Starting phenix.real_space_refine on Wed Sep 17 06:47:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbq_39907/09_2025/8zbq_39907_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbq_39907/09_2025/8zbq_39907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zbq_39907/09_2025/8zbq_39907_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbq_39907/09_2025/8zbq_39907_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zbq_39907/09_2025/8zbq_39907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbq_39907/09_2025/8zbq_39907.map" } resolution = 3.03 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= 0.002 sd= 0.081 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 36 5.16 5 C 4072 2.51 5 N 1052 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s 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: 6346 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1476 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Time building chain proxies: 1.38, per 1000 atoms: 0.22 Number of scatterers: 6346 At special positions: 0 Unit cell: (75.9, 97.9, 105.6, 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 36 16.00 O 1186 8.00 N 1052 7.00 C 4072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.01 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: 0.54 Conformation dependent library (CDL) restraints added in 316.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 53.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 53 Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.514A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 172 through 193 Proline residue: D 178 - end of helix removed outlier: 3.616A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 247 removed outlier: 3.748A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 292 through 296 removed outlier: 4.113A pdb=" N ASP D 295 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.978A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.726A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.072A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 421' Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.737A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.542A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.226A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.706A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 6.071A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.604A pdb=" N ALA F 344 " --> pdb=" O VAL F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 371 Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.509A pdb=" N VAL F 407 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'F' and resid 354 through 358 removed outlier: 4.755A pdb=" N ILE F 434 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 452 through 454 280 hydrogen bonds defined for protein. 753 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: 0.95 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1060 1.31 - 1.44: 1921 1.44 - 1.58: 3494 1.58 - 1.72: 0 1.72 - 1.86: 57 Bond restraints: 6532 Sorted by residual: bond pdb=" CA ALA F 348 " pdb=" C ALA F 348 " ideal model delta sigma weight residual 1.527 1.419 0.108 1.35e-02 5.49e+03 6.35e+01 bond pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.31e-02 5.83e+03 5.67e+01 bond pdb=" C ASP F 442 " pdb=" O ASP F 442 " ideal model delta sigma weight residual 1.232 1.171 0.061 1.01e-02 9.80e+03 3.61e+01 bond pdb=" N GLU D 110 " pdb=" CA GLU D 110 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.17e-02 7.31e+03 2.77e+01 bond pdb=" C LYS F 478 " pdb=" O LYS F 478 " ideal model delta sigma weight residual 1.241 1.184 0.057 1.14e-02 7.69e+03 2.50e+01 ... (remaining 6527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 8587 2.25 - 4.51: 224 4.51 - 6.76: 46 6.76 - 9.02: 11 9.02 - 11.27: 7 Bond angle restraints: 8875 Sorted by residual: angle pdb=" C LYS F 478 " pdb=" CA LYS F 478 " pdb=" CB LYS F 478 " ideal model delta sigma weight residual 110.33 101.27 9.06 1.02e+00 9.61e-01 7.88e+01 angle pdb=" N ASN F 477 " pdb=" CA ASN F 477 " pdb=" C ASN F 477 " ideal model delta sigma weight residual 112.41 123.68 -11.27 1.30e+00 5.92e-01 7.52e+01 angle pdb=" N PRO F 499 " pdb=" CA PRO F 499 " pdb=" C PRO F 499 " ideal model delta sigma weight residual 113.98 103.70 10.28 1.29e+00 6.01e-01 6.35e+01 angle pdb=" N VAL D 298 " pdb=" CA VAL D 298 " pdb=" C VAL D 298 " ideal model delta sigma weight residual 113.71 106.57 7.14 9.50e-01 1.11e+00 5.66e+01 angle pdb=" N TYR D 158 " pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 114.04 105.17 8.87 1.24e+00 6.50e-01 5.12e+01 ... (remaining 8870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3367 