Starting phenix.real_space_refine on Tue Jan 14 15:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iw3_60944/01_2025/9iw3_60944_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iw3_60944/01_2025/9iw3_60944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iw3_60944/01_2025/9iw3_60944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iw3_60944/01_2025/9iw3_60944.map" model { file = "/net/cci-nas-00/data/ceres_data/9iw3_60944/01_2025/9iw3_60944_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iw3_60944/01_2025/9iw3_60944_neut.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 51 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4226 2.51 5 N 1211 2.21 5 O 1368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6879 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "B" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5834 Classifications: {'peptide': 712} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 30, 'TRANS': 681} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.66 Number of scatterers: 6879 At special positions: 0 Unit cell: (78.288, 96.928, 116.5, 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 22 16.00 P 51 15.00 Mg 1 11.99 O 1368 8.00 N 1211 7.00 C 4226 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: 1.78 Conformation dependent library (CDL) restraints added in 785.9 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 37.1% alpha, 20.2% beta 11 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.588A pdb=" N GLY A 92 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 removed outlier: 3.545A pdb=" N LEU A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.582A pdb=" N LEU A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.576A pdb=" N LYS A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.872A pdb=" N TRP A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 Processing helix chain 'A' and resid 528 through 540 Processing helix chain 'A' and resid 541 through 544 removed outlier: 4.140A pdb=" N SER A 544 " --> pdb=" O PRO A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 544' Processing helix chain 'A' and resid 548 through 562 removed outlier: 3.564A pdb=" N GLY A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 585 through 598 removed outlier: 3.561A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 680 removed outlier: 4.303A pdb=" N ASP A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 671 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 694 through 711 removed outlier: 4.094A pdb=" N LYS A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 5.210A pdb=" N LYS A 15 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.537A pdb=" N PHE A 69 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127 removed outlier: 4.063A pdb=" N LEU A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 142 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 removed outlier: 4.063A pdb=" N LEU A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 196 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 178 removed outlier: 4.596A pdb=" N ILE A 175 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA7, first strand: chain 'A' and resid 254 through 258 removed outlier: 4.297A pdb=" N SER A 257 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 622 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 629 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N HIS A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 11.623A pdb=" N PHE A 634 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 636 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN A 497 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU A 498 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 490 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 500 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP A 488 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE A 422 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 433 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 453 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 435 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 removed outlier: 6.241A pdb=" N SER A 276 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 324 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN A 278 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 326 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A 280 " --> pdb=" O VAL A 326 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2046 1.34 - 1.46: 1654 1.46 - 1.58: 3289 1.58 - 1.70: 98 1.70 - 1.82: 39 Bond restraints: 7126 Sorted by residual: bond pdb=" C1' DA D 12 " pdb=" N9 DA D 12 " ideal model delta sigma weight residual 1.460 1.364 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1' DA C 31 " pdb=" N9 DA C 31 " ideal model delta sigma weight residual 1.460 1.368 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C1' DG C 47 " pdb=" N9 DG C 47 " ideal model delta sigma weight residual 1.460 1.372 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1' DA C 38 " pdb=" N9 DA C 38 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O3' DA C 45 " pdb=" P DC C 46 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.58e+01 ... (remaining 7121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 9738 3.47 - 6.95: 81 6.95 - 10.42: 13 10.42 - 13.89: 5 13.89 - 17.36: 2 Bond angle restraints: 9839 Sorted by residual: angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 114.31 97.82 16.49 1.29e+00 6.01e-01 1.63e+02 angle pdb=" O3' DA D 10 " pdb=" C3' DA D 10 " pdb=" C2' DA D 10 " ideal model delta sigma weight residual 111.50 98.99 12.51 1.50e+00 4.44e-01 6.95e+01 angle pdb=" N SER A 547 " pdb=" CA SER A 547 " pdb=" C SER A 547 " ideal model delta sigma weight residual 110.80 128.16 -17.36 2.13e+00 2.20e-01 6.65e+01 angle pdb=" C4' DA B 3 " pdb=" C3' DA B 3 " pdb=" O3' DA B 3 " ideal model delta sigma weight residual 110.00 122.06 -12.06 1.50e+00 4.44e-01 6.47e+01 angle pdb=" N ALA A 37 " pdb=" CA ALA A 37 " pdb=" C ALA A 37 " ideal model delta sigma weight residual 111.75 122.04 -10.29 1.28e+00 6.10e-01 6.47e+01 ... (remaining 9834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 3696 29.98 - 59.96: 460 59.96 - 89.93: 42 89.93 - 119.91: 2 119.91 - 149.89: 2 Dihedral angle restraints: 4202 sinusoidal: 2101 harmonic: 2101 Sorted by residual: dihedral pdb=" C SER A 36 " pdb=" N SER A 36 " pdb=" CA SER A 36 " pdb=" CB SER A 36 " ideal model delta harmonic sigma weight residual -122.60 -138.52 15.92 0 2.50e+00 1.60e-01 4.05e+01 dihedral pdb=" N SER A 36 " pdb=" C SER A 36 " pdb=" CA SER A 36 " pdb=" CB SER A 36 " ideal model delta harmonic sigma weight residual 122.80 134.13 -11.33 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" C4' DT C 34 " pdb=" C3' DT C 34 " pdb=" O3' DT C 34 " pdb=" P DT C 35 " ideal model delta sinusoidal sigma weight residual 220.00 70.11 149.89 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 4199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1047 0.121 - 0.241: 27 0.241 - 0.362: 2 0.362 - 0.482: 2 0.482 - 0.603: 2 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA SER A 36 " pdb=" N SER A 36 " pdb=" C SER A 36 " pdb=" CB SER A 36 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" C3' DA C 45 " pdb=" C4' DA C 45 " pdb=" O3' DA C 45 " pdb=" C2' DA C 45 " both_signs ideal model delta sigma weight residual False -2.66 -2.14 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CA SER A 547 " pdb=" N SER A 547 " pdb=" C SER A 547 " pdb=" CB SER A 547 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 1077 not shown) Planarity restraints: 1087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 250 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C HIS A 250 " -0.054 2.00e-02 2.50e+03 pdb=" O HIS A 250 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS A 251 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 39 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C LYS A 39 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS A 39 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 40 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 7 " 0.031 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" N1 DT D 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DT D 7 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT D 7 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DT D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT D 7 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT D 7 " 0.021 2.00e-02 2.50e+03 pdb=" C5 DT D 7 " -0.009 2.00e-02 2.50e+03 pdb=" C7 DT D 7 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT D 7 " -0.018 2.00e-02 2.50e+03 ... (remaining 1084 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 75 2.52 - 3.12: 5161 3.12 - 3.71: 11526 3.71 - 4.31: 15281 4.31 - 4.90: 24429 Nonbonded interactions: 56472 Sorted by model distance: nonbonded pdb=" OP1 DA C 49 " pdb=" CB ARG A 585 " model vdw 1.930 3.440 nonbonded pdb=" OP2 DG B 2 " pdb=" N THR A 352 " model vdw 2.144 3.120 nonbonded pdb=" O LEU A 260 " pdb=" OH TYR A 690 " model vdw 2.151 3.040 nonbonded pdb=" C7 DT B 1 " pdb=" CZ TYR A 339 " model vdw 2.192 3.680 nonbonded pdb=" OP1 DA B 3 " pdb="MG MG B 101 " model vdw 2.217 2.170 ... (remaining 56467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.040 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.005 0.096 7126 Z= 0.284 Angle : 0.909 17.364 9839 Z= 0.548 Chirality : 0.058 0.603 1080 Planarity : 0.004 0.050 1087 Dihedral : 23.443 149.891 2842 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.76 % Favored : 92.82 % Rotamer: Outliers : 2.34 % Allowed : 24.38 % Favored : 73.28 % Cbeta Deviations : 0.29 % 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: -0.43 (0.31), residues: 710 helix: 1.10 (0.35), residues: 225 sheet: -0.09 (0.44), residues: 150 loop : -1.35 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 484 HIS 0.002 0.000 HIS A 350 PHE 0.010 0.001 PHE A 673 TYR 0.010 0.001 TYR A 481 ARG 0.004 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.720 Fit side-chains REVERT: A 709 ARG cc_start: 0.8343 (tpt170) cc_final: 0.8009 (ttm-80) outliers start: 15 outliers final: 3 residues processed: 59 average time/residue: 0.2534 time to fit residues: 19.7176 Evaluate side-chains 41 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 429 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 282 GLN A 298 HIS A 319 GLN A 376 HIS A 495 ASN A 555 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058694 restraints weight = 21924.