Starting phenix.real_space_refine on Sun Apr 27 16:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gz3_51721/04_2025/9gz3_51721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gz3_51721/04_2025/9gz3_51721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gz3_51721/04_2025/9gz3_51721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gz3_51721/04_2025/9gz3_51721.map" model { file = "/net/cci-nas-00/data/ceres_data/9gz3_51721/04_2025/9gz3_51721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gz3_51721/04_2025/9gz3_51721.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3941 2.51 5 N 1051 2.21 5 O 1152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6147 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.94, per 1000 atoms: 0.80 Number of scatterers: 6180 At special positions: 0 Unit cell: (71.514, 92.064, 129.876, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 3 15.00 Mg 1 11.99 O 1152 8.00 N 1051 7.00 C 3941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 922.5 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 54.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 4.430A pdb=" N VAL A 8 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 131 through 134 removed outlier: 3.938A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.780A pdb=" N VAL A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.891A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.869A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.532A pdb=" N VAL A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 removed outlier: 4.047A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.990A pdb=" N ASP A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.247A pdb=" N MET A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.555A pdb=" N TYR A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.548A pdb=" N LEU A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 4.203A pdb=" N TYR A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 4.016A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 524 " --> pdb=" O CYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 537 removed outlier: 4.040A pdb=" N GLU A 535 " --> pdb=" O MET A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 614 through 621 Processing helix chain 'A' and resid 646 through 662 Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 697 through 708 removed outlier: 4.032A pdb=" N CYS A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 737 through 748 removed outlier: 4.024A pdb=" N SER A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 748 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 796 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 removed outlier: 7.162A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.137A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER A 173 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLN A 172 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU A 460 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A 174 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 245 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.641A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1498 1.33 - 1.45: 1233 1.45 - 1.57: 3518 1.57 - 1.69: 5 1.69 - 1.80: 56 Bond restraints: 6310 Sorted by residual: bond pdb=" O3 PO4 A1203 " pdb=" P PO4 A1203 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" O4 PO4 A1203 " pdb=" P PO4 A1203 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O2 PO4 A1203 " pdb=" P PO4 A1203 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O1 PO4 A1203 " pdb=" P PO4 A1203 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" N LYS A 572 " pdb=" CA LYS A 572 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.05e+00 ... (remaining 6305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 8128 2.36 - 4.72: 341 4.72 - 7.07: 38 7.07 - 9.43: 5 9.43 - 11.79: 1 Bond angle restraints: 8513 Sorted by residual: angle pdb=" CA LYS A 542 " pdb=" CB LYS A 542 " pdb=" CG LYS A 542 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" C2' ADP A1202 " pdb=" C3' ADP A1202 " pdb=" C4' ADP A1202 " ideal model delta sigma weight residual 111.00 99.21 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" N ILE A 591 " pdb=" CA ILE A 591 " pdb=" C ILE A 591 " ideal model delta sigma weight residual 108.93 114.14 -5.21 1.35e+00 5.49e-01 1.49e+01 angle pdb=" C LYS A 598 " pdb=" N ASP A 599 " pdb=" CA ASP A 599 " ideal model delta sigma weight residual 121.80 130.24 -8.44 2.44e+00 1.68e-01 1.20e+01 angle