170372 restraints weight = 6315.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.170024 restraints weight = 6647.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.171511 restraints weight = 5532.778| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5165 Z= 0.196 Angle : 0.588 7.870 6999 Z= 0.311 Chirality : 0.038 0.135 803 Planarity : 0.005 0.067 909 Dihedral : 4.458 21.994 700 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.64 % Allowed : 15.88 % Favored : 82.48 % 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: -0.96 (0.34), residues: 638 helix: 0.15 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -1.88 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G -2 HIS 0.005 0.001 HIS D 166 PHE 0.008 0.001 PHE D 284 TYR 0.020 0.001 TYR D 472 ARG 0.004 0.000 ARG D 171 *********************** 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 84 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.588 Fit side-chains REVERT: D 163 TYR cc_start: 0.8552 (t80) cc_final: 0.8167 (t80) REVERT: D 290 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.6022 (mm) REVERT: D 399 ASN cc_start: 0.7763 (t0) cc_final: 0.7508 (t0) REVERT: D 423 ASN cc_start: 0.7702 (m-40) cc_final: 0.7339 (t0) REVERT: D 544 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7849 (ptp90) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.2225 time to fit residues: 23.6627 Evaluate side-chains 65 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.0060 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN D 511 ASN G -19 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.193035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.164302 restraints weight = 6276.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163676 restraints weight = 6824.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165573 restraints weight = 5222.469| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2105 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= 0.266 Angle : 0.607 7.789 6999 Z= 0.321 Chirality : 0.039 0.124 803 Planarity : 0.005 0.067 909 Dihedral : 4.496 22.471 700 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 2.19 % Allowed : 18.25 % Favored : 79.56 % 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: 0.15 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G -2 HIS 0.005 0.001 HIS D 166 PHE 0.009 0.001 PHE D 623 TYR 0.017 0.002 TYR D 472 ARG 0.006 0.001 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 83 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.608 Fit side-chains REVERT: D 1 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6096 (ptp) REVERT: D 69 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.4949 (p90) REVERT: D 163 TYR cc_start: 0.8580 (t80) cc_final: 0.8267 (t80) REVERT: D 290 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.5857 (mm) REVERT: D 342 ASP cc_start: 0.7440 (t70) cc_final: 0.7190 (t0) REVERT: D 399 ASN cc_start: 0.7797 (t0) cc_final: 0.7547 (t0) REVERT: D 423 ASN cc_start: 0.7710 (m-40) cc_final: 0.7386 (t0) REVERT: D 544 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7934 (ptp90) outliers start: 12 outliers final: 4 residues processed: 78 average time/residue: 0.2328 time to fit residues: 24.2408 Evaluate side-chains 71 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET 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 438 ASP 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 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 HIS G -19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.167770 restraints weight = 6375.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165877 restraints weight = 6003.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167019 restraints weight = 5110.612| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2276 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= 0.254 Angle : 0.610 9.302 6999 Z= 0.321 Chirality : 0.039 0.128 803 Planarity : 0.005 0.066 909 Dihedral : 4.515 22.451 700 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.10 % Allowed : 18.98 % Favored : 77.92 % 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: -0.96 (0.34), residues: 638 helix: 0.15 (0.27), residues: 396 sheet: None (None), residues: 0 loop : -1.94 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 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 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 85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.558 Fit side-chains REVERT: D 1 MET cc_start: 0.6671 (pmm) cc_final: 0.6181 (ptp) REVERT: D 38 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: D 69 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.4642 (p90) REVERT: D 163 TYR cc_start: 0.8711 (t80) cc_final: 0.8333 (t80) REVERT: D 290 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.5716 (mm) REVERT: D 342 ASP cc_start: 0.7567 (t70) cc_final: 0.7209 (t0) REVERT: D 399 ASN cc_start: 0.7922 (t0) cc_final: 0.7654 (t0) REVERT: D 423 ASN cc_start: 0.7919 (m-40) cc_final: 0.7410 (t0) REVERT: D 544 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.8070 (ptp90) outliers start: 17 outliers final: 8 residues processed: 81 average time/residue: 0.1616 time to fit residues: 17.7253 Evaluate side-chains 75 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 TYR 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 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 4 optimal weight: 0.0030 chunk 58 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.199318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169583 restraints weight = 6338.