17.97 - 35.95: 365 35.95 - 53.92: 79 53.92 - 71.90: 27 71.90 - 89.87: 11 Dihedral angle restraints: 3849 sinusoidal: 1559 harmonic: 2290 Sorted by residual: dihedral pdb=" CB CYS F 336 " pdb=" SG CYS F 336 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual 93.00 22.87 70.13 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" C LYS F 478 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" CB LYS F 478 " ideal model delta harmonic sigma weight residual -122.60 -107.54 -15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 3846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 743 0.055 - 0.109: 144 0.109 - 0.164: 23 0.164 - 0.218: 6 0.218 - 0.273: 2 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA GLU D 110 " pdb=" N GLU D 110 " pdb=" C GLU D 110 " pdb=" CB GLU D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LYS D 234 " pdb=" N LYS D 234 " pdb=" C LYS D 234 " pdb=" CB LYS D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP D 111 " pdb=" N ASP D 111 " pdb=" C ASP D 111 " pdb=" CB ASP D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 915 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 476 " -0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C GLY F 476 " 0.075 2.00e-02 2.50e+03 pdb=" O GLY F 476 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN F 477 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG F 498 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO F 499 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 499 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 499 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 233 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ILE D 233 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE D 233 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS D 234 " 0.019 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1774 2.79 - 3.32: 6510 3.32 - 3.84: 11877 3.84 - 4.37: 14524 4.37 - 4.90: 23235 Nonbonded interactions: 57920 Sorted by model distance: nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU D 527 " pdb=" NE2 GLN D 531 " model vdw 2.273 3.120 nonbonded pdb=" O SER D 47 " pdb=" ND2 ASN D 51 " model vdw 2.292 3.120 nonbonded pdb=" NH2 ARG F 454 " pdb=" O ASP F 467 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG D 482 " pdb=" O THR D 608 " model vdw 2.300 3.120 ... (remaining 57915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.510 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.810 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.006 0.108 6538 Z= 0.376 Angle : 0.923 11.273 8887 Z= 0.585 Chirality : 0.048 0.273 918 Planarity : 0.006 0.082 1150 Dihedral : 16.508 89.870 2361 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 6.41 % Allowed : 3.50 % Favored : 90.09 % Cbeta Deviations : 0.27 % 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: -2.05 (0.30), residues: 775 helix: -0.65 (0.28), residues: 351 sheet: -1.62 (0.82), residues: 39 loop : -2.01 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 482 TYR 0.021 0.001 TYR D 381 PHE 0.022 0.002 PHE F 375 TRP 0.035 0.002 TRP F 353 HIS 0.008 0.002 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 6532) covalent geometry : angle 0.91905 ( 8875) SS BOND : bond 0.01246 ( 6) SS BOND : angle 2.38743 ( 12) hydrogen bonds : bond 0.19583 ( 280) hydrogen bonds : angle 7.56001 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7280 (m110) cc_final: 0.6761 (m110) REVERT: D 111 ASP cc_start: 0.7840 (p0) cc_final: 0.7559 (p0) REVERT: D 189 GLU cc_start: 0.7186 (mp0) cc_final: 0.6453 (mp0) REVERT: D 192 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6956 (mtt90) REVERT: F 500 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6573 (t) outliers start: 44 outliers final: 6 residues processed: 165 average time/residue: 0.0874 time to fit residues: 18.7667 Evaluate side-chains 113 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 ASN D 175 GLN D 300 GLN D 378 HIS F 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.165788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135037 restraints weight = 7481.149| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.46 r_work: 0.3322 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6538 Z= 0.167 Angle : 0.629 6.411 8887 Z= 0.336 Chirality : 0.045 0.149 918 Planarity : 0.005 0.052 1150 Dihedral : 6.228 57.039 858 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.50 % Allowed : 11.22 % Favored : 85.28 % 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: -1.59 (0.30), residues: 775 helix: -0.50 (0.27), residues: 365 sheet: -1.56 (0.87), residues: 36 loop : -1.51 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 