pdb=" C LEU A 749 " pdb=" N ASP A 750 " pdb=" CA ASP A 750 " ideal model delta sigma weight residual 122.46 127.20 -4.74 1.41e+00 5.03e-01 1.13e+01 ... (remaining 8508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3462 17.63 - 35.26: 265 35.26 - 52.89: 49 52.89 - 70.52: 15 70.52 - 88.15: 16 Dihedral angle restraints: 3807 sinusoidal: 1581 harmonic: 2226 Sorted by residual: dihedral pdb=" CA LYS A 367 " pdb=" C LYS A 367 " pdb=" N GLN A 368 " pdb=" CA GLN A 368 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN A 44 " pdb=" C GLN A 44 " pdb=" N GLU A 45 " pdb=" CA GLU A 45 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ARG A 281 " pdb=" C ARG A 281 " pdb=" N ASP A 282 " pdb=" CA ASP A 282 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 3804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 578 0.051 - 0.101: 243 0.101 - 0.152: 79 0.152 - 0.203: 17 0.203 - 0.253: 5 Chirality restraints: 922 Sorted by residual: chirality pdb=" CA ASN A 224 " pdb=" N ASN A 224 " pdb=" C ASN A 224 " pdb=" CB ASN A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE A 730 " pdb=" CA ILE A 730 " pdb=" CG1 ILE A 730 " pdb=" CG2 ILE A 730 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL A 763 " pdb=" CA VAL A 763 " pdb=" CG1 VAL A 763 " pdb=" CG2 VAL A 763 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 919 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 712 " 0.263 9.50e-02 1.11e+02 1.22e-01 2.03e+01 pdb=" NE ARG A 712 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 712 " -0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG A 712 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 712 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 570 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LYS A 570 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS A 570 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY A 571 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 671 " -0.191 9.50e-02 1.11e+02 8.76e-02 9.21e+00 pdb=" NE ARG A 671 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 671 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 671 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 671 " -0.019 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 81 2.65 - 3.21: 5659 3.21 - 3.78: 9356 3.78 - 4.34: 13042 4.34 - 4.90: 21332 Nonbonded interactions: 49470 Sorted by model distance: nonbonded pdb=" OG SER A 242 " pdb="MG MG A1201 " model vdw 2.088 2.170 nonbonded pdb="MG MG A1201 " pdb=" O1B ADP A1202 " model vdw 2.093 2.170 nonbonded pdb=" OG1 THR A 185 " pdb="MG MG A1201 " model vdw 2.147 2.170 nonbonded pdb=" OG1 THR A 185 " pdb=" O1B ADP A1202 " model vdw 2.291 3.040 nonbonded pdb=" O SER A 664 " pdb=" OG SER A 664 " model vdw 2.300 3.040 ... (remaining 49465 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 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: 2.900 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.007 0.094 6310 Z= 0.305 Angle : 1.067 11.790 8513 Z= 0.612 Chirality : 0.063 0.253 922 Planarity : 0.009 0.122 1097 Dihedral : 14.737 88.150 2373 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.56 % Favored : 96.17 % Rotamer: Outliers : 0.15 % Allowed : 1.81 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.27), residues: 758 helix: -1.53 (0.23), residues: 359 sheet: -1.52 (0.59), residues: 69 loop : -0.80 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 438 HIS 0.008 0.002 HIS A 576 PHE 0.028 0.003 PHE A 489 TYR 0.027 0.004 TYR A 117 ARG 0.059 0.006 ARG A 712 Details of bonding type rmsd hydrogen bonds : bond 0.22728 ( 295) hydrogen bonds : angle 8.14992 ( 837) covalent geometry : bond 0.00695 ( 6310) covalent geometry : angle 1.06737 ( 8513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 470 PHE cc_start: 0.7779 (t80) cc_final: 0.7492 (t80) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.2383 time to fit residues: 36.5312 Evaluate side-chains 79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.0060 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 104 ASN A 160 ASN A 471 ASN A 490 ASN A 492 HIS ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147056 restraints weight = 7714.254| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.29 r_work: 0.3683 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6310 Z= 0.129 Angle : 0.608 7.044 8513 Z= 0.312 Chirality : 0.044 0.135 922 Planarity : 0.003 0.031 1097 Dihedral : 6.432 68.495 843 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.06 % Allowed : 6.94 