Starting phenix.real_space_refine on Tue Aug 4 22:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izp_61038/08_2026/9izp_61038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izp_61038/08_2026/9izp_61038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izp_61038/08_2026/9izp_61038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izp_61038/08_2026/9izp_61038.map" model { file = "/net/cci-nas-00/data/ceres_data/9izp_61038/08_2026/9izp_61038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izp_61038/08_2026/9izp_61038.cif" } resolution = 2.89 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 ------------------------------------------------------------------------------- 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= 0.014 sd= 0.231 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 92 5.49 5 Mg 3 5.21 5 S 25 5.16 5 C 4263 2.51 5 N 1199 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7186 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5246 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 8, 'TRANS': 619} Chain breaks: 1 Chain: "B" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1127 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 20} Link IDs: {'rna2p': 9, 'rna3p': 43} Chain: "C" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.93, per 1000 atoms: 0.27 Number of scatterers: 7186 At special positions: 0 Unit cell: (89.64, 94.62, 110.805, 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 25 16.00 P 92 15.00 Mg 3 11.99 O 1604 8.00 N 1199 7.00 C 4263 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: 0.70 Conformation dependent library (CDL) restraints added in 346.5 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 57.0% alpha, 10.0% beta 37 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.591A pdb=" N ILE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.762A pdb=" N THR A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 165 removed outlier: 3.577A pdb=" N GLN A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.807A pdb=" N TRP A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.691A pdb=" N TYR A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 203 " --> pdb=" O CYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.520A pdb=" N TYR A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.556A pdb=" N LYS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 397 through 418 Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.733A pdb=" N GLY A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 removed outlier: 6.686A pdb=" N ASP A 472 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 517 removed outlier: 3.645A pdb=" N ASN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.795A pdb=" N MET A 606 " --> pdb=" O PHE A 602 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 608 " --> pdb=" O ASN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 4.370A pdb=" N SER A 305 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN A 290 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.942A pdb=" N VAL A 377 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 332 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 335 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY A 322 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 10.210A pdb=" N LYS A 337 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N THR A 320 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS A 319 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA A 524 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 321 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU A 526 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 323 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 577 removed outlier: 3.792A pdb=" N ASP A 586 " --> pdb=" O ILE A 577 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1212 1.33 - 1.45: 2355 1.45 - 1.57: 3722 1.57 - 1.69: 182 1.69 - 1.81: 39 Bond restraints: 7510 Sorted by residual: bond pdb=" C3' DC D 19 " pdb=" C2' DC D 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.91e+00 bond pdb=" C3' DA D 24 " pdb=" C2' DA D 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.62e+00 bond pdb=" C3' DA C 2 " pdb=" C2' DA C 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.62e+00 bond pdb=" C3' DA C -1 " pdb=" C2' DA C -1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DA D 23 " pdb=" C2' DA D 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 ... (remaining 7505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 9694 1.14 - 2.29: 632 2.29 - 3.43: 194 3.43 - 4.57: 8 4.57 - 5.71: 2 Bond angle restraints: 10530 Sorted by residual: angle pdb=" O5' U B -19 " pdb=" C5' U B -19 " pdb=" C4' U B -19 " ideal model delta sigma weight residual 109.40 113.19 -3.79 8.00e-01 1.56e+00 2.25e+01 angle pdb=" O5' A B -3 " pdb=" C5' A B -3 " pdb=" C4' A B -3 " ideal model delta sigma weight residual 109.40 113.10 -3.70 8.00e-01 1.56e+00 2.13e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" O4' DC D 20 " pdb=" C4' DC D 20 " pdb=" C3' DC D 20 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT C -6 " pdb=" C4 DT C -6 " pdb=" O4 DT C -6 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 10525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 3810 18.07 - 36.13: 432 36.13 - 54.20: 171 54.20 - 72.26: 95 72.26 - 90.33: 7 Dihedral angle restraints: 4515 sinusoidal: 2636 harmonic: 1879 Sorted by residual: dihedral pdb=" CA GLN A 272 " pdb=" C GLN A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N TRP A 69 " pdb=" CA TRP A 69 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASN A 270 " pdb=" C ASN A 270 " pdb=" N ARG A 271 " pdb=" CA ARG A 271 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 696 0.035 - 0.071: 304 0.071 - 0.106: 121 0.106 - 0.141: 69 0.141 - 0.177: 8 Chirality restraints: 1198 Sorted by residual: chirality pdb=" C1' G B 1 " pdb=" O4' G B 1 " pdb=" C2' G B 1 " pdb=" N9 G B 1 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" C1' G B -33 " pdb=" O4' G B -33 " pdb=" C2' G B -33 " pdb=" N9 G B -33 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" C2' U B 10 " pdb=" C3' U B 10 " pdb=" O2' U B 10 " pdb=" C1' U B 10 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1195 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " -0.031 2.00e-02 2.50e+03 1.32e-02 5.25e+00 pdb=" N9 G B 1 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B 1 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 1 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G B 1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -33 " -0.025 2.00e-02 2.50e+03 1.10e-02 3.66e+00 pdb=" N9 G B -33 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G B -33 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B -33 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B -33 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B -33 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B -33 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B -33 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B -33 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B -33 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G B -33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B -33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 7 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.15e+00 pdb=" N9 A B 7 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B 7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 7 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 7 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 7 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 7 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 7 " 0.006 2.00e-02 2.50e+03 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 28 2.57 - 3.15: 5448 3.15 - 3.73: 11763 3.73 - 4.32: 17565 4.32 - 4.90: 25896 Nonbonded interactions: 60700 Sorted by model distance: nonbonded pdb=" OP1 G B -30 " pdb="MG MG A 801 " model vdw 1.984 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A 801 " model vdw 2.100 2.170 nonbonded pdb=" O4 U B -23 " pdb="MG MG B 102 " model vdw 2.149 2.170 nonbonded pdb=" O2' C B -1 " pdb=" OP1 G B 1 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 437 " pdb=" O PHE A 602 " model vdw 2.251 3.040 ... (remaining 60695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.240 Find NCS groups from input model: 0.030 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 0.058 7510 Z= 0.392 Angle : 0.667 5.713 10530 Z= 0.532 Chirality : 0.052 0.177 1198 Planarity : 0.003 0.042 1005 Dihedral : 18.573 90.329 3303 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.33), residues: 624 helix: 0.51 (0.29), residues: 322 sheet: 1.16 (0.84), residues: 41 loop : -1.06 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.021 0.002 TYR A 92 PHE 0.012 0.002 PHE A 382 TRP 0.007 