Starting phenix.real_space_refine on Wed Jun 4 17:45:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgz_60093/06_2025/8zgz_60093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgz_60093/06_2025/8zgz_60093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgz_60093/06_2025/8zgz_60093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgz_60093/06_2025/8zgz_60093.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgz_60093/06_2025/8zgz_60093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgz_60093/06_2025/8zgz_60093.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 24 5.16 5 C 2415 2.51 5 N 578 2.21 5 O 605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3622 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3622 Classifications: {'peptide': 471} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.35, per 1000 atoms: 0.92 Number of scatterers: 3622 At special positions: 0 Unit cell: (75.7092, 76.6105, 73.0053, 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 24 16.00 O 605 8.00 N 578 7.00 C 2415 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: 0.98 Conformation dependent library (CDL) restraints added in 471.4 milliseconds 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 removed outlier: 3.524A pdb=" N SER A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 3.643A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.582A pdb=" N ALA A 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 72 removed outlier: 4.130A pdb=" N TRP A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Proline residue: A 67 - end of helix removed outlier: 4.160A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.647A pdb=" N TRP A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 135 Processing helix chain 'A' and resid 142 through 159 Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.569A pdb=" N ASP A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.725A pdb=" N TYR A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.723A pdb=" N LEU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.702A pdb=" N MET A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.560A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.724A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.711A pdb=" N GLY A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 362 through 379 removed outlier: 4.363A pdb=" N TYR A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.683A pdb=" N GLU A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 378 " --> pdb=" O TRP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.541A pdb=" N TYR A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 402 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.801A pdb=" N TYR A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.877A pdb=" N LEU A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLY A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 440 " --> pdb=" O CYS A 436 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 449 " --> pdb=" O MET A 445 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 485 removed outlier: 3.661A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 720 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: 1.04 Time building geometry restraints manager: 1.17 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: 1094 1.34 - 1.46: 893 1.46 - 1.58: 1681 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 3710 Sorted by residual: bond pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " ideal model delta sigma weight residual 1.533 1.549 -0.015 1.51e-02 4.39e+03 1.02e+00 bond pdb=" CA LEU A 244 " pdb=" C LEU A 244 " ideal model delta sigma weight residual 1.523 1.510 0.014 1.80e-02 3.09e+03 5.81e-01 bond pdb=" CA ALA A 276 " pdb=" C ALA A 276 " ideal model delta sigma weight residual 1.523 1.514 0.009 1.30e-02 5.92e+03 5.18e-01 bond pdb=" CA GLU A 102 " pdb=" CB GLU A 102 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.68e-02 3.54e+03 5.05e-01 bond pdb=" CB GLN A 36 " pdb=" CG GLN A 36 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.67e-01 ... (remaining 3705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4882 1.28 - 2.56: 130 2.56 - 3.84: 22 3.84 - 5.12: 12 5.12 - 6.41: 3 Bond angle restraints: 5049 Sorted by residual: angle pdb=" C ALA A 392 " pdb=" N VAL A 393 " pdb=" CA VAL A 393 " ideal model delta sigma weight residual 120.33 122.67 -2.34 8.00e-01 1.56e+00 8.56e+00 angle pdb=" N MET A 242 " pdb=" CA MET A 242 " pdb=" C MET A 242 " ideal model delta sigma weight residual 108.31 104.43 3.88 1.52e+00 4.33e-01 6.52e+00 angle pdb=" C PRO A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.92e+00 angle pdb=" N ALA A 257 " pdb=" CA ALA A 257 " pdb=" C ALA A 257 " ideal model delta sigma weight residual 111.28 114.15 -2.87 1.35e+00 5.49e-01 4.52e+00 angle pdb=" C VAL A 393 " pdb=" CA VAL A 393 " pdb=" CB VAL A 393 " ideal model delta sigma weight residual 114.00 111.53 2.47 1.31e+00 5.83e-01 3.55e+00 ... (remaining 5044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 1775 14.79 - 29.58: 233 29.58 - 44.36: 88 44.36 - 59.15: 19 59.15 - 73.94: 9 Dihedral angle restraints: 2124 sinusoidal: 787 harmonic: 1337 Sorted by residual: dihedral pdb=" CA ALA A 257 " pdb=" C ALA A 257 " pdb=" N GLY A 258 " pdb=" CA GLY A 258 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA PHE A 240 " pdb=" C PHE A 240 " pdb=" N ALA A 241 " pdb=" CA ALA A 241 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CG ARG A 365 " pdb=" CD ARG A 365 " pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sinusoidal sigma weight residual -90.00 -132.87 42.87 2 1.50e+01 4.44e-03 9.88e+00 ... (remaining 2121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 306 0.022 - 0.043: 166 0.043 - 0.065: 