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169606 restraints weight = 6057.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.171433 restraints weight = 4874.630| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5165 Z= 0.191 Angle : 0.582 10.347 6999 Z= 0.306 Chirality : 0.037 0.128 803 Planarity : 0.004 0.066 909 Dihedral : 4.400 21.675 700 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.92 % Allowed : 20.07 % Favored : 77.01 % 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: -0.76 (0.34), residues: 638 helix: 0.32 (0.27), residues: 396 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.005 0.001 PHE D 623 TYR 0.023 0.001 TYR D 472 ARG 0.007 0.000 ARG D 264 *********************** 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 88 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.900 Fit side-chains REVERT: D 1 MET cc_start: 0.6715 (pmm) cc_final: 0.5970 (ptm) REVERT: D 36 LEU cc_start: 0.6487 (mp) cc_final: 0.6187 (mp) REVERT: D 38 TYR cc_start: 0.5440 (OUTLIER) cc_final: 0.5073 (m-80) REVERT: D 69 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.4968 (p90) REVERT: D 163 TYR cc_start: 0.8661 (t80) cc_final: 0.8328 (t80) REVERT: D 290 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5521 (mm) REVERT: D 399 ASN cc_start: 0.7712 (t0) cc_final: 0.7469 (t0) REVERT: D 423 ASN cc_start: 0.7725 (m-40) cc_final: 0.7382 (t0) REVERT: D 544 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8015 (ptp90) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.1999 time to fit residues: 21.6278 Evaluate side-chains 72 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 TYR 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 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 511 ASN Chi-restraints excluded: chain D residue 544 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 58 optimal weight: 0.0570 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167870 restraints weight = 6230.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167224 restraints weight = 6544.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.168746 restraints weight = 5385.668| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2458 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= 0.237 Angle : 0.612 10.958 6999 Z= 0.318 Chirality : 0.038 0.129 803 Planarity : 0.004 0.065 909 Dihedral : 4.402 22.066 700 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 4.01 % Allowed : 20.99 % Favored : 75.00 % 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: -0.84 (0.34), residues: 638 helix: 0.25 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G -2 HIS 0.008 0.001 HIS D 166 PHE 0.007 0.001 PHE D 623 TYR 0.022 0.001 TYR D 472 ARG 0.007 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 89 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.514 Fit side-chains REVERT: D 36 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6260 (mp) REVERT: D 38 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.5129 (m-80) REVERT: D 69 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.4945 (p90) REVERT: D 163 TYR cc_start: 0.8699 (t80) cc_final: 0.8364 (t80) REVERT: D 200 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7289 (mt) REVERT: D 399 ASN cc_start: 0.7738 (t0) cc_final: 0.7493 (t0) REVERT: D 423 ASN cc_start: 0.7708 (m-40) cc_final: 0.7407 (t0) REVERT: D 544 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8055 (ptp90) outliers start: 22 outliers final: 12 residues processed: 82 average time/residue: 0.1499 time to fit residues: 16.5201 Evaluate side-chains 80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 64 LEU 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 317 ILE Chi-restraints excluded: chain D residue 364 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 511 ASN Chi-restraints excluded: chain D residue 544 ARG Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.195752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165994 restraints weight = 6328.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165487 restraints weight = 6044.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.166831 restraints weight = 5114.359| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2542 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= 0.268 Angle : 0.638 11.830 6999 Z= 0.330 Chirality : 0.039 0.127 803 Planarity : 0.005 0.064 909 Dihedral : 4.451 22.411 700 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.83 % Allowed : 21.17 % Favored : 75.00 % 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: -0.83 (0.34), residues: 638 helix: 0.26 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.008 0.001 PHE D 623 TYR 0.022 0.001 TYR D 472 ARG 0.013 0.001 ARG D 482 *********************** 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 87 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.518 Fit side-chains REVERT: D 36 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6240 (mp) REVERT: D 38 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: D 69 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.4946 (p90) REVERT: D 163 TYR cc_start: 0.8705 (t80) cc_final: 0.8386 (t80) REVERT: D 200 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7318 (mt) REVERT: D 399 ASN cc_start: 0.7767 (t0) cc_final: 0.7520 (t0) REVERT: D 423 ASN cc_start: 0.7775 (m-40) cc_final: 0.7472 (t0) REVERT: D 544 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (ptp90) REVERT: D 557 ILE cc_start: 0.8478 (tt) cc_final: 0.8239 (tt) outliers start: 21 outliers final: 15 residues processed: 81 average time/residue: 0.1947 time to fit residues: 21.2351 Evaluate side-chains 84 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 TYR 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 73 THR 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 364 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 511 ASN Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 544 ARG Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.192949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.167659 restraints weight = 6279.