Starting phenix.real_space_refine on Wed Sep 17 04:02:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgz_60093/09_2025/8zgz_60093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgz_60093/09_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_60093/09_2025/8zgz_60093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgz_60093/09_2025/8zgz_60093.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgz_60093/09_2025/8zgz_60093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgz_60093/09_2025/8zgz_60093.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.10, per 1000 atoms: 0.30 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: 0.31 Conformation dependent library (CDL) restraints added in 148.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.12 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: 0.59 Time building geometry restraints manager: 0.41 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: 2.290 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.670 Find NCS groups from input model: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 251 TYR 0.011 0.001 TYR A 278 PHE 0.011 0.001 PHE A 248 TRP 0.010 0.001 TRP A 170 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3710) covalent geometry : angle 0.54598 ( 5049) hydrogen bonds : bond 0.27913 ( 245) hydrogen bonds : angle 8.80345 ( 720) *********************** 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 : 0.138 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: 0.0493 time to fit residues: 6.1272 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 : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.180209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.165207 restraints weight = 4205.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.166693 restraints weight = 2960.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.167705 restraints weight = 2285.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.168038 restraints weight = 1895.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.168054 restraints weight = 1726.166| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3710 Z= 0.199 Angle : 0.696 6.880 5049 Z= 0.357 Chirality : 0.040 0.124 599 Planarity : 0.005 0.036 610 Dihedral : 5.252 18.236 501 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.68 % Allowed : 23.51 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.38), residues: 467 helix: -0.23 (0.26), residues: 362 sheet: None (None), residues: 0 loop : -0.52 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 285 TYR 0.026 0.002 TYR A 385 PHE 0.014 0.002 PHE A 349 TRP 0.017 0.001 TRP A 374 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3710) covalent geometry : angle 0.69630 ( 5049) hydrogen bonds : bond 0.05715 ( 245) hydrogen bonds : angle 5.92884 ( 720) *********************** 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 102 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.126 Fit side-chains outliers start: 21 outliers final: 6 residues processed: 92 average time/residue: 0.0549 time to fit residues: 6.5143 Evaluate side-chains 77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 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 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.171414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.157390 restraints weight = 4380.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.156362 restraints weight = 4385.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.157620 restraints weight = 3887.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.157902 restraints weight = 3011.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.158082 restraints weight = 2601.865| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3710 Z= 0.192 Angle : 0.672 7.912 5049 Z= 0.342 Chirality : 0.039 0.119 599 Planarity : 0.004 0.039 610 Dihedral : 5.240 19.009 501 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.41 % Allowed : 23.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.38), residues: 467 helix: -0.13 (0.26), residues: 363 sheet: None (None), residues: 0 loop : -0.68 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 365 TYR 0.023 0.002 TYR A 385 PHE 0.011 0.001 PHE A 375 TRP 0.013 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3710) covalent geometry : angle 0.67241 ( 5049) hydrogen bonds : bond 0.05115 ( 245) hydrogen bonds : angle 5.51167 ( 720) *********************** 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 100 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.093 Fit side-chains REVERT: A 13 LYS cc_start: 0.7998 (tppt) cc_final: 0.7730 (tppt) REVERT: A 39 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7888 (mtt) REVERT: A 292 LEU cc_start: 0.8235 (mm) cc_final: 0.7996 (mt) outliers start: 20 outliers final: 12 residues processed: 90 average time/residue: 0.0507 time to fit residues: 5.9811 Evaluate side-chains 88 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 302 SER 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 6 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.172284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.157043 restraints weight = 4361.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.158319 restraints weight = 3146.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.159299 restraints weight = 2494.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.159973 restraints weight = 2102.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.159975 restraints weight = 1848.029| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3710 Z= 0.155 Angle : 0.636 10.152 5049 Z= 0.319 Chirality : 0.037 0.120 599 Planarity : 0.004 0.035 610 Dihedral : 5.237 19.309 501 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.86 % Allowed : 25.41 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.38), residues: 467 helix: -0.02 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.74 (0.67), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.022 0.002 TYR A 385 PHE 0.010 0.001 PHE A 255 TRP 0.015 0.001 TRP A 374 HIS 0.001 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3710) covalent geometry : angle 0.63597 ( 5049) hydrogen bonds : bond 0.04480 ( 245) hydrogen bonds : angle 5.19625 ( 720) *********************** 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 90 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.124 Fit side-chains REVERT: A 13 LYS cc_start: 0.7916 (tppt) cc_final: 0.7152 (ttpp) REVERT: A 39 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8016 (mtp) REVERT: A 292 LEU cc_start: 0.8248 (mm) cc_final: 0.7924 (mm) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.0418 time to fit residues: 4.7342 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 : 0.082 ------------------------------------------------------------------------------- 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 158 VAL 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 405 THR 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 35 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.175894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.160445 restraints weight = 4339.