Starting phenix.real_space_refine on Sat May 10 04:41:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqi_37746/05_2025/8wqi_37746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqi_37746/05_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_37746/05_2025/8wqi_37746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqi_37746/05_2025/8wqi_37746.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqi_37746/05_2025/8wqi_37746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqi_37746/05_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-5687/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: 5.78, per 1000 atoms: 1.14 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: 1.24 Conformation dependent library (CDL) restraints added in 612.8 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: 0.54 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: 1.30 Time building geometry restraints manager: 1.47 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: 12.070 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- 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= 0.143 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 Details of bonding type rmsd hydrogen bonds : bond 0.16255 ( 227) hydrogen bonds : angle 5.98237 ( 666) covalent geometry : bond 0.00329 ( 5165) covalent geometry : angle 0.62047 ( 6999) *********************** 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 : 0.545 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: 0.2213 time to fit residues: 31.7471 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 : 0.665 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 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= 0.207 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 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 227) hydrogen bonds : angle 4.59154 ( 666) covalent geometry : bond 0.00493 ( 5165) covalent geometry : angle 0.63501 ( 6999) *********************** 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 : 0.567 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: 0.1975 time to fit residues: 20.4573 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 : 1.112 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.9990 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 = 0.200056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.170518 restraints weight = 6317.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.170354 restraints weight = 6194.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171879 restraints weight = 5235.007| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1801 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= 0.129 Angle : 0.586 7.831 6999 Z= 0.310 Chirality : 0.038 0.134 803 Planarity : 0.005 0.067 909 Dihedral : 4.454 21.988 700 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 1.64 % Allowed : 15.69 % Favored : 82.66 % 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: -0.95 (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 0.008 0.001 TRP G -2 HIS 0.006 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 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 227) hydrogen bonds : angle 4.32138 ( 666) covalent geometry : bond 0.00295 ( 5165) covalent geometry : angle 0.58567 ( 6999) *********************** 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 : 0.502 Fit side-chains REVERT: D 163 TYR cc_start: 0.8610 (t80) cc_final: 0.8206 (t80) REVERT: D 290 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5990 (mm) REVERT: D 399 ASN cc_start: 0.7847 (t0) cc_final: 0.7585 (t0) REVERT: D 423 ASN cc_start: 0.7776 (m-40) cc_final: 0.7306 (t0) REVERT: D 544 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.7866 (ptp90) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.1762 time to fit residues: 18.5316 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 : 0.534 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 511 ASN G -19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.195372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166158 restraints weight = 6391.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165496 restraints weight = 7333.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167076 restraints weight = 5932.189| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5165 Z= 0.188 Angle : 0.626 8.106 6999 Z= 0.329 Chirality : 0.040 0.125 803 Planarity : 0.005 0.068 909 Dihedral : 4.525 22.772 700 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 2.55 % Allowed : 17.52 % Favored : 79.93 % 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: -1.04 (0.34), residues: 638 helix: 0.10 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -1.97 (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 0.018 0.002 TYR D 472 ARG 0.005 0.001 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 227) hydrogen bonds : angle 4.35457 ( 666) covalent geometry : bond 0.00447 ( 5165) covalent geometry : angle 0.62581 ( 6999) *********************** 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 85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.557 Fit side-chains REVERT: D 1 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6041 (ptm) REVERT: D 69 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.4934 (p90) REVERT: D 163 TYR cc_start: 0.8574 (t80) cc_final: 0.8263 (t80) REVERT: D 342 ASP cc_start: 0.7452 (t70) cc_final: 0.7199 (t0) REVERT: D 399 ASN cc_start: 0.7848 (t0) cc_final: 0.7584 (t0) REVERT: D 423 ASN cc_start: 0.7712 (m-40) cc_final: 0.7402 (t0) REVERT: D 544 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7956 (ptp90) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 0.1670 time to fit residues: 17.8383 Evaluate side-chains 74 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 73 THR 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 511 ASN 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: 0.9980 chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN G -19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.195331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166406 restraints weight = 6366.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164955 restraints weight = 6975.