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166985 restraints weight = 8724.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.167469 restraints weight = 7021.899| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2584 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= 0.255 Angle : 0.639 13.049 6999 Z= 0.328 Chirality : 0.039 0.140 803 Planarity : 0.004 0.063 909 Dihedral : 4.440 22.310 700 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.83 % Allowed : 22.45 % Favored : 73.72 % 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: 0.25 (0.26), residues: 398 sheet: None (None), residues: 0 loop : -1.87 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.008 0.001 PHE D 623 TYR 0.022 0.001 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 88 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.688 Fit side-chains REVERT: D 36 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6345 (mp) REVERT: D 38 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: D 69 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5074 (p90) REVERT: D 163 TYR cc_start: 0.8627 (t80) cc_final: 0.8322 (t80) REVERT: D 200 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7410 (mt) REVERT: D 399 ASN cc_start: 0.7714 (t0) cc_final: 0.7471 (t0) REVERT: D 544 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (ptp90) REVERT: D 557 ILE cc_start: 0.8435 (tt) cc_final: 0.8185 (tt) outliers start: 21 outliers final: 14 residues processed: 81 average time/residue: 0.1688 time to fit residues: 19.0009 Evaluate side-chains 81 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 TYR 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 73 THR 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 364 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 511 ASN Chi-restraints excluded: chain D residue 544 ARG Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.190972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161046 restraints weight = 6436.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.160188 restraints weight = 7676.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.162014 restraints weight = 5415.763| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5165 Z= 0.209 Angle : 0.627 13.318 6999 Z= 0.321 Chirality : 0.038 0.132 803 Planarity : 0.004 0.064 909 Dihedral : 4.388 21.745 700 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.28 % Allowed : 23.36 % 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: -0.68 (0.34), residues: 638 helix: 0.34 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.77 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.007 0.001 PHE D 623 TYR 0.021 0.001 TYR D 472 ARG 0.005 0.000 ARG D 171 ********************** 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 84 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 1.067 Fit side-chains REVERT: D 36 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6379 (mp) REVERT: D 38 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.5089 (m-80) REVERT: D 69 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.4922 (p90) REVERT: D 163 TYR cc_start: 0.8730 (t80) cc_final: 0.8415 (t80) REVERT: D 200 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7345 (mt) REVERT: G -2 TRP cc_start: 0.7381 (m-10) cc_final: 0.6970 (m-10) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 0.2187 time to fit residues: 23.4982 Evaluate side-chains 79 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 68 HIS 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 317 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 511 ASN Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 44 optimal weight: 0.1980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.192207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162416 restraints weight = 6550.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163243 restraints weight = 7335.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164681 restraints weight = 5571.672| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2673 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= 0.191 Angle : 0.620 13.086 6999 Z= 0.317 Chirality : 0.038 0.134 803 Planarity : 0.004 0.065 909 Dihedral : 4.343 21.486 700 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 2.74 % Allowed : 23.91 % 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: -0.57 (0.34), residues: 638 helix: 0.43 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.71 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.006 0.001 PHE D 623 TYR 0.020 0.001 TYR D 472 ARG 0.004 0.000 ARG D 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3345.96 seconds wall clock time: 62 minutes 4.29 seconds (3724.29 seconds total)