86 0.065 - 0.086: 28 0.086 - 0.108: 13 Chirality restraints: 599 Sorted by residual: chirality pdb=" CA PRO A 394 " pdb=" N PRO A 394 " pdb=" C PRO A 394 " pdb=" CB PRO A 394 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.89e-01 chirality pdb=" CA PRO A 27 " pdb=" N PRO A 27 " pdb=" C PRO A 27 " pdb=" CB PRO A 27 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.80e-01 chirality pdb=" CA PRO A 214 " pdb=" N PRO A 214 " pdb=" C PRO A 214 " pdb=" CB PRO A 214 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.78e-01 ... (remaining 596 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 66 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 67 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 11 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.11e+00 pdb=" N PRO A 12 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 393 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 394 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.019 5.00e-02 4.00e+02 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1015 2.80 - 3.33: 3864 3.33 - 3.85: 6296 3.85 - 4.38: 7724 4.38 - 4.90: 12017 Nonbonded interactions: 30916 Sorted by model distance: nonbonded pdb=" OG1 THR A 87 " pdb=" O CYS A 120 " model vdw 2.277 3.040 nonbonded pdb=" O SER A 358 " pdb=" OG SER A 361 " model vdw 2.282 3.040 nonbonded pdb=" O GLY A 155 " pdb=" OG SER A 159 " model vdw 2.287 3.040 nonbonded pdb=" O VAL A 232 " pdb=" NH2 ARG A 365 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN A 223 " pdb=" OG1 THR A 405 " model vdw 2.298 3.120 ... (remaining 30911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 0.030 3710 Z= 0.135 Angle : 0.546 6.405 5049 Z= 0.304 Chirality : 0.035 0.108 599 Planarity : 0.004 0.038 610 Dihedral : 16.597 73.942 1270 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.81 % Allowed : 25.14 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.38), residues: 467 helix: -0.20 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.79 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 170 HIS 0.003 0.001 HIS A 420 PHE 0.011 0.001 PHE A 248 TYR 0.011 0.001 TYR A 278 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.27913 ( 245) hydrogen bonds : angle 8.80345 ( 720) covalent geometry : bond 0.00274 ( 3710) covalent geometry : angle 0.54598 ( 5049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.342 Fit side-chains REVERT: A 43 ASN cc_start: 0.8413 (m-40) cc_final: 0.8166 (m-40) REVERT: A 98 MET cc_start: 0.7871 (tpp) cc_final: 0.7516 (ttp) REVERT: A 166 MET cc_start: 0.7622 (mtm) cc_final: 0.7352 (ttt) REVERT: A 176 MET cc_start: 0.7914 (tmm) cc_final: 0.7629 (tmm) REVERT: A 222 ASN cc_start: 0.8184 (t0) cc_final: 0.7468 (t0) REVERT: A 277 LEU cc_start: 0.7182 (tp) cc_final: 0.6907 (mp) REVERT: A 278 TYR cc_start: 0.7400 (t80) cc_final: 0.6708 (t80) REVERT: A 319 MET cc_start: 0.8246 (ttp) cc_final: 0.7921 (ttp) REVERT: A 342 MET cc_start: 0.7506 (mmt) cc_final: 0.7121 (mtm) REVERT: A 354 PHE cc_start: 0.8483 (t80) cc_final: 0.8199 (t80) REVERT: A 445 MET cc_start: 0.5839 (mpt) cc_final: 0.5145 (mmm) outliers start: 3 outliers final: 0 residues processed: 93 average time/residue: 0.1147 time to fit residues: 14.0124 Evaluate side-chains 70 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 223 ASN A 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.183151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.168317 restraints weight = 4126.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.169704 restraints weight = 2900.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.170756 restraints weight = 2252.269| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3710 Z= 0.175 Angle : 0.674 7.134 5049 Z= 0.347 Chirality : 0.039 0.122 599 Planarity : 0.005 0.036 610 Dihedral : 5.172 17.960 501 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.68 % Allowed : 22.97 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.38), residues: 467 helix: -0.14 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.46 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 374 HIS 0.002 0.001 HIS A 379 PHE 0.017 0.002 PHE A 349 TYR 0.024 0.002 TYR A 385 ARG 0.006 0.001 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.05823 ( 245) hydrogen bonds : angle 5.97658 ( 720) covalent geometry : bond 0.00362 ( 3710) covalent geometry : angle 0.67377 ( 5049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.391 Fit side-chains REVERT: A 222 ASN cc_start: 0.8080 (t0) cc_final: 0.7822 (t0) REVERT: A 445 MET cc_start: 0.6035 (mpt) cc_final: 0.5831 (mmt) outliers start: 21 outliers final: 6 residues processed: 88 average time/residue: 0.0982 time to fit residues: 11.8588 Evaluate side-chains 74 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.173963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.158327 restraints weight = 4235.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.157551 restraints weight = 4921.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.158991 restraints weight = 4533.584| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3710 Z= 0.189 Angle : 0.694 8.876 5049 Z= 0.354 Chirality : 0.040 0.157 599 Planarity : 0.004 0.040 610 Dihedral : 5.258 19.041 501 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.95 % Allowed : 21.89 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.38), residues: 467 helix: -0.16 (0.26), residues: 364 sheet: None (None), residues: 0 loop : -0.79 (0.61), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 PHE 0.011 0.002 PHE A 456 TYR 0.026 0.002 TYR A 385 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 245) hydrogen bonds : angle 5.48747 ( 720) covalent geometry : bond 0.00406 ( 3710) covalent geometry : angle 0.69396 ( 5049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.7886 (tppt) cc_final: 0.7679 (tppt) REVERT: A 39 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7890 (mtt) outliers start: 22 outliers final: 12 residues processed: 91 average time/residue: 0.1244 time to fit residues: 14.5043 Evaluate side-chains 85 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 405 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.172859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.157450 restraints weight = 4352.