454 TYR 0.028 0.002 TYR D 385 PHE 0.019 0.002 PHE D 523 TRP 0.016 0.002 TRP F 353 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6532) covalent geometry : angle 0.62832 ( 8875) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.06370 ( 12) hydrogen bonds : bond 0.05080 ( 280) hydrogen bonds : angle 5.35613 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.231 Fit side-chains REVERT: D 62 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7281 (ttt) REVERT: D 63 ASN cc_start: 0.7346 (m110) cc_final: 0.6725 (m110) REVERT: D 192 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7428 (mtt180) REVERT: D 228 HIS cc_start: 0.7975 (m170) cc_final: 0.7551 (m-70) REVERT: D 307 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7995 (mt) REVERT: D 483 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: D 531 GLN cc_start: 0.8142 (mt0) cc_final: 0.7815 (mt0) REVERT: D 559 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7995 (ttm-80) REVERT: F 346 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4767 (tmm160) outliers start: 24 outliers final: 12 residues processed: 137 average time/residue: 0.0805 time to fit residues: 14.5314 Evaluate side-chains 125 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 501 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.2980 chunk 17 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN D 330 ASN D 340 GLN D 345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130358 restraints weight = 7473.748| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.45 r_work: 0.3289 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6538 Z= 0.169 Angle : 0.606 6.016 8887 Z= 0.320 Chirality : 0.044 0.139 918 Planarity : 0.005 0.054 1150 Dihedral : 5.630 45.866 850 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.64 % Allowed : 14.58 % Favored : 81.78 % 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: -1.32 (0.30), residues: 775 helix: -0.23 (0.27), residues: 357 sheet: -1.70 (0.85), residues: 36 loop : -1.39 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 454 TYR 0.023 0.002 TYR D 385 PHE 0.018 0.002 PHE D 523 TRP 0.019 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6532) covalent geometry : angle 0.60554 ( 8875) SS BOND : bond 0.00451 ( 6) SS BOND : angle 0.82023 ( 12) hydrogen bonds : bond 0.04857 ( 280) hydrogen bonds : angle 5.07023 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 62 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7142 (ttt) REVERT: D 63 ASN cc_start: 0.7284 (m110) cc_final: 0.6723 (m110) REVERT: D 81 GLN cc_start: 0.7411 (mm110) cc_final: 0.7180 (mm-40) REVERT: D 86 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8177 (tm-30) REVERT: D 192 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7411 (mtt180) REVERT: D 227 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: D 306 ARG cc_start: 0.7490 (ttt180) cc_final: 0.7063 (ttt180) REVERT: D 307 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7967 (mt) REVERT: D 323 MET cc_start: 0.8016 (mmm) cc_final: 0.7768 (mmt) REVERT: D 472 GLN cc_start: 0.8631 (mt0) cc_final: 0.8392 (mt0) REVERT: D 474 MET cc_start: 0.8871 (mmp) cc_final: 0.8623 (mmp) REVERT: D 483 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8275 (pp20) REVERT: D 531 GLN cc_start: 0.8183 (mt0) cc_final: 0.7964 (mt0) REVERT: D 559 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8173 (ttp80) REVERT: F 439 ASN cc_start: 0.8228 (t0) cc_final: 0.7854 (t0) outliers start: 25 outliers final: 15 residues processed: 134 average time/residue: 0.0849 time to fit residues: 15.0077 Evaluate side-chains 128 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.161676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130498 restraints weight = 7499.521| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.45 r_work: 0.3284 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6538 Z= 0.166 Angle : 0.589 6.177 8887 Z= 0.312 Chirality : 0.044 0.138 918 Planarity : 0.004 0.054 1150 Dihedral : 5.570 45.375 850 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.79 % Allowed : 16.03 % Favored : 80.17 % 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: -1.33 (0.30), residues: 775 helix: -0.08 (0.28), residues: 352 sheet: -1.55 (0.85), residues: 38 loop : -1.56 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 482 TYR 0.021 0.002 TYR D 385 PHE 0.020 0.001 PHE D 523 TRP 0.018 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6532) covalent geometry : angle 0.58696 ( 8875) SS BOND : bond 0.00737 ( 6) SS BOND : angle 1.54115 ( 12) hydrogen bonds : bond 0.04713 ( 280) hydrogen bonds : angle 4.94146 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 