Starting phenix.real_space_refine on Tue Aug 4 21:22:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iw3_60944/08_2026/9iw3_60944_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iw3_60944/08_2026/9iw3_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_60944/08_2026/9iw3_60944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iw3_60944/08_2026/9iw3_60944.map" model { file = "/net/cci-nas-00/data/ceres_data/9iw3_60944/08_2026/9iw3_60944_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iw3_60944/08_2026/9iw3_60944_neut.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 1.83, per 1000 atoms: 0.27 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: 0.72 Conformation dependent library (CDL) restraints added in 298.9 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: 0.95 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: 1.32 Time building geometry restraints manager: 0.81 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 1.468 1.364 0.104 1.40e-02 5.10e+03 5.54e+01 bond pdb=" C1' DA C 31 " pdb=" N9 DA C 31 " ideal model delta sigma weight residual 1.468 1.368 0.100 1.40e-02 5.10e+03 5.07e+01 bond pdb=" C1' DG C 47 " pdb=" N9 DG C 47 " ideal model delta sigma weight residual 1.468 1.372 0.096 1.40e-02 5.10e+03 4.71e+01 bond pdb=" C1' DA C 38 " pdb=" N9 DA C 38 " ideal model delta sigma weight residual 1.468 1.377 0.091 1.40e-02 5.10e+03 4.21e+01 bond pdb=" C1' DC C 51 " pdb=" N1 DC C 51 " ideal model delta sigma weight residual 1.468 1.554 -0.086 1.40e-02 5.10e+03 3.78e+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: 14 10.42 - 13.89: 4 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=" 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=" 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 angle pdb=" N ASP A 40 " pdb=" CA ASP A 40 " pdb=" C ASP A 40 " ideal model delta sigma weight residual 111.24 103.12 8.12 1.29e+00 6.01e-01 3.96e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" CB ASP A 548 " ideal model delta sigma weight residual 110.90 118.31 -7.41 1.33e+00 5.65e-01 3.11e+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: 1048 0.121 - 0.241: 26 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 -2.73 -2.14 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" C3' DA B 3 " pdb=" C4' DA B 3 " pdb=" O3' DA B 3 " pdb=" C2' DA B 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.28 -0.45 2.00e-01 2.50e+01 5.05e+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: 1.560 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.980 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.104 7126 Z= 0.390 Angle : 0.889 17.364 9839 Z= 0.576 Chirality : 0.059 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 502 TYR 0.010 0.001 TYR A 481 PHE 0.010 0.001 PHE A 673 TRP 0.005 0.001 TRP A 484 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.39 ( 7126) covalent geometry : angle 0.88910 / 0.58 ( 9839) hydrogen bonds : bond 0.23860 / 25.95 ( 253) hydrogen bonds : angle 8.60734 / 10.27 ( 714) *********************** 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 : 0.251 Fit side-chains REVERT: A 651 ASN cc_start: 0.8432 (m110) cc_final: 0.8169 (t0) REVERT: A 709 ARG cc_start: 0.8343 (tpt170) cc_final: 0.8009 (ttm-80) outliers start: 15 outliers final: 4 residues processed: 59 average time/residue: 0.1018 time to fit residues: 7.9537 Evaluate side-chains 43 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 698 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.0060 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 282 GLN A 298 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060560 restraints weight = 22022.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062539 restraints weight = 11306.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063855 restraints weight = 7454.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064648 restraints weight = 5702.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065219 restraints weight = 4841.482| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7126 Z= 0.176 Angle : 0.760 9.582 9839 Z= 0.409 Chirality : 0.051 0.254 1080 Planarity : 0.005 0.052 1087 Dihedral : 24.867 155.053 1355 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.49 % Favored : 94.23 % Rotamer: Outliers : 3.12 % Allowed : 24.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.31), residues: 710 helix: 1.29 (0.33), residues: 237 sheet: -0.17 (0.42), residues: 155 loop : -1.26 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 328 TYR 0.017 0.001 TYR A 638 PHE 0.020 0.001 PHE A 673 TRP 0.007 0.001 TRP A 484 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 ( 7126) covalent geometry : angle 0.75977 / 0.41 ( 9839) hydrogen bonds : bond 0.05977 / 6.34 ( 253) hydrogen bonds : angle 5.38169 / 6.94 ( 714) *********************** 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: 20 poor density : 44 time to evaluate : 0.252 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 61 average time/residue: 0.0816 time to fit residues: 6.8658 Evaluate side-chains 48 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 398 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 682 VAL Chi-restraints excluded: chain A residue 698 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** A 651 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 = 0.3266 r_free = 0.3266 target = 0.072496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056627 restraints weight = 22339.