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.166324 restraints weight = 5688.222| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2282 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= 0.172 Angle : 0.619 8.884 6999 Z= 0.327 Chirality : 0.039 0.125 803 Planarity : 0.005 0.067 909 Dihedral : 4.554 22.615 700 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.55 % Allowed : 19.71 % Favored : 77.74 % 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: -1.06 (0.34), residues: 638 helix: 0.08 (0.26), residues: 396 sheet: None (None), residues: 0 loop : -1.99 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.008 0.001 PHE D 623 TYR 0.026 0.002 TYR D 472 ARG 0.004 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 227) hydrogen bonds : angle 4.26186 ( 666) covalent geometry : bond 0.00408 ( 5165) covalent geometry : angle 0.61868 ( 6999) *********************** 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 84 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.520 Fit side-chains REVERT: D 1 MET cc_start: 0.6651 (pmm) cc_final: 0.6191 (ptp) REVERT: D 69 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.4886 (p90) REVERT: D 163 TYR cc_start: 0.8642 (t80) cc_final: 0.8280 (t80) REVERT: D 290 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5831 (mm) REVERT: D 342 ASP cc_start: 0.7472 (t70) cc_final: 0.7223 (t0) REVERT: D 399 ASN cc_start: 0.7856 (t0) cc_final: 0.7598 (t0) REVERT: D 423 ASN cc_start: 0.7749 (m-40) cc_final: 0.7442 (t0) REVERT: D 544 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.8035 (ptp90) REVERT: D 557 ILE cc_start: 0.8403 (tt) cc_final: 0.8175 (tt) outliers start: 14 outliers final: 5 residues processed: 80 average time/residue: 0.1759 time to fit residues: 18.4430 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 : 0.510 ------------------------------------------------------------------------------- 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 364 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.192151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.163232 restraints weight = 6196.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162637 restraints weight = 6577.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164404 restraints weight = 5011.199| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5165 Z= 0.157 Angle : 0.604 10.300 6999 Z= 0.318 Chirality : 0.038 0.126 803 Planarity : 0.005 0.066 909 Dihedral : 4.500 22.305 700 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.47 % Allowed : 20.26 % Favored : 76.28 % 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: -0.93 (0.34), residues: 638 helix: 0.18 (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 0.005 0.001 TRP G -2 HIS 0.006 0.001 HIS D 627 PHE 0.008 0.001 PHE D 623 TYR 0.023 0.002 TYR D 472 ARG 0.007 0.001 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 227) hydrogen bonds : angle 4.12527 ( 666) covalent geometry : bond 0.00371 ( 5165) covalent geometry : angle 0.60446 ( 6999) *********************** 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 to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.556 Fit side-chains REVERT: D 1 MET cc_start: 0.6665 (pmm) cc_final: 0.6148 (ptp) REVERT: D 36 LEU cc_start: 0.6662 (mp) cc_final: 0.6447 (mp) REVERT: D 69 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4997 (p90) REVERT: D 163 TYR cc_start: 0.8626 (t80) cc_final: 0.8280 (t80) REVERT: D 200 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7305 (mt) REVERT: D 290 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5700 (mm) REVERT: D 399 ASN cc_start: 0.7779 (t0) cc_final: 0.7516 (t0) REVERT: D 423 ASN cc_start: 0.7691 (m-40) cc_final: 0.7432 (t0) REVERT: D 482 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7897 (ptm160) REVERT: D 544 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8059 (ptp90) REVERT: D 557 ILE cc_start: 0.8365 (tt) cc_final: 0.8141 (tt) outliers start: 19 outliers final: 9 residues processed: 84 average time/residue: 0.1671 time to fit residues: 18.4967 Evaluate side-chains 74 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 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 609 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 58 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.194118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.165007 restraints weight = 6245.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.163766 restraints weight = 7087.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.165214 restraints weight = 5909.258| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2535 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= 0.196 Angle : 0.650 10.604 6999 Z= 0.337 Chirality : 0.039 0.127 803 Planarity : 0.005 0.066 909 Dihedral : 4.616 22.801 700 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 3.47 % Allowed : 20.99 % Favored : 75.55 % 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: -1.05 (0.33), residues: 638 helix: 0.13 (0.26), residues: 395 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 93 HIS 0.008 0.001 HIS D 166 PHE 0.009 0.001 PHE D 623 TYR 0.023 0.002 TYR D 472 ARG 0.007 0.001 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 227) hydrogen bonds : angle 4.22340 ( 666) covalent geometry : bond 0.00469 ( 5165) covalent geometry : angle 0.65002 ( 6999) *********************** 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 87 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.517 Fit side-chains REVERT: D 36 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6261 (mp) REVERT: D 69 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.4984 (p90) REVERT: D 163 TYR cc_start: 0.8690 (t80) cc_final: 0.8343 (t80) REVERT: D 200 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7338 (mt) REVERT: D 399 ASN cc_start: 0.7890 (t0) cc_final: 0.7614 (t0) REVERT: D 423 ASN cc_start: 0.7758 (m-40) cc_final: 0.7500 (t0) REVERT: D 482 ARG cc_start: 0.8458 (ptm160) cc_final: 0.8038 (ptm160) REVERT: D 557 ILE cc_start: 0.8401 (tt) cc_final: 0.8175 (tt) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.1534 time to fit residues: 17.0076 Evaluate side-chains 77 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 438 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 582 THR 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: 0.0980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 511 ASN G -19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.193820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168827 restraints weight = 6260.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167524 restraints weight = 7247.