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.30), residues: 758 helix: 0.46 (0.27), residues: 365 sheet: -1.07 (0.63), residues: 63 loop : -0.24 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 593 HIS 0.003 0.001 HIS A 284 PHE 0.016 0.001 PHE A 252 TYR 0.013 0.001 TYR A 117 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 295) hydrogen bonds : angle 4.82742 ( 837) covalent geometry : bond 0.00290 ( 6310) covalent geometry : angle 0.60830 ( 8513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 77 MET cc_start: 0.5805 (ptm) cc_final: 0.5602 (ptp) REVERT: A 146 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8126 (mtmt) REVERT: A 386 TYR cc_start: 0.8011 (t80) cc_final: 0.7775 (t80) REVERT: A 433 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7669 (tt0) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.2069 time to fit residues: 25.4164 Evaluate side-chains 76 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 482 ASN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140471 restraints weight = 7935.994| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.36 r_work: 0.3626 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6310 Z= 0.150 Angle : 0.587 6.686 8513 Z= 0.295 Chirality : 0.044 0.133 922 Planarity : 0.003 0.032 1097 Dihedral : 5.790 60.506 839 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.11 % Allowed : 9.50 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.30), residues: 758 helix: 0.61 (0.27), residues: 373 sheet: -1.03 (0.66), residues: 58 loop : -0.32 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 508 HIS 0.005 0.001 HIS A 284 PHE 0.012 0.002 PHE A 252 TYR 0.014 0.001 TYR A 117 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 295) hydrogen bonds : angle 4.49656 ( 837) covalent geometry : bond 0.00357 ( 6310) covalent geometry : angle 0.58748 ( 8513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 92 MET cc_start: 0.7531 (mmm) cc_final: 0.7112 (mmp) REVERT: A 330 MET cc_start: 0.7341 (mtt) cc_final: 0.7080 (mtt) REVERT: A 378 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8744 (m) REVERT: A 386 TYR cc_start: 0.8035 (t80) cc_final: 0.7825 (t80) REVERT: A 433 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7638 (tt0) REVERT: A 470 PHE cc_start: 0.7605 (t80) cc_final: 0.7374 (t80) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.1902 time to fit residues: 23.0955 Evaluate side-chains 84 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 576 HIS A 581 HIS ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142696 restraints weight = 8026.403| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.43 r_work: 0.3627 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6310 Z= 0.127 Angle : 0.540 6.961 8513 Z= 0.269 Chirality : 0.042 0.133 922 Planarity : 0.003 0.028 1097 Dihedral : 5.484 53.981 839 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.11 % Allowed : 10.41 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 758 helix: 0.82 (0.27), residues: 371 sheet: -1.06 (0.67), residues: 58 loop : -0.17 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.003 0.001 HIS A 284 PHE 0.012 0.001 PHE A 252 TYR 0.012 0.001 TYR A 266 ARG 0.003 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 295) hydrogen bonds : angle 4.29055 ( 837) covalent geometry : bond 0.00298 ( 6310) covalent geometry : angle 0.54005 ( 8513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 92 MET cc_start: 0.7519 (mmm) cc_final: 0.7077 (mmp) REVERT: A 195 PHE cc_start: 0.7181 (m-80) cc_final: 0.6961 (m-10) REVERT: A 378 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8701 (m) REVERT: A 433 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7707 (tt0) REVERT: A 470 PHE cc_start: 0.7706 (t80) cc_final: 0.7440 (t80) REVERT: A 574 GLU cc_start: 0.6129 (tp30) cc_final: 0.5533 (pt0) outliers start: 14 outliers final: 6 residues processed: 86 average time/residue: 0.2026 time to fit residues: 23.6746 Evaluate side-chains 76 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136922 restraints weight = 7908.483| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.40 r_work: 0.3574 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6310 Z= 0.166 Angle : 0.570 7.457 8513 Z= 0.283 Chirality : 0.043 0.135 922 Planarity : 0.003 0.037 1097 Dihedral : 5.571 54.002 839 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.26 % Allowed : 11.61 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 758 helix: 0.75 (0.27), residues: 371 sheet: -1.22 (0.70), residues: 58 loop : -0.22 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 