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058445 restraints weight = 11468.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059678 restraints weight = 7658.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060470 restraints weight = 5914.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060798 restraints weight = 5019.804| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7126 Z= 0.282 Angle : 0.749 9.198 9839 Z= 0.400 Chirality : 0.050 0.280 1080 Planarity : 0.005 0.052 1087 Dihedral : 24.687 162.675 1354 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % Favored : 93.24 % Rotamer: Outliers : 3.59 % Allowed : 23.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.31), residues: 710 helix: 1.56 (0.35), residues: 228 sheet: -0.49 (0.41), residues: 162 loop : -1.40 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 184 TYR 0.016 0.002 TYR A 638 PHE 0.021 0.002 PHE A 673 TRP 0.013 0.002 TRP A 484 HIS 0.004 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 ( 7126) covalent geometry : angle 0.74936 / 0.40 ( 9839) hydrogen bonds : bond 0.05228 / 5.72 ( 253) hydrogen bonds : angle 5.16824 / 6.74 ( 714) *********************** 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 62 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8444 (t0) outliers start: 23 outliers final: 9 residues processed: 56 average time/residue: 0.0756 time to fit residues: 5.9243 Evaluate side-chains 46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 341 VAL 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 651 ASN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 698 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3284 r_free = 0.3284 target = 0.073437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057499 restraints weight = 22193.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.059464 restraints weight = 10943.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060786 restraints weight = 7043.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061603 restraints weight = 5312.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.062229 restraints weight = 4454.079| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7126 Z= 0.162 Angle : 0.661 7.880 9839 Z= 0.356 Chirality : 0.046 0.229 1080 Planarity : 0.005 0.049 1087 Dihedral : 24.527 164.825 1353 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.07 % Favored : 94.51 % Rotamer: Outliers : 3.28 % Allowed : 24.84 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.32), residues: 710 helix: 1.83 (0.35), residues: 227 sheet: -0.43 (0.41), residues: 165 loop : -1.36 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.018 0.001 TYR A 638 PHE 0.014 0.001 PHE A 673 TRP 0.004 0.001 TRP A 484 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 7126) covalent geometry : angle 0.66135 / 0.36 ( 9839) hydrogen bonds : bond 0.04347 / 4.48 ( 253) hydrogen bonds : angle 4.85007 / 6.33 ( 714) *********************** 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 61 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9097 (p) REVERT: A 584 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8720 (ttpt) REVERT: A 651 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8524 (t0) outliers start: 21 outliers final: 10 residues processed: 54 average time/residue: 0.0789 time to fit residues: 5.8559 Evaluate side-chains 47 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR 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 326 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 698 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 0.0170 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 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 = 0.3309 r_free = 0.3309 target = 0.074459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058451 restraints weight = 22193.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060446 restraints weight = 10835.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061738 restraints weight = 6953.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062652 restraints weight = 5265.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063072 restraints weight = 4355.869| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7126 Z= 0.133 Angle : 0.644 7.961 9839 Z= 0.345 Chirality : 0.045 0.210 1080 Planarity : 0.004 0.048 1087 Dihedral : 24.454 165.695 1353 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.35 % Favored : 94.23 % Rotamer: Outliers : 2.50 % Allowed : 25.47 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.31), residues: 710 helix: 1.75 (0.34), residues: 227 sheet: -0.24 (0.41), residues: 164 loop : -1.28 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 540 TYR 0.015 0.001 TYR A 638 PHE 0.014 0.001 PHE A 673 TRP 0.003 0.000 TRP A 48 HIS 0.003 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 7126) covalent geometry : angle 0.64372 / 0.35 ( 9839) hydrogen bonds : bond 0.04142 / 4.29 ( 253) hydrogen bonds : angle 4.76920 / 6.16 ( 714) *********************** 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 59 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 584 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8684 (ttpt) REVERT: A 651 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8507 (t0) outliers start: 16 outliers final: 8 residues processed: 54 average time/residue: 0.0595 time to fit residues: 4.5429 Evaluate side-chains 45 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 351 LEU 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 625 THR Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 698 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN A 557 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058997 restraints weight = 22252.