62 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7357 (ttt) REVERT: D 63 ASN cc_start: 0.7353 (m110) cc_final: 0.6811 (m110) REVERT: D 192 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7506 (mtt180) REVERT: D 306 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7089 (ttt180) REVERT: D 307 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7937 (mt) REVERT: D 472 GLN cc_start: 0.8660 (mt0) cc_final: 0.8425 (mt0) REVERT: D 474 MET cc_start: 0.9020 (mmp) cc_final: 0.8406 (mmp) REVERT: D 483 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8256 (pp20) REVERT: D 531 GLN cc_start: 0.8160 (mt0) cc_final: 0.7921 (mt0) REVERT: F 439 ASN cc_start: 0.8292 (t0) cc_final: 0.7897 (t0) outliers start: 26 outliers final: 20 residues processed: 126 average time/residue: 0.0751 time to fit residues: 12.8325 Evaluate side-chains 130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 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 = 0.3700 r_free = 0.3700 target = 0.156337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124449 restraints weight = 7583.386| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.47 r_work: 0.3230 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6538 Z= 0.189 Angle : 0.605 6.712 8887 Z= 0.320 Chirality : 0.045 0.142 918 Planarity : 0.004 0.052 1150 Dihedral : 5.614 45.996 850 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.08 % Allowed : 16.62 % Favored : 79.30 % 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: -1.38 (0.30), residues: 775 helix: -0.27 (0.27), residues: 363 sheet: -1.50 (0.85), residues: 36 loop : -1.48 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 482 TYR 0.021 0.002 TYR D 385 PHE 0.020 0.002 PHE D 523 TRP 0.013 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6532) covalent geometry : angle 0.60422 ( 8875) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.16496 ( 12) hydrogen bonds : bond 0.04868 ( 280) hydrogen bonds : angle 4.93414 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7561 (mm-30) REVERT: D 63 ASN cc_start: 0.7387 (m110) cc_final: 0.6809 (m110) REVERT: D 189 GLU cc_start: 0.7514 (mp0) cc_final: 0.6828 (mt-10) REVERT: D 192 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7468 (mtt180) REVERT: D 306 ARG cc_start: 0.7564 (ttt180) cc_final: 0.7279 (ttt180) REVERT: D 307 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8024 (mt) REVERT: D 472 GLN cc_start: 0.8769 (mt0) cc_final: 0.8524 (mt0) REVERT: D 474 MET cc_start: 0.9051 (mmp) cc_final: 0.8461 (mmp) REVERT: D 483 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: D 531 GLN cc_start: 0.8204 (mt0) cc_final: 0.7982 (mt0) REVERT: F 439 ASN cc_start: 0.8349 (t0) cc_final: 0.7929 (t0) outliers start: 28 outliers final: 23 residues processed: 127 average time/residue: 0.0771 time to fit residues: 13.3511 Evaluate side-chains 128 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 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 = 0.3704 r_free = 0.3704 target = 0.156474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124083 restraints weight = 7512.399| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.55 r_work: 0.3211 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6538 Z= 0.194 Angle : 0.603 7.158 8887 Z= 0.318 Chirality : 0.045 0.164 918 Planarity : 0.004 0.052 1150 Dihedral : 5.649 46.206 850 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.96 % Allowed : 16.62 % Favored : 78.43 % 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: -1.27 (0.30), residues: 775 helix: -0.19 (0.27), residues: 355 sheet: -1.29 (0.86), residues: 36 loop : -1.40 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 482 TYR 0.019 0.002 TYR D 385 PHE 0.022 0.002 PHE D 523 TRP 0.024 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6532) covalent geometry : angle 0.60056 ( 8875) SS BOND : bond 0.00748 ( 6) SS BOND : angle 1.56980 ( 12) hydrogen bonds : bond 0.04839 ( 280) hydrogen bonds : angle 4.92641 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7632 (mm-30) REVERT: D 63 ASN cc_start: 0.7404 (m110) cc_final: 0.6822 (m110) REVERT: D 192 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7563 (mtt180) REVERT: D 306 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7282 (ttt180) REVERT: D 307 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8058 (mt) REVERT: D 472 GLN cc_start: 0.8793 (mt0) cc_final: 0.8478 (mt0) REVERT: D 474 MET cc_start: 0.9042 (mmp) cc_final: 0.8597 (mmp) REVERT: D 499 ASP cc_start: 0.8454 (m-30) cc_final: 0.8154 (m-30) REVERT: D 531 GLN cc_start: 0.8211 (mt0) cc_final: 0.7966 (mt0) REVERT: F 439 ASN cc_start: 0.8419 (t0) cc_final: 0.8011 (t0) outliers