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.158672 restraints weight = 3239.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.159595 restraints weight = 2581.234| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3710 Z= 0.171 Angle : 0.667 10.020 5049 Z= 0.334 Chirality : 0.038 0.140 599 Planarity : 0.004 0.037 610 Dihedral : 5.259 19.792 501 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.86 % Allowed : 24.59 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.38), residues: 467 helix: -0.12 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -0.87 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 PHE 0.015 0.001 PHE A 456 TYR 0.019 0.002 TYR A 385 ARG 0.005 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 245) hydrogen bonds : angle 5.31913 ( 720) covalent geometry : bond 0.00378 ( 3710) covalent geometry : angle 0.66744 ( 5049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.364 Fit side-chains REVERT: A 13 LYS cc_start: 0.8016 (tppt) cc_final: 0.7231 (ttpp) REVERT: A 39 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: A 223 ASN cc_start: 0.8337 (m-40) cc_final: 0.7060 (m-40) outliers start: 18 outliers final: 11 residues processed: 84 average time/residue: 0.1178 time to fit residues: 13.0438 Evaluate side-chains 84 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.170404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.153471 restraints weight = 4452.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.155056 restraints weight = 3072.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.155916 restraints weight = 2333.408| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3710 Z= 0.173 Angle : 0.644 10.278 5049 Z= 0.324 Chirality : 0.037 0.118 599 Planarity : 0.004 0.035 610 Dihedral : 5.248 20.364 501 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.68 % Allowed : 24.86 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.39), residues: 467 helix: -0.12 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.88 (0.67), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 PHE 0.033 0.002 PHE A 390 TYR 0.020 0.002 TYR A 385 ARG 0.005 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 245) hydrogen bonds : angle 5.25751 ( 720) covalent geometry : bond 0.00375 ( 3710) covalent geometry : angle 0.64406 ( 5049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.385 Fit side-chains REVERT: A 39 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8026 (mtp) REVERT: A 72 TYR cc_start: 0.4330 (t80) cc_final: 0.4006 (t80) REVERT: A 176 MET cc_start: 0.8411 (tmm) cc_final: 0.8136 (tmm) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1070 time to fit residues: 12.0138 Evaluate side-chains 85 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.174016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.157939 restraints weight = 4351.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.159200 restraints weight = 3089.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.159864 restraints weight = 2438.387| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3710 Z= 0.143 Angle : 0.622 9.827 5049 Z= 0.310 Chirality : 0.036 0.119 599 Planarity : 0.004 0.034 610 Dihedral : 5.167 20.729 501 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.05 % Allowed : 26.76 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.39), residues: 467 helix: 0.03 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.98 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 PHE 0.021 0.002 PHE A 390 TYR 0.021 0.002 TYR A 385 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 245) hydrogen bonds : angle 5.10109 ( 720) covalent geometry : bond 0.00313 ( 3710) covalent geometry : angle 0.62172 ( 5049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.398 Fit side-chains REVERT: A 72 TYR cc_start: 0.4212 (t80) cc_final: 0.3821 (t80) REVERT: A 176 MET cc_start: 0.8374 (tmm) cc_final: 0.8155 (tmm) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.1269 time to fit residues: 13.3482 Evaluate side-chains 74 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.0070 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 40 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.177329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.161215 restraints weight = 4328.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.162464 restraints weight = 3119.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.163107 restraints weight = 2497.780| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3710 Z= 0.131 Angle : 0.616 7.691 5049 Z= 0.304 Chirality : 0.037 0.207 599 Planarity : 0.003 0.033 610 Dihedral : 5.085 22.045 501 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.05 % Allowed : 27.03 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.39), residues: 467 helix: 0.15 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.95 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 PHE 0.019 0.001 PHE A 390 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 245) hydrogen bonds : angle 4.97934 ( 720) covalent geometry : bond 0.00282 ( 3710) covalent geometry : angle 0.61560 ( 5049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.379 Fit side-chains REVERT: A 176 MET cc_start: 0.8367 (tmm) cc_final: 0.8059 (tmm) REVERT: A 298 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7512 (tp) REVERT: A 332 MET cc_start: 0.6215 (ttm) cc_final: 0.5867 (mtp) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.1121 time to fit residues: 11.9693 Evaluate side-chains 80 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.183077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.168622 restraints weight = 4329.