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060547 restraints weight = 11240.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.061814 restraints weight = 7422.967| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7126 Z= 0.263 Angle : 0.653 6.568 9839 Z= 0.361 Chirality : 0.042 0.180 1080 Planarity : 0.005 0.053 1087 Dihedral : 24.688 168.503 1351 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.77 % Favored : 93.94 % Rotamer: Outliers : 2.50 % Allowed : 24.06 % Favored : 73.44 % 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: -0.34 (0.31), residues: 710 helix: 1.36 (0.34), residues: 231 sheet: -0.36 (0.41), residues: 161 loop : -1.35 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 484 HIS 0.002 0.000 HIS A 298 PHE 0.017 0.001 PHE A 673 TYR 0.016 0.001 TYR A 638 ARG 0.004 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 671 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8555 (tp30) outliers start: 16 outliers final: 6 residues processed: 61 average time/residue: 0.2102 time to fit residues: 17.4112 Evaluate side-chains 45 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 671 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 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 = 0.3273 r_free = 0.3273 target = 0.072572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056523 restraints weight = 22526.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058463 restraints weight = 11002.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059792 restraints weight = 7066.451| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7126 Z= 0.281 Angle : 0.621 7.775 9839 Z= 0.338 Chirality : 0.040 0.155 1080 Planarity : 0.005 0.052 1087 Dihedral : 24.635 176.870 1349 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.49 % Favored : 94.08 % Rotamer: Outliers : 4.06 % Allowed : 22.97 % Favored : 72.97 % 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: -0.26 (0.31), residues: 710 helix: 1.69 (0.35), residues: 227 sheet: -0.50 (0.41), residues: 162 loop : -1.37 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 528 HIS 0.002 0.000 HIS A 350 PHE 0.017 0.001 PHE A 673 TYR 0.017 0.001 TYR A 638 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8776 (mmt) cc_final: 0.8484 (mmt) REVERT: A 88 LEU cc_start: 0.8856 (tp) cc_final: 0.8471 (tp) REVERT: A 91 MET cc_start: 0.9221 (tmm) cc_final: 0.9014 (tmm) REVERT: A 366 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8786 (tp) REVERT: A 376 HIS cc_start: 0.8834 (m90) cc_final: 0.8522 (m-70) REVERT: A 584 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8750 (ttpt) REVERT: A 679 MET cc_start: 0.9023 (mmm) cc_final: 0.8673 (mtt) outliers start: 26 outliers final: 11 residues processed: 61 average time/residue: 0.1812 time to fit residues: 15.3591 Evaluate side-chains 49 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 598 ASN Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN A 325 GLN A 557 GLN ** A 592 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 = 0.3262 r_free = 0.3262 target = 0.071906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.055824 restraints weight = 22547.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.057718 restraints weight = 11322.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058918 restraints weight = 7415.848| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7126 Z= 0.279 Angle : 0.607 8.854 9839 Z= 0.330 Chirality : 0.040 0.160 1080 Planarity : 0.005 0.050 1087 Dihedral : 24.531 174.708 1349 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.92 % Favored : 93.66 % Rotamer: Outliers : 2.81 % Allowed : 23.75 % Favored : 73.44 % 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: -0.16 (0.32), residues: 710 helix: 1.85 (0.35), residues: 226 sheet: -0.40 (0.42), residues: 164 loop : -1.40 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 528 HIS 0.002 0.000 HIS A 350 PHE 0.018 0.001 PHE A 673 TYR 0.016 0.001 TYR A 638 ARG 0.002 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.8611 (mmt) cc_final: 0.8384 (mmm) REVERT: A 88 LEU cc_start: 0.8818 (tp) cc_final: 0.8612 (tp) REVERT: A 91 MET cc_start: 0.9251 (tmm) cc_final: 0.9029 (tmm) REVERT: A 584 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8824 (ttpt) REVERT: A 679 MET cc_start: 0.9039 (mmm) cc_final: 0.8687 (mtt) outliers start: 18 outliers final: 11 residues processed: 52 average time/residue: 0.2301 time to fit residues: 16.1491 Evaluate side-chains 44 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.0170 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS A 557 GLN ** A 592 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 = 0.3310 r_free = 0.3310 target = 0.074343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058196 restraints weight = 22296.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060153 restraints weight = 11204.