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.161747 restraints weight = 3093.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.162292 restraints weight = 2433.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.163310 restraints weight = 2137.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.163310 restraints weight = 1838.469| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3710 Z= 0.129 Angle : 0.612 9.276 5049 Z= 0.304 Chirality : 0.035 0.115 599 Planarity : 0.004 0.034 610 Dihedral : 5.175 20.489 501 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.86 % Allowed : 25.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.39), residues: 467 helix: 0.24 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.99 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.020 0.001 TYR A 385 PHE 0.032 0.001 PHE A 390 TRP 0.009 0.001 TRP A 374 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3710) covalent geometry : angle 0.61234 ( 5049) hydrogen bonds : bond 0.04194 ( 245) hydrogen bonds : angle 5.02619 ( 720) *********************** 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 93 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8207 (mm) cc_final: 0.7862 (mm) REVERT: A 417 MET cc_start: 0.5516 (ppp) cc_final: 0.5079 (ppp) outliers start: 18 outliers final: 11 residues processed: 88 average time/residue: 0.0476 time to fit residues: 5.6366 Evaluate side-chains 82 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 317 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 405 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 27 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 overall best weight: 0.2216 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.176989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.161507 restraints weight = 4311.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.162979 restraints weight = 3022.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.163900 restraints weight = 2354.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.164111 restraints weight = 1963.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.164141 restraints weight = 1830.992| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3710 Z= 0.122 Angle : 0.609 8.002 5049 Z= 0.302 Chirality : 0.035 0.119 599 Planarity : 0.004 0.034 610 Dihedral : 5.093 22.574 501 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.05 % Allowed : 25.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.39), residues: 467 helix: 0.40 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.91 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.021 0.001 TYR A 385 PHE 0.022 0.001 PHE A 390 TRP 0.015 0.001 TRP A 374 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3710) covalent geometry : angle 0.60928 ( 5049) hydrogen bonds : bond 0.03988 ( 245) hydrogen bonds : angle 4.82689 ( 720) *********************** 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 87 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.162 Fit side-chains REVERT: A 417 MET cc_start: 0.5582 (ppp) cc_final: 0.5100 (ppp) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.0435 time to fit residues: 4.8409 Evaluate side-chains 81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 253 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 LEU 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 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.175878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.159701 restraints weight = 4446.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.161062 restraints weight = 3142.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.162140 restraints weight = 2443.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.162140 restraints weight = 2068.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.162140 restraints weight = 2068.642| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.5466 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= 0.133 Angle : 0.608 7.833 5049 Z= 0.301 Chirality : 0.037 0.177 599 Planarity : 0.004 0.033 610 Dihedral : 5.069 21.140 501 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.32 % Allowed : 25.68 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.39), residues: 467 helix: 0.42 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.92 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.020 0.001 TYR A 385 PHE 0.018 0.001 PHE A 390 TRP 0.008 0.001 TRP A 374 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3710) covalent geometry : angle 0.60816 ( 5049) hydrogen bonds : bond 0.03969 ( 245) hydrogen bonds : angle 4.83009 ( 720) *********************** 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 89 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.136 Fit side-chains REVERT: A 90 LEU cc_start: 0.7868 (tp) cc_final: 0.7623 (tp) REVERT: A 176 MET cc_start: 0.8289 (tmm) cc_final: 0.8007 (tmm) REVERT: A 180 MET cc_start: 0.7594 (mmm) cc_final: 0.7361 (mmm) outliers start: 16 outliers final: 15 residues processed: 81 average time/residue: 0.0523 time to fit residues: 5.6849 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 : 0.156 ------------------------------------------------------------------------------- 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 253 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 LEU 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 44 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.175759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.159382 restraints weight = 4365.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.160550 restraints weight = 3172.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.161510 restraints weight = 2530.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.162108 restraints weight = 2181.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.162375 restraints weight = 1959.471| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3710 Z= 0.143 Angle : 0.623 7.398 5049 Z= 0.306 Chirality : 0.037 0.200 599 Planarity : 0.004 0.032 610 Dihedral : 5.110 20.918 501 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.59 % Allowed : 27.