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.167644 restraints weight = 5430.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.168906 restraints weight = 4594.102| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3710 Z= 0.153 Angle : 0.647 9.393 5049 Z= 0.317 Chirality : 0.038 0.191 599 Planarity : 0.004 0.034 610 Dihedral : 5.048 21.574 501 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.32 % Allowed : 27.30 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.39), residues: 467 helix: 0.13 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.97 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 374 HIS 0.000 0.000 HIS A 379 PHE 0.022 0.002 PHE A 289 TYR 0.027 0.002 TYR A 72 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 245) hydrogen bonds : angle 4.98499 ( 720) covalent geometry : bond 0.00338 ( 3710) covalent geometry : angle 0.64717 ( 5049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.383 Fit side-chains REVERT: A 318 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 396 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6877 (mp) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.1007 time to fit residues: 11.0537 Evaluate side-chains 82 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.175209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.158665 restraints weight = 4228.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.160084 restraints weight = 3077.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.160152 restraints weight = 2440.369| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3710 Z= 0.168 Angle : 0.655 7.826 5049 Z= 0.324 Chirality : 0.038 0.164 599 Planarity : 0.004 0.036 610 Dihedral : 5.158 22.241 501 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.32 % Allowed : 27.30 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.39), residues: 467 helix: 0.07 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.99 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 109 HIS 0.001 0.000 HIS A 315 PHE 0.018 0.002 PHE A 289 TYR 0.010 0.001 TYR A 152 ARG 0.004 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 245) hydrogen bonds : angle 5.11935 ( 720) covalent geometry : bond 0.00375 ( 3710) covalent geometry : angle 0.65518 ( 5049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.341 Fit side-chains REVERT: A 152 TYR cc_start: 0.8264 (t80) cc_final: 0.7734 (t80) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 0.1144 time to fit residues: 13.4606 Evaluate side-chains 87 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.181825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.164606 restraints weight = 4259.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.166139 restraints weight = 2969.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.166868 restraints weight = 2303.923| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3710 Z= 0.164 Angle : 0.662 7.642 5049 Z= 0.326 Chirality : 0.039 0.174 599 Planarity : 0.004 0.036 610 Dihedral : 5.228 22.535 501 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.05 % Allowed : 27.03 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.40), residues: 467 helix: 0.09 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.05 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 109 HIS 0.001 0.000 HIS A 379 PHE 0.017 0.002 PHE A 289 TYR 0.012 0.002 TYR A 385 ARG 0.006 0.001 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 245) hydrogen bonds : angle 5.12141 ( 720) covalent geometry : bond 0.00366 ( 3710) covalent geometry : angle 0.66213 ( 5049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.389 Fit side-chains REVERT: A 100 PHE cc_start: 0.7731 (m-10) cc_final: 0.7512 (m-80) REVERT: A 152 TYR cc_start: 0.8285 (t80) cc_final: 0.7702 (t80) REVERT: A 278 TYR cc_start: 0.7101 (t80) cc_final: 0.6851 (t80) REVERT: A 332 MET cc_start: 0.6046 (ttm) cc_final: 0.5823 (mtp) REVERT: A 396 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6841 (mp) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1056 time to fit residues: 12.5544 Evaluate side-chains 88 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.171645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.155005 restraints weight = 4317.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.156150 restraints weight = 3166.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.156440 restraints weight = 2578.211| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3710 Z= 0.183 Angle : 0.677 7.833 5049 Z= 0.335 Chirality : 0.039 0.162 599 Planarity : 0.004 0.037 610 Dihedral : 5.329 23.356 501 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.35 % Favored : 94.43 % Rotamer: Outliers : 3.78 % Allowed : 27.84 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.39), residues: 467 helix: 0.01 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.15 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 109 HIS 0.001 0.000 HIS A 379 PHE 0.018 0.002 PHE A 240 TYR 0.012 0.002 TYR A 385 ARG 0.006 0.001 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 245) hydrogen bonds : angle 5.18223 ( 720) covalent geometry : bond 0.00406 ( 3710) covalent geometry : angle 0.67665 ( 5049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1532.82 seconds wall clock time: 27 minutes 11.90 seconds (1631.90 seconds total)