438 HIS 0.004 0.001 HIS A 284 PHE 0.012 0.002 PHE A 473 TYR 0.013 0.001 TYR A 266 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 295) hydrogen bonds : angle 4.32066 ( 837) covalent geometry : bond 0.00401 ( 6310) covalent geometry : angle 0.57001 ( 8513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8016 (tm-30) REVERT: A 195 PHE cc_start: 0.7354 (m-80) cc_final: 0.7084 (m-10) REVERT: A 378 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 433 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7714 (tt0) REVERT: A 574 GLU cc_start: 0.6258 (tp30) cc_final: 0.5575 (pt0) REVERT: A 753 HIS cc_start: 0.7231 (m-70) cc_final: 0.7023 (m-70) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.1942 time to fit residues: 23.6262 Evaluate side-chains 82 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 784 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 37 optimal weight: 0.0020 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142853 restraints weight = 7799.836| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.39 r_work: 0.3632 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.003 0.042 6310 Z= 0.110 Angle : 0.541 8.172 8513 Z= 0.266 Chirality : 0.041 0.128 922 Planarity : 0.003 0.029 1097 Dihedral : 5.221 47.598 839 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.26 % Allowed : 12.22 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 758 helix: 0.94 (0.27), residues: 370 sheet: -1.22 (0.70), residues: 58 loop : -0.10 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.003 0.000 HIS A 284 PHE 0.011 0.001 PHE A 473 TYR 0.011 0.001 TYR A 266 ARG 0.003 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 295) hydrogen bonds : angle 4.15933 ( 837) covalent geometry : bond 0.00257 ( 6310) covalent geometry : angle 0.54054 ( 8513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 92 MET cc_start: 0.7550 (mmp) cc_final: 0.6803 (mtm) REVERT: A 195 PHE cc_start: 0.7247 (m-80) cc_final: 0.6989 (m-10) REVERT: A 378 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8629 (m) REVERT: A 433 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7714 (tt0) REVERT: A 470 PHE cc_start: 0.7814 (t80) cc_final: 0.7496 (t80) REVERT: A 574 GLU cc_start: 0.6267 (tp30) cc_final: 0.5660 (pt0) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.1860 time to fit residues: 22.4740 Evaluate side-chains 79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 3 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143997 restraints weight = 7826.512| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.39 r_work: 0.3644 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6310 Z= 0.106 Angle : 0.535 8.653 8513 Z= 0.264 Chirality : 0.042 0.159 922 Planarity : 0.003 0.029 1097 Dihedral : 4.928 42.044 839 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.11 % Allowed : 12.37 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.31), residues: 758 helix: 1.06 (0.28), residues: 373 sheet: -1.25 (0.67), residues: 58 loop : -0.05 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.003 0.000 HIS A 97 PHE 0.011 0.001 PHE A 473 TYR 0.014 0.001 TYR A 422 ARG 0.003 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 295) hydrogen bonds : angle 4.02472 ( 837) covalent geometry : bond 0.00246 ( 6310) covalent geometry : angle 0.53521 ( 8513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 92 MET cc_start: 0.7482 (mmp) cc_final: 0.6787 (mtm) REVERT: A 433 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7695 (tt0) REVERT: A 470 PHE cc_start: 0.7805 (t80) cc_final: 0.7449 (t80) REVERT: A 574 GLU cc_start: 0.6331 (tp30) cc_final: 0.5739 (pt0) outliers start: 14 outliers final: 7 residues processed: 90 average time/residue: 0.2015 time to fit residues: 24.8271 Evaluate side-chains 79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 5.9990 chunk 30 optimal weight: 0.0020 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.0270 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.174052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142760 restraints weight = 7765.481| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.37 r_work: 0.3641 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6310 Z= 0.106 Angle : 0.560 9.341 8513 Z= 0.269 Chirality : 0.041 0.126 922 Planarity : 0.003 0.028 1097 Dihedral : 4.833 40.629 839 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.66 % Allowed : 12.97 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 758 helix: 1.07 (0.27), residues: 373 sheet: -1.07 (0.59), residues: 73 loop : 0.01 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.003 0.000 HIS A 97 PHE 0.011 0.001 PHE A 473 TYR 0.010 0.001 TYR A 266 ARG 0.002 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 295) hydrogen bonds : angle 3.97863 ( 837) covalent geometry : bond 0.00246 ( 6310) covalent geometry : angle 0.56017 ( 8513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 92 MET cc_start: 0.7475 (mmp) cc_final: 0.6761 (mtm) REVERT: A 374 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6427 (tt0) REVERT: A 388 MET cc_start: 0.8456 (mtt) cc_final: 0.8182 (mtt) REVERT: A 574 GLU cc_start: 0.6273 (tp30) cc_final: 0.5730 (pt0) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 0.2450 time to fit residues: 28.7368 Evaluate side-chains 85 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139996 restraints weight = 7814.131| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.36 r_work: 0.3606 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6310 Z= 0.136 Angle : 0.570 10.193 8513 Z= 0.276 Chirality : 0.042 0.128 922 Planarity : 0.003 0.029 1097 Dihedral : 4.954 40.844 839 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.36 % Allowed : 13.42 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 758 helix: 1.01 (0.27), residues: 373 sheet: -1.26 (0.65), residues: 58 loop : -0.11 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.003 0.001 HIS A 284 PHE 0.011 0.001 PHE A 473 TYR 0.011 0.001 TYR A 266 ARG 0.003 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 295) hydrogen bonds : angle 4.06301 ( 837) covalent geometry : bond 0.00327 ( 6310) covalent geometry : angle 0.56981 ( 8513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 92 MET cc_start: 0.7509 (mmp) cc_final: 0.6771 (mtm) REVERT: A 374 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6395 (tt0) REVERT: A 574 GLU cc_start: 0.6293 (tp30) cc_final: 0.5733 (pt0) REVERT: A 783 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8049 (ttm110) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.2576 time to fit residues: 27.9641 Evaluate side-chains 83 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 74 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141842 restraints weight = 7866.188| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.43 r_work: 0.3623 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6310 Z= 0.119 Angle : 0.565 10.436 8513 Z= 0.271 Chirality : 0.042 0.128 922 Planarity : 0.003 0.028 1097 Dihedral : 4.907 40.519 839 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.21 % Allowed : 13.42 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 758 helix: 1.05 (0.27), residues: 374 sheet: -1.31 (0.66), residues: 58 loop : -0.10 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.002 0.000 HIS A 284 PHE 0.010 0.001 PHE A 473 TYR 0.012 0.001 TYR A 310 ARG 0.003 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 295) hydrogen bonds : angle 4.04809 ( 837) covalent geometry : bond 0.00282 ( 6310) covalent geometry : angle 0.56513 ( 8513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7982 (tm-30) REVERT: A 92 MET cc_start: 0.7450 (mmp) cc_final: 0.6689 (mtm) REVERT: A 374 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6306 (tt0) REVERT: A 388 MET cc_start: 0.8488 (mtt) cc_final: 0.8214 (mtt) REVERT: A 470 PHE cc_start: 0.7912 (t80) cc_final: 0.7534 (t80) REVERT: A 574 GLU cc_start: 0.6318 (tp30) cc_final: 0.5716 (pt0) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.2025 time to fit residues: 22.0994 Evaluate side-chains 80 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 723 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142271 restraints weight = 7920.136| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.38 r_work: 0.3607 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6310 Z= 0.119 Angle : 0.576 10.765 8513 Z= 0.275 Chirality : 0.042 0.127 922 Planarity : 0.003 0.030 1097 Dihedral : 4.871 39.825 839 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.36 % Allowed : 13.42 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 758 helix: 1.02 (0.27), residues: 374 sheet: -1.27 (0.66), residues: 58 loop : -0.12 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.002 0.001 HIS A 284 PHE 0.011 0.001 PHE A 473 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 295) hydrogen bonds : angle 4.07431 ( 837) covalent geometry : bond 0.00284 ( 6310) covalent geometry : angle 0.57599 ( 8513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.33 seconds wall clock time: 59 minutes 21.61 seconds (3561.61 seconds total)