start: 34 outliers final: 28 residues processed: 129 average time/residue: 0.0776 time to fit residues: 13.5428 Evaluate side-chains 125 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.155925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124367 restraints weight = 7482.544| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.47 r_work: 0.3236 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6538 Z= 0.173 Angle : 0.583 7.221 8887 Z= 0.308 Chirality : 0.044 0.139 918 Planarity : 0.004 0.052 1150 Dihedral : 5.607 46.671 850 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.25 % Allowed : 17.35 % Favored : 77.41 % 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: -1.22 (0.30), residues: 775 helix: -0.13 (0.27), residues: 355 sheet: -1.55 (0.75), residues: 46 loop : -1.33 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 582 TYR 0.018 0.002 TYR D 385 PHE 0.021 0.002 PHE D 523 TRP 0.022 0.002 TRP D 302 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6532) covalent geometry : angle 0.58179 ( 8875) SS BOND : bond 0.00671 ( 6) SS BOND : angle 1.29751 ( 12) hydrogen bonds : bond 0.04686 ( 280) hydrogen bonds : angle 4.90535 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 63 ASN cc_start: 0.7401 (m110) cc_final: 0.6814 (m110) REVERT: D 171 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: D 192 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7410 (mtt90) REVERT: D 307 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8030 (mt) REVERT: D 472 GLN cc_start: 0.8786 (mt0) cc_final: 0.8534 (mt0) REVERT: D 474 MET cc_start: 0.9012 (mmp) cc_final: 0.8559 (mmp) REVERT: D 499 ASP cc_start: 0.8431 (m-30) cc_final: 0.8159 (m-30) REVERT: D 531 GLN cc_start: 0.8166 (mt0) cc_final: 0.7898 (mt0) REVERT: F 439 ASN cc_start: 0.8437 (t0) cc_final: 0.8091 (t0) outliers start: 36 outliers final: 32 residues processed: 129 average time/residue: 0.0735 time to fit residues: 13.0920 Evaluate side-chains 131 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.155549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124018 restraints weight = 7560.940| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.47 r_work: 0.3238 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6538 Z= 0.177 Angle : 0.586 6.862 8887 Z= 0.310 Chirality : 0.044 0.141 918 Planarity : 0.004 0.052 1150 Dihedral : 5.607 47.253 850 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.10 % Allowed : 17.49 % Favored : 77.41 % 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: -1.16 (0.30), residues: 775 helix: -0.14 (0.27), residues: 357 sheet: -1.37 (0.77), residues: 46 loop : -1.26 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 582 TYR 0.019 0.002 TYR D 385 PHE 0.022 0.002 PHE D 523 TRP 0.028 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6532) covalent geometry : angle 0.58522 ( 8875) SS BOND : bond 0.00631 ( 6) SS BOND : angle 1.16102 ( 12) hydrogen bonds : bond 0.04712 ( 280) hydrogen bonds : angle 4.88251 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7582 (mm-30) REVERT: D 150 GLU cc_start: 0.7813 (mp0) cc_final: 0.7509 (mp0) REVERT: D 171 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: D 192 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7420 (mtt90) REVERT: D 307 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8018 (mt) REVERT: D 472 GLN cc_start: 0.8794 (mt0) cc_final: 0.8543 (mt0) REVERT: D 474 MET cc_start: 0.9028 (mmp) cc_final: 0.8569 (mmp) REVERT: D 499 ASP cc_start: 0.8432 (m-30) cc_final: 0.8176 (m-30) REVERT: D 531 GLN cc_start: 0.8160 (mt0) cc_final: 0.7867 (mt0) REVERT: F 439 ASN cc_start: 0.8461 (t0) cc_final: 0.8115 (t0) outliers start: 35 outliers final: 32 residues processed: 132 average time/residue: 0.0728 time to fit residues: 13.2424 Evaluate side-chains 137 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 66 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 7 optimal weight: 0.0770 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.1938 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.163216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132088 restraints weight = 7531.493| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.56 r_work: 0.3317 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6538 Z= 0.114 Angle : 0.537 6.599 8887 Z= 0.284 Chirality : 0.041 0.141 918 Planarity : 0.004 0.051 1150 Dihedral : 5.346 47.196 850 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.94 % Allowed : 18.95 % Favored : 77.11 % 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: -0.90 (0.31), residues: 775 helix: 0.16 (0.28), residues: 352 sheet: -1.25 (0.76), residues: 48 loop : -1.19 