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061484 restraints weight = 7324.042| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7126 Z= 0.179 Angle : 0.567 7.675 9839 Z= 0.308 Chirality : 0.038 0.139 1080 Planarity : 0.004 0.050 1087 Dihedral : 24.583 173.375 1349 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.35 % Favored : 94.23 % Rotamer: Outliers : 2.19 % Allowed : 25.16 % Favored : 72.66 % 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: 0.08 (0.32), residues: 710 helix: 2.10 (0.35), residues: 226 sheet: -0.22 (0.42), residues: 163 loop : -1.34 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 528 HIS 0.002 0.000 HIS A 250 PHE 0.013 0.001 PHE A 673 TYR 0.014 0.001 TYR A 638 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.8651 (mmt) cc_final: 0.8409 (mmm) REVERT: A 88 LEU cc_start: 0.8697 (tp) cc_final: 0.8298 (mt) REVERT: A 91 MET cc_start: 0.9183 (tmm) cc_final: 0.8968 (tmm) REVERT: A 584 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8709 (ttpt) REVERT: A 679 MET cc_start: 0.9045 (mmm) cc_final: 0.8685 (mtt) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.1899 time to fit residues: 13.9934 Evaluate side-chains 46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN A 376 HIS A 557 GLN ** A 592 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 = 0.3319 r_free = 0.3319 target = 0.074663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058525 restraints weight = 22463.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.060514 restraints weight = 11087.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061859 restraints weight = 7167.081| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7126 Z= 0.174 Angle : 0.562 7.387 9839 Z= 0.303 Chirality : 0.038 0.138 1080 Planarity : 0.004 0.048 1087 Dihedral : 24.609 173.440 1349 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.92 % Favored : 93.66 % Rotamer: Outliers : 1.88 % Allowed : 25.47 % Favored : 72.66 % 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 (0.32), residues: 710 helix: 2.18 (0.35), residues: 226 sheet: -0.07 (0.42), residues: 162 loop : -1.28 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 368 HIS 0.001 0.000 HIS A 350 PHE 0.013 0.001 PHE A 673 TYR 0.015 0.001 TYR A 638 ARG 0.001 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8616 (mmt) cc_final: 0.8362 (mmm) REVERT: A 18 MET cc_start: 0.9344 (mmt) cc_final: 0.8987 (mmt) REVERT: A 88 LEU cc_start: 0.8611 (tp) cc_final: 0.8335 (tp) REVERT: A 91 MET cc_start: 0.9258 (tmm) cc_final: 0.8952 (tmm) REVERT: A 507 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9302 (mt) REVERT: A 584 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8688 (ttpt) REVERT: A 611 LEU cc_start: 0.9076 (mt) cc_final: 0.8578 (tt) REVERT: A 679 MET cc_start: 0.9093 (mmm) cc_final: 0.8709 (mtt) outliers start: 12 outliers final: 5 residues processed: 49 average time/residue: 0.2139 time to fit residues: 14.5710 Evaluate side-chains 45 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS A 557 GLN ** A 592 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 = 0.3333 r_free = 0.3333 target = 0.075432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.059452 restraints weight = 22151.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061458 restraints weight = 10900.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062713 restraints weight = 6996.879| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7126 Z= 0.177 Angle : 0.574 8.966 9839 Z= 0.309 Chirality : 0.038 0.136 1080 Planarity : 0.004 0.048 1087 Dihedral : 24.669 173.930 1349 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.92 % Favored : 93.66 % Rotamer: Outliers : 1.41 % Allowed : 25.16 % Favored : 73.44 % 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: 0.26 (0.32), residues: 710 helix: 2.11 (0.35), residues: 227 sheet: 0.01 (0.42), residues: 162 loop : -1.19 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 528 HIS 0.001 0.000 HIS A 350 PHE 0.013 0.001 PHE A 673 TYR 0.015 0.001 TYR A 638 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8587 (mmt) cc_final: 0.8333 (mmm) REVERT: A 88 LEU cc_start: 0.8610 (tp) cc_final: 0.8387 (tp) REVERT: A 91 MET cc_start: 0.9221 (tmm) cc_final: 0.8911 (tmm) REVERT: A 584 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8626 (ttpt) REVERT: A 611 LEU cc_start: 0.9062 (mt) cc_final: 0.8538 (tt) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.2089 time to fit residues: 13.0428 Evaluate side-chains 44 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS ** A 592 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 = 0.3345 r_free = 0.3345 target = 0.075985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060006 restraints weight = 22350.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.062039 restraints weight = 10944.