Starting phenix.real_space_refine on Sat May 10 12:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gz3_51721/05_2025/9gz3_51721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gz3_51721/05_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_51721/05_2025/9gz3_51721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gz3_51721/05_2025/9gz3_51721.map" model { file = "/net/cci-nas-00/data/ceres_data/9gz3_51721/05_2025/9gz3_51721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gz3_51721/05_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-5687/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: 4.66, per 1000 atoms: 0.75 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: 1.62 Conformation dependent library (CDL) restraints added in 924.5 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: 0.74 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: 1.89 Time building geometry restraints manager: 1.87 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: 2.550 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- 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 : 0.745 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: 0.2306 time to fit residues: 35.2782 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 : 0.665 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147004 restraints weight = 7714.254| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.30 r_work: 0.3680 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 77 MET cc_start: 0.5803 (ptm) cc_final: 0.5598 (ptp) REVERT: A 146 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8126 (mtmt) REVERT: A 386 TYR cc_start: 0.8011 (t80) cc_final: 0.7774 (t80) REVERT: A 433 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7668 (tt0) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.2107 time to fit residues: 25.9462 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 : 0.713 ------------------------------------------------------------------------------- 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: 0.0470 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 0.0060 chunk 56 optimal weight: 0.8980 overall best weight: 0.5294 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.176668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146625 restraints weight = 7880.825| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.24 r_work: 0.3672 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6310 Z= 0.122 Angle : 0.560 6.959 8513 Z= 0.281 Chirality : 0.042 0.131 922 Planarity : 0.003 0.033 1097 Dihedral : 5.680 62.345 839 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.81 % Allowed : 9.35 % Favored : 88.84 % 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: 0.84 (0.27), residues: 367 sheet: -1.31 (0.62), residues: 63 loop : -0.09 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 508 HIS 0.004 0.001 HIS A 284 PHE 0.012 0.001 PHE A 252 TYR 0.014 0.001 TYR A 117 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 295) hydrogen bonds : angle 4.42257 ( 837) covalent geometry : bond 0.00283 ( 6310) covalent geometry : angle 0.56001 ( 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 98 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 92 MET cc_start: 0.7488 (mmm) cc_final: 0.7038 (mmp) REVERT: A 330 MET cc_start: 0.7350 (mtt) cc_final: 0.7127 (mtt) REVERT: A 378 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8705 (m) REVERT: A 433 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7648 (tt0) REVERT: A 470 PHE cc_start: 0.7563 (t80) cc_final: 0.7350 (t80) REVERT: A 574 GLU cc_start: 0.6126 (tp30) cc_final: 0.5474 (pt0) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 0.1874 time to fit residues: 23.1890 Evaluate side-chains 82 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 674 ILE Chi-restraints excluded: chain A residue 695 CYS 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: 0.9980 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 43 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS A 581 HIS ** 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 = 0.4111 r_free = 0.4111 target = 0.176752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145930 restraints weight = 7909.969| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.37 r_work: 0.3661 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6310 Z= 0.111 Angle : 0.528 6.843 8513 Z= 0.263 Chirality : 0.042 0.129 922 Planarity : 0.003 0.028 1097 Dihedral : 5.345 56.064 839 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.11 % Allowed : 10.56 % Favored : 87.33 % 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: 0.40 (0.30), residues: 758 helix: 0.93 (0.27), residues: 374 sheet: -1.07 (0.66), residues: 58 loop : -0.11 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 508 HIS 0.002 0.001 HIS A 153 PHE 0.014 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 0.03230 ( 295) hydrogen bonds : angle 4.22980 ( 837) covalent geometry : bond 0.00257 ( 6310) covalent geometry : angle 0.52756 ( 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 91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 378 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8666 (m) REVERT: A 433 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7679 (tt0) REVERT: A 470 PHE cc_start: 0.7606 (t80) cc_final: 0.7319 (t80) REVERT: A 574 GLU cc_start: 0.6310 (tp30) cc_final: 0.5654 (pt0) outliers start: 14 outliers final: 7 residues processed: 86 average time/residue: 0.1737 time to fit residues: 