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060973 restraints weight = 10818.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062321 restraints weight = 6919.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063120 restraints weight = 5217.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.063723 restraints weight = 4372.215| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2695 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= 0.130 Angle : 0.644 10.600 9839 Z= 0.335 Chirality : 0.044 0.214 1080 Planarity : 0.004 0.056 1087 Dihedral : 24.369 167.038 1353 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.07 % Favored : 94.51 % Rotamer: Outliers : 2.50 % Allowed : 25.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.32), residues: 710 helix: 1.93 (0.35), residues: 227 sheet: -0.13 (0.41), residues: 163 loop : -1.24 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 589 TYR 0.014 0.001 TYR A 638 PHE 0.016 0.001 PHE A 673 TRP 0.006 0.001 TRP A 48 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7126) covalent geometry : angle 0.64392 / 0.34 ( 9839) hydrogen bonds : bond 0.03953 / 3.97 ( 253) hydrogen bonds : angle 4.62976 / 5.94 ( 714) *********************** 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 56 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8544 (mmm) cc_final: 0.8293 (mmt) REVERT: A 584 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8727 (ttpt) REVERT: A 611 LEU cc_start: 0.9149 (mm) cc_final: 0.8594 (tt) outliers start: 16 outliers final: 7 residues processed: 50 average time/residue: 0.0729 time to fit residues: 5.0707 Evaluate side-chains 41 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 72 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 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 = 0.3296 r_free = 0.3296 target = 0.073706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057441 restraints weight = 22206.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059416 restraints weight = 11072.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.060650 restraints weight = 7184.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061551 restraints weight = 5532.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.062011 restraints weight = 4612.809| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7126 Z= 0.179 Angle : 0.638 8.818 9839 Z= 0.334 Chirality : 0.043 0.225 1080 Planarity : 0.004 0.055 1087 Dihedral : 24.256 161.957 1349 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.92 % Favored : 93.66 % Rotamer: Outliers : 2.03 % Allowed : 25.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.32), residues: 710 helix: 2.03 (0.35), residues: 226 sheet: -0.21 (0.41), residues: 164 loop : -1.25 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.016 0.001 TYR A 638 PHE 0.015 0.001 PHE A 673 TRP 0.006 0.001 TRP A 528 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 7126) covalent geometry : angle 0.63750 / 0.33 ( 9839) hydrogen bonds : bond 0.03938 / 4.02 ( 253) hydrogen bonds : angle 4.63373 / 6.02 ( 714) *********************** 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 48 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 584 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8756 (ttpt) REVERT: A 611 LEU cc_start: 0.9169 (mm) cc_final: 0.8598 (tt) outliers start: 13 outliers final: 9 residues processed: 44 average time/residue: 0.0820 time to fit residues: 5.0704 Evaluate side-chains 42 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 ILE 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 563 MET 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 35 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** A 165 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 = 0.3312 r_free = 0.3312 target = 0.074615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058508 restraints weight = 22307.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060505 restraints weight = 10807.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061778 restraints weight = 6921.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062715 restraints weight = 5257.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063096 restraints weight = 4334.121| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7126 Z= 0.132 Angle : 0.617 9.206 9839 Z= 0.325 Chirality : 0.042 0.232 1080 Planarity : 0.004 0.054 1087 Dihedral : 24.251 164.022 1349 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.49 % Favored : 94.08 % Rotamer: Outliers : 1.41 % Allowed : 25.78 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.32), residues: 710 helix: 2.06 (0.35), residues: 227 sheet: -0.13 (0.42), residues: 163 loop : -1.23 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 652 TYR 0.016 0.001 TYR A 638 PHE 0.014 0.001 PHE A 673 TRP 0.003 0.001 TRP A 528 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 7126) covalent geometry : angle 0.61685 / 0.32 ( 9839) hydrogen bonds : bond 0.03707 / 3.73 ( 253) hydrogen bonds : angle 4.49978 / 5.83 ( 714) *********************** 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 48 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8523 (mmt) cc_final: 0.8095 (mmt) REVERT: A 584 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8730 (ttpt) REVERT: A 611 LEU cc_start: 0.9171 (mm) cc_final: 0.8584 (tt) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.0944 time to fit residues: 5.9081 Evaluate side-chains 43 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 223 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3282 r_free = 0.3282 target = 0.073159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057191 restraints weight = 22262.