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 582 TYR 0.016 0.001 TYR D 385 PHE 0.017 0.001 PHE D 523 TRP 0.025 0.001 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6532) covalent geometry : angle 0.53654 ( 8875) SS BOND : bond 0.00477 ( 6) SS BOND : angle 0.91001 ( 12) hydrogen bonds : bond 0.04138 ( 280) hydrogen bonds : angle 4.68270 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 63 ASN cc_start: 0.7355 (m110) cc_final: 0.6738 (m110) REVERT: D 150 GLU cc_start: 0.7606 (mp0) cc_final: 0.7097 (mp0) REVERT: D 192 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7447 (mtt180) REVERT: D 227 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: D 307 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7804 (mt) REVERT: D 472 GLN cc_start: 0.8678 (mt0) cc_final: 0.8406 (mt0) REVERT: D 474 MET cc_start: 0.8999 (mmp) cc_final: 0.8395 (mmp) REVERT: D 483 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (pp20) REVERT: D 531 GLN cc_start: 0.8087 (mt0) cc_final: 0.7836 (mt0) REVERT: D 578 ASN cc_start: 0.6888 (t0) cc_final: 0.6422 (p0) REVERT: F 439 ASN cc_start: 0.8427 (t0) cc_final: 0.8064 (t0) outliers start: 27 outliers final: 20 residues processed: 133 average time/residue: 0.0690 time to fit residues: 12.3845 Evaluate side-chains 130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.0470 chunk 17 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.162526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131061 restraints weight = 7371.837| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.53 r_work: 0.3269 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6538 Z= 0.154 Angle : 0.574 6.329 8887 Z= 0.304 Chirality : 0.043 0.136 918 Planarity : 0.004 0.052 1150 Dihedral : 5.398 48.249 850 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.94 % Allowed : 18.51 % Favored : 77.55 % 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: -0.97 (0.30), residues: 775 helix: 0.09 (0.28), residues: 354 sheet: -1.15 (0.77), residues: 48 loop : -1.24 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 582 TYR 0.015 0.001 TYR D 497 PHE 0.020 0.001 PHE D 523 TRP 0.029 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6532) covalent geometry : angle 0.57341 ( 8875) SS BOND : bond 0.00531 ( 6) SS BOND : angle 1.04034 ( 12) hydrogen bonds : bond 0.04461 ( 280) hydrogen bonds : angle 4.70752 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7528 (mm-30) REVERT: D 63 ASN cc_start: 0.7339 (m110) cc_final: 0.6739 (m110) REVERT: D 150 GLU cc_start: 0.7671 (mp0) cc_final: 0.7229 (mp0) REVERT: D 192 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7427 (mtt180) REVERT: D 307 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7930 (mt) REVERT: D 472 GLN cc_start: 0.8785 (mt0) cc_final: 0.8539 (mt0) REVERT: D 474 MET cc_start: 0.9026 (mmp) cc_final: 0.8571 (mmp) REVERT: D 483 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8310 (pp20) REVERT: D 499 ASP cc_start: 0.8436 (m-30) cc_final: 0.8137 (m-30) REVERT: D 531 GLN cc_start: 0.8130 (mt0) cc_final: 0.7859 (mt0) REVERT: D 578 ASN cc_start: 0.6923 (t0) cc_final: 0.6408 (p0) REVERT: F 439 ASN cc_start: 0.8444 (t0) cc_final: 0.8071 (t0) outliers start: 27 outliers final: 24 residues processed: 126 average time/residue: 0.0706 time to fit residues: 12.1972 Evaluate side-chains 133 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.0270 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 0.0020 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 overall best weight: 0.2246 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.165646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135059 restraints weight = 7441.174| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.53 r_work: 0.3330 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6538 Z= 0.120 Angle : 0.546 6.505 8887 Z= 0.289 Chirality : 0.042 0.135 918 Planarity : 0.004 0.052 1150 Dihedral : 5.255 48.609 850 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.08 % Allowed : 18.51 % Favored : 77.41 % 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: -0.82 (0.30), residues: 775 helix: 0.24 (0.28), residues: 353 sheet: -1.05 (0.77), residues: 48 loop : -1.21 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.015 0.001 TYR D 385 PHE 0.016 0.001 PHE D 523 TRP 0.027 0.001 TRP F 353 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6532) covalent geometry : angle 0.54517 ( 8875) SS BOND : bond 0.00461 ( 6) SS BOND : angle 0.89057 ( 12) hydrogen bonds : bond 0.04161 ( 280) hydrogen bonds : angle 4.58728 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.48 seconds wall clock time: 33 minutes 30.74 seconds (2010.74 seconds total)