20.2953 Evaluate side-chains 78 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 235 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 695 CYS 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: 0.8980 chunk 61 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.141509 restraints weight = 7825.476| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.36 r_work: 0.3612 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6310 Z= 0.142 Angle : 0.552 7.229 8513 Z= 0.274 Chirality : 0.043 0.134 922 Planarity : 0.003 0.032 1097 Dihedral : 5.274 46.854 839 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.11 % Allowed : 11.01 % Favored : 86.88 % 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: 0.31 (0.30), residues: 758 helix: 0.86 (0.27), residues: 374 sheet: -1.21 (0.68), residues: 58 loop : -0.15 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.004 0.001 HIS A 284 PHE 0.011 0.001 PHE A 473 TYR 0.012 0.001 TYR A 266 ARG 0.003 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 295) hydrogen bonds : angle 4.21935 ( 837) covalent geometry : bond 0.00338 ( 6310) covalent geometry : angle 0.55230 ( 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 89 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 92 MET cc_start: 0.7584 (mmp) cc_final: 0.6809 (mtm) REVERT: A 195 PHE cc_start: 0.7286 (m-80) cc_final: 0.7057 (m-10) REVERT: A 378 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8648 (m) REVERT: A 433 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7676 (tt0) outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 0.1860 time to fit residues: 20.8009 Evaluate side-chains 77 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 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: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.171235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139747 restraints weight = 7829.806| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.35 r_work: 0.3596 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6310 Z= 0.161 Angle : 0.581 7.904 8513 Z= 0.287 Chirality : 0.043 0.134 922 Planarity : 0.003 0.034 1097 Dihedral : 5.253 44.481 839 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 11.76 % Favored : 85.97 % 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: 0.21 (0.30), residues: 758 helix: 0.77 (0.27), residues: 374 sheet: -1.28 (0.70), residues: 58 loop : -0.17 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 593 HIS 0.004 0.001 HIS A 753 PHE 0.012 0.001 PHE A 473 TYR 0.013 0.001 TYR A 266 ARG 0.004 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 295) hydrogen bonds : angle 4.20806 ( 837) covalent geometry : bond 0.00388 ( 6310) covalent geometry : angle 0.58082 ( 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 91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 195 PHE cc_start: 0.7292 (m-80) cc_final: 0.7067 (m-10) REVERT: A 357 MET cc_start: 0.7907 (mtt) cc_final: 0.7632 (mtp) REVERT: A 374 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6553 (tt0) REVERT: A 378 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8692 (m) REVERT: A 433 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7720 (tt0) REVERT: A 574 GLU cc_start: 0.6077 (tp30) cc_final: 0.5450 (pt0) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.1700 time to fit residues: 20.1862 Evaluate side-chains 82 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137678 restraints weight = 7895.526| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.37 r_work: 0.3595 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6310 Z= 0.162 Angle : 0.582 8.241 8513 Z= 0.286 Chirality : 0.043 0.135 922 Planarity : 0.003 0.031 1097 Dihedral : 5.181 42.766 839 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 0.20 (0.30), residues: 758 helix: 0.78 (0.27), residues: 374 sheet: -1.39 (0.68), residues: 58 loop : -0.19 (0.34), residues: 326 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 0.012 0.001 PHE A 473 TYR 0.013 0.001 TYR A 266 ARG 0.003 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 295) hydrogen bonds : angle 4.16973 ( 837) covalent geometry : bond 0.00390 ( 6310) covalent geometry : angle 0.58177 ( 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 85 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 92 MET cc_start: 0.7558 (mmp) cc_final: 0.6872 (mtm) REVERT: A 374 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6510 (tt0) REVERT: A 378 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 433 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7731 (tt0) REVERT: A 574 GLU cc_start: 0.6100 (tp30) cc_final: 0.5620 (pt0) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.2130 time to fit residues: 23.1633 Evaluate side-chains 78 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 300 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.169206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137663 restraints weight = 7821.496| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.35 r_work: 0.3587 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6310 Z= 0.160 Angle : 0.588 8.403 8513 Z= 0.289 Chirality : 0.043 0.135 922 Planarity : 0.003 0.030 1097 Dihedral : 5.207 42.607 839 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.41 % Allowed : 12.52 % Favored : 85.07 % 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: 0.19 (0.31), residues: 758 helix: 0.76 (0.27), residues: 374 sheet: -1.35 (0.67), residues: 58 loop : -0.20 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.003 