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.168226 restraints weight = 6366.977| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5165 Z= 0.147 Angle : 0.632 11.992 6999 Z= 0.327 Chirality : 0.038 0.129 803 Planarity : 0.005 0.065 909 Dihedral : 4.517 22.131 700 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.74 % Allowed : 22.81 % 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: -0.89 (0.34), residues: 638 helix: 0.25 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -2.00 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.006 0.001 ARG D 544 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 227) hydrogen bonds : angle 4.05228 ( 666) covalent geometry : bond 0.00346 ( 5165) covalent geometry : angle 0.63172 ( 6999) *********************** 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 80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.620 Fit side-chains REVERT: D 36 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6265 (mp) REVERT: D 69 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.5106 (p90) REVERT: D 163 TYR cc_start: 0.8634 (t80) cc_final: 0.8307 (t80) REVERT: D 290 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5528 (mm) REVERT: D 399 ASN cc_start: 0.7705 (t0) cc_final: 0.7462 (t0) REVERT: D 482 ARG cc_start: 0.8319 (ptm160) cc_final: 0.7922 (ptm160) REVERT: D 557 ILE cc_start: 0.8433 (tt) cc_final: 0.8205 (tt) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.2251 time to fit residues: 23.6219 Evaluate side-chains 76 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 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 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: 0.0010 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.189402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160826 restraints weight = 6249.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161149 restraints weight = 7857.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162250 restraints weight = 6143.573| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2662 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= 0.169 Angle : 0.647 12.466 6999 Z= 0.335 Chirality : 0.039 0.129 803 Planarity : 0.005 0.066 909 Dihedral : 4.514 22.470 700 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 3.10 % Allowed : 23.18 % 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: -0.92 (0.34), residues: 638 helix: 0.22 (0.26), residues: 397 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 241 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 0.022 0.001 TYR D 472 ARG 0.005 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 227) hydrogen bonds : angle 4.09484 ( 666) covalent geometry : bond 0.00401 ( 5165) covalent geometry : angle 0.64725 ( 6999) *********************** 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 to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.564 Fit side-chains REVERT: D 36 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6326 (mp) REVERT: D 69 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5048 (p90) REVERT: D 163 TYR cc_start: 0.8658 (t80) cc_final: 0.8335 (t80) REVERT: D 200 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7409 (mt) REVERT: D 399 ASN cc_start: 0.7813 (t0) cc_final: 0.7558 (t0) REVERT: D 482 ARG cc_start: 0.8468 (ptm160) cc_final: 0.8065 (ptm160) REVERT: D 557 ILE cc_start: 0.8429 (tt) cc_final: 0.8190 (tt) outliers start: 17 outliers final: 12 residues processed: 77 average time/residue: 0.1450 time to fit residues: 15.4151 Evaluate side-chains 76 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 528 VAL 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: 0.0270 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.0370 overall best weight: 0.2674 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.192830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163154 restraints weight = 6439.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.162379 restraints weight = 7620.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163911 restraints weight = 5770.282| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2699 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= 0.124 Angle : 0.628 13.188 6999 Z= 0.323 Chirality : 0.038 0.136 803 Planarity : 0.004 0.066 909 Dihedral : 4.424 21.472 700 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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: -0.70 (0.34), residues: 638 helix: 0.37 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.87 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 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 0.005 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 227) hydrogen bonds : angle 3.96271 ( 666) covalent geometry : bond 0.00284 ( 5165) covalent geometry : angle 0.62754 ( 6999) ********************** 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 80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.540 Fit side-chains REVERT: D 69 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.4974 (p90) REVERT: D 163 TYR cc_start: 0.8697 (t80) cc_final: 0.8361 (t80) REVERT: D 200 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7342 (mt) REVERT: D 290 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5299 (mm) REVERT: D 482 ARG cc_start: 0.8514 (ptm160) cc_final: 0.8139 (ptm160) REVERT: G -2 TRP cc_start: 0.7347 (m-10) cc_final: 0.7021 (m-10) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.1437 time to fit residues: 15.2756 Evaluate side-chains 68 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 364 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 619 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 0.0970 chunk 56 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.193169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163149 restraints weight = 6529.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164775 restraints weight = 7472.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165952 restraints weight = 5007.170| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5165 Z= 0.122 Angle : 0.631 12.874 6999 Z= 0.321 Chirality : 0.038 0.133 803 Planarity : 0.004 0.067 909 Dihedral : 4.352 21.364 700 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.01 % Allowed : 24.64 % 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: -0.60 (0.34), residues: 638 helix: 0.45 (0.27), residues: 398 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G -2 HIS 0.006 0.001 HIS D 166 PHE 0.006 0.001 PHE D 284 TYR 0.020 0.001 TYR D 472 ARG 0.006 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 227) hydrogen bonds : angle 3.97590 ( 666) covalent geometry : bond 0.00281 ( 5165) covalent geometry : angle 0.63064 ( 6999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.86 seconds wall clock time: 42 minutes 19.99 seconds (2539.99 seconds total)