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.39), residues: 467 helix: 0.35 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.07 (0.65), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.011 0.001 TYR A 385 PHE 0.017 0.001 PHE A 390 TRP 0.013 0.001 TRP A 374 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3710) covalent geometry : angle 0.62263 ( 5049) hydrogen bonds : bond 0.04008 ( 245) hydrogen bonds : angle 4.80939 ( 720) *********************** 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 88 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.086 Fit side-chains REVERT: A 90 LEU cc_start: 0.7900 (tp) cc_final: 0.7646 (tp) REVERT: A 152 TYR cc_start: 0.8302 (t80) cc_final: 0.7603 (t80) REVERT: A 176 MET cc_start: 0.8409 (tmm) cc_final: 0.8170 (tmm) REVERT: A 319 MET cc_start: 0.7404 (tpp) cc_final: 0.7181 (tpp) outliers start: 17 outliers final: 14 residues processed: 81 average time/residue: 0.0577 time to fit residues: 6.0428 Evaluate side-chains 82 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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 302 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 LEU 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 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.177658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.160685 restraints weight = 4335.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.162159 restraints weight = 3126.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.162818 restraints weight = 2486.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.162948 restraints weight = 2162.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.163560 restraints weight = 2065.624| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.5774 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 : 0.627 7.408 5049 Z= 0.306 Chirality : 0.037 0.176 599 Planarity : 0.003 0.032 610 Dihedral : 5.084 20.528 501 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.05 % Allowed : 28.38 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.39), residues: 467 helix: 0.36 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.04 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 221 TYR 0.008 0.001 TYR A 152 PHE 0.023 0.001 PHE A 289 TRP 0.015 0.001 TRP A 374 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3710) covalent geometry : angle 0.62690 ( 5049) hydrogen bonds : bond 0.03945 ( 245) hydrogen bonds : angle 4.79197 ( 720) *********************** 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 90 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.130 Fit side-chains REVERT: A 90 LEU cc_start: 0.7915 (tp) cc_final: 0.7642 (tp) REVERT: A 152 TYR cc_start: 0.8261 (t80) cc_final: 0.7627 (t80) REVERT: A 375 PHE cc_start: 0.7714 (t80) cc_final: 0.7495 (t80) outliers start: 15 outliers final: 15 residues processed: 83 average time/residue: 0.0457 time to fit residues: 5.2782 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 : 0.170 ------------------------------------------------------------------------------- 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 253 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 LEU 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 42 optimal weight: 0.0170 chunk 34 optimal weight: 0.0980 chunk 26 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.161191 restraints weight = 4379.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.162433 restraints weight = 3134.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.163327 restraints weight = 2481.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.163485 restraints weight = 2125.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.164092 restraints weight = 2008.068| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3710 Z= 0.130 Angle : 0.627 7.506 5049 Z= 0.306 Chirality : 0.038 0.181 599 Planarity : 0.004 0.032 610 Dihedral : 5.065 20.901 501 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.51 % Allowed : 28.92 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.40), residues: 467 helix: 0.37 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.00 (0.69), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.020 0.002 TYR A 385 PHE 0.020 0.001 PHE A 289 TRP 0.013 0.001 TRP A 374 HIS 0.000 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3710) covalent geometry : angle 0.62722 ( 5049) hydrogen bonds : bond 0.03930 ( 245) hydrogen bonds : angle 4.81845 ( 720) ********************** 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 81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.114 Fit side-chains REVERT: A 60 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8123 (t) REVERT: A 90 LEU cc_start: 0.7923 (tp) cc_final: 0.7671 (tp) REVERT: A 184 LEU cc_start: 0.7501 (mt) cc_final: 0.6913 (mt) REVERT: A 319 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6965 (tpp) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.0416 time to fit residues: 4.3008 Evaluate side-chains 76 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 302 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 343 THR 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 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.177564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.160501 restraints weight = 4292.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.162018 restraints weight = 3105.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.162656 restraints weight = 2463.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.163232 restraints weight = 2144.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.163232 restraints weight = 1946.408| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3710 Z= 0.136 Angle : 0.644 7.403 5049 Z= 0.314 Chirality : 0.037 0.172 599 Planarity : 0.004 0.032 610 Dihedral : 5.103 20.045 501 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.05 % Allowed : 27.84 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.40), residues: 467 helix: 0.39 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.26 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.010 0.001 TYR A 152 PHE 0.020 0.001 PHE A 289 TRP 0.013 0.001 TRP A 374 HIS 0.000 0.000 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3710) covalent geometry : angle 0.64427 ( 5049) hydrogen bonds : bond 0.03887 ( 245) hydrogen bonds : angle 4.75028 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 839.45 seconds wall clock time: 15 minutes 21.22 seconds (921.22 seconds total)