0.001 HIS A 753 PHE 0.012 0.001 PHE A 473 TYR 0.013 0.001 TYR A 266 ARG 0.003 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 295) hydrogen bonds : angle 4.18761 ( 837) covalent geometry : bond 0.00385 ( 6310) covalent geometry : angle 0.58824 ( 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 88 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 92 MET cc_start: 0.7573 (mmp) cc_final: 0.6873 (mtm) REVERT: A 433 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7745 (tt0) REVERT: A 470 PHE cc_start: 0.7934 (t80) cc_final: 0.7591 (t80) REVERT: A 574 GLU cc_start: 0.6142 (tp30) cc_final: 0.5507 (pt0) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.1791 time to fit residues: 20.0544 Evaluate side-chains 81 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 300 MET Chi-restraints excluded: chain A residue 304 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 698 VAL 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: 1.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 67 optimal weight: 0.2980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.175132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144035 restraints weight = 7782.653| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.35 r_work: 0.3636 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6310 Z= 0.100 Angle : 0.542 8.779 8513 Z= 0.263 Chirality : 0.041 0.134 922 Planarity : 0.003 0.028 1097 Dihedral : 4.903 41.026 839 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.46 (0.31), residues: 758 helix: 1.01 (0.28), residues: 374 sheet: -1.25 (0.68), residues: 58 loop : -0.08 (0.35), residues: 326 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 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 295) hydrogen bonds : angle 4.05151 ( 837) covalent geometry : bond 0.00230 ( 6310) covalent geometry : angle 0.54210 ( 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 87 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 92 MET cc_start: 0.7511 (mmp) cc_final: 0.6828 (mtm) REVERT: A 195 PHE cc_start: 0.7253 (m-80) cc_final: 0.7007 (m-10) REVERT: A 357 MET cc_start: 0.7840 (mtt) cc_final: 0.7596 (mtp) REVERT: A 374 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6279 (tt0) REVERT: A 433 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7675 (tt0) REVERT: A 470 PHE cc_start: 0.7908 (t80) cc_final: 0.7558 (t80) REVERT: A 517 LEU cc_start: 0.7584 (mt) cc_final: 0.7378 (mt) REVERT: A 574 GLU cc_start: 0.6135 (tp30) cc_final: 0.5608 (pt0) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.1907 time to fit residues: 21.2787 Evaluate side-chains 78 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 420 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 552 LEU 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: 3.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.170665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138617 restraints weight = 7910.245| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.39 r_work: 0.3608 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6310 Z= 0.140 Angle : 0.576 9.976 8513 Z= 0.280 Chirality : 0.043 0.130 922 Planarity : 0.003 0.029 1097 Dihedral : 5.014 40.748 839 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 0.37 (0.31), residues: 758 helix: 0.93 (0.27), residues: 375 sheet: -1.36 (0.67), residues: 58 loop : -0.12 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.002 0.001 HIS A 753 PHE 0.021 0.001 PHE A 38 TYR 0.015 0.001 TYR A 310 ARG 0.003 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 295) hydrogen bonds : angle 4.11864 ( 837) covalent geometry : bond 0.00336 ( 6310) covalent geometry : angle 0.57631 ( 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 84 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 92 MET cc_start: 0.7484 (mmp) cc_final: 0.6769 (mtm) REVERT: A 195 PHE cc_start: 0.7304 (m-80) cc_final: 0.7100 (m-10) REVERT: A 357 MET cc_start: 0.7829 (mtt) cc_final: 0.7548 (mtp) REVERT: A 374 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6306 (tt0) REVERT: A 433 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7726 (tt0) REVERT: A 470 PHE cc_start: 0.7988 (t80) cc_final: 0.7650 (t80) REVERT: A 574 GLU cc_start: 0.6119 (tp30) cc_final: 0.5592 (pt0) REVERT: A 783 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.8516 (ttm110) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.1790 time to fit residues: 19.4191 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 : 0.634 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.172755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140356 restraints weight = 8068.369| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.48 r_work: 0.3632 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3582 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= 0.112 Angle : 0.548 9.830 8513 Z= 0.266 Chirality : 0.042 0.128 922 Planarity : 0.003 0.031 1097 Dihedral : 4.865 40.363 839 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 0.50 (0.31), residues: 758 helix: 1.06 (0.27), residues: 374 sheet: -1.34 (0.68), residues: 58 loop : -0.05 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.002 0.000 HIS A 97 PHE 0.010 0.001 PHE A 473 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 295) hydrogen bonds : angle 4.06623 ( 837) covalent geometry : bond 0.00263 ( 6310) covalent geometry : angle 0.54803 ( 8513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.69 seconds wall clock time: 53 minutes 14.19 seconds (3194.19 seconds total)