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059135 restraints weight = 11012.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060471 restraints weight = 7117.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061279 restraints weight = 5359.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061791 restraints weight = 4498.448| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7126 Z= 0.176 Angle : 0.636 9.058 9839 Z= 0.333 Chirality : 0.044 0.239 1080 Planarity : 0.004 0.056 1087 Dihedral : 24.329 169.354 1349 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.48 % Favored : 93.10 % Rotamer: Outliers : 1.72 % Allowed : 25.47 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.32), residues: 710 helix: 2.12 (0.35), residues: 226 sheet: -0.24 (0.41), residues: 164 loop : -1.25 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.014 0.001 TYR A 638 PHE 0.016 0.001 PHE A 673 TRP 0.008 0.001 TRP A 484 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 7126) covalent geometry : angle 0.63558 / 0.33 ( 9839) hydrogen bonds : bond 0.03900 / 4.01 ( 253) hydrogen bonds : angle 4.54636 / 5.96 ( 714) *********************** 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 44 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 584 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8754 (ttpt) REVERT: A 611 LEU cc_start: 0.9173 (mm) cc_final: 0.8595 (tt) outliers start: 11 outliers final: 7 residues processed: 41 average time/residue: 0.0884 time to fit residues: 5.1661 Evaluate side-chains 40 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR 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 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 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 0.0370 chunk 59 optimal weight: 0.0980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3325 r_free = 0.3325 target = 0.075352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059249 restraints weight = 22110.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061210 restraints weight = 10806.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062606 restraints weight = 6947.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063308 restraints weight = 5198.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064001 restraints weight = 4404.075| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7126 Z= 0.118 Angle : 0.621 10.138 9839 Z= 0.323 Chirality : 0.042 0.228 1080 Planarity : 0.004 0.055 1087 Dihedral : 24.323 166.202 1349 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.49 % Favored : 94.08 % Rotamer: Outliers : 1.09 % Allowed : 26.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.32), residues: 710 helix: 2.16 (0.35), residues: 226 sheet: -0.16 (0.41), residues: 163 loop : -1.26 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.017 0.001 TYR A 638 PHE 0.017 0.001 PHE A 472 TRP 0.002 0.000 TRP A 48 HIS 0.001 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 7126) covalent geometry : angle 0.62134 / 0.32 ( 9839) hydrogen bonds : bond 0.03630 / 3.62 ( 253) hydrogen bonds : angle 4.39127 / 5.70 ( 714) ********************** 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 46 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 584 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8693 (ttpt) REVERT: A 611 LEU cc_start: 0.9199 (mm) cc_final: 0.8597 (tt) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.0721 time to fit residues: 4.4068 Evaluate side-chains 41 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059273 restraints weight = 21921.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061241 restraints weight = 10732.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.062596 restraints weight = 6887.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063485 restraints weight = 5171.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064042 restraints weight = 4288.569| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7126 Z= 0.118 Angle : 0.625 10.018 9839 Z= 0.322 Chirality : 0.042 0.227 1080 Planarity : 0.004 0.056 1087 Dihedral : 24.325 165.348 1349 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.35 % Favored : 94.23 % Rotamer: Outliers : 1.09 % Allowed : 26.09 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.32), residues: 710 helix: 2.13 (0.35), residues: 227 sheet: -0.01 (0.42), residues: 162 loop : -1.27 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 589 TYR 0.014 0.001 TYR A 638 PHE 0.014 0.001 PHE A 673 TRP 0.003 0.001 TRP A 368 HIS 0.001 0.000 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 7126) covalent geometry : angle 0.62541 / 0.32 ( 9839) hydrogen bonds : bond 0.03586 / 3.57 ( 253) hydrogen bonds : angle 4.35787 / 5.63 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1004.02 seconds wall clock time: 18 minutes 3.48 seconds (1083.48 seconds total)