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063366 restraints weight = 6994.476| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7126 Z= 0.169 Angle : 0.558 8.104 9839 Z= 0.301 Chirality : 0.038 0.133 1080 Planarity : 0.004 0.047 1087 Dihedral : 24.678 173.856 1349 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.06 % Favored : 93.52 % Rotamer: Outliers : 1.56 % Allowed : 25.16 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.32), residues: 710 helix: 2.23 (0.35), residues: 226 sheet: 0.06 (0.43), residues: 162 loop : -1.20 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 528 HIS 0.001 0.000 HIS A 350 PHE 0.012 0.001 PHE A 673 TYR 0.015 0.001 TYR A 638 ARG 0.003 0.000 ARG A 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8586 (mmt) cc_final: 0.8331 (mmm) REVERT: A 18 MET cc_start: 0.9233 (mmt) cc_final: 0.8832 (tpp) REVERT: A 64 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: A 88 LEU cc_start: 0.8622 (tp) cc_final: 0.8387 (tp) REVERT: A 91 MET cc_start: 0.9219 (tmm) cc_final: 0.8834 (tmm) REVERT: A 584 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8659 (ttpt) REVERT: A 611 LEU cc_start: 0.9057 (mt) cc_final: 0.8545 (tt) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.2082 time to fit residues: 13.4436 Evaluate side-chains 46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS ** A 592 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 = 0.3357 r_free = 0.3357 target = 0.076419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.060567 restraints weight = 22151.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062580 restraints weight = 10761.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063895 restraints weight = 6886.263| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7126 Z= 0.159 Angle : 0.557 8.112 9839 Z= 0.299 Chirality : 0.038 0.150 1080 Planarity : 0.004 0.047 1087 Dihedral : 24.662 173.903 1349 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.77 % Favored : 93.80 % Rotamer: Outliers : 1.72 % Allowed : 25.31 % Favored : 72.97 % 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: 0.37 (0.32), residues: 710 helix: 2.18 (0.35), residues: 231 sheet: 0.14 (0.43), residues: 162 loop : -1.18 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 528 HIS 0.001 0.000 HIS A 376 PHE 0.011 0.001 PHE A 673 TYR 0.015 0.001 TYR A 638 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8576 (mmt) cc_final: 0.8319 (mmm) REVERT: A 64 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: A 91 MET cc_start: 0.9215 (tmm) cc_final: 0.8886 (tmm) REVERT: A 584 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8561 (ttpt) REVERT: A 611 LEU cc_start: 0.9035 (mt) cc_final: 0.8518 (tt) REVERT: A 679 MET cc_start: 0.9096 (mmm) cc_final: 0.7869 (mpp) REVERT: A 702 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8260 (mm-30) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.2135 time to fit residues: 14.7018 Evaluate side-chains 47 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS ** A 592 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 = 0.3338 r_free = 0.3338 target = 0.075449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059466 restraints weight = 22278.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061475 restraints weight = 10940.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062760 restraints weight = 7005.676| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7126 Z= 0.192 Angle : 0.576 8.738 9839 Z= 0.304 Chirality : 0.038 0.162 1080 Planarity : 0.004 0.048 1087 Dihedral : 24.639 176.728 1349 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.49 % Favored : 94.08 % Rotamer: Outliers : 1.41 % Allowed : 26.09 % Favored : 72.50 % 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 (0.32), residues: 710 helix: 2.18 (0.35), residues: 231 sheet: 0.13 (0.43), residues: 162 loop : -1.15 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 528 HIS 0.001 0.000 HIS A 202 PHE 0.012 0.001 PHE A 673 TYR 0.015 0.001 TYR A 638 ARG 0.005 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8609 (mmt) cc_final: 0.8348 (mmm) REVERT: A 64 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: A 91 MET cc_start: 0.9247 (tmm) cc_final: 0.8872 (tmm) REVERT: A 584 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8677 (ttpt) REVERT: A 611 LEU cc_start: 0.9069 (mt) cc_final: 0.8552 (tt) REVERT: A 679 MET cc_start: 0.9119 (mmm) cc_final: 0.7876 (mpp) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.1907 time to fit residues: 12.6525 Evaluate side-chains 49 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS ** A 592 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 = 0.3336 r_free = 0.3336 target = 0.075322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059387 restraints weight = 22294.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.061366 restraints weight = 10690.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062725 restraints weight = 6835.403| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7126 Z= 0.194 Angle : 0.565 8.466 9839 Z= 0.302 Chirality : 0.038 0.136 1080 Planarity : 0.004 0.047 1087 Dihedral : 24.620 176.278 1349 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.77 % Favored : 93.80 % Rotamer: Outliers : 2.03 % Allowed : 25.62 % Favored : 72.34 % 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 (0.32), residues: 710 helix: 2.18 (0.35), residues: 231 sheet: 0.12 (0.43), residues: 162 loop : -1.15 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 528 HIS 0.001 0.000 HIS A 376 PHE 0.014 0.001 PHE A 673 TYR 0.015 0.001 TYR A 638 ARG 0.006 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.85 seconds wall clock time: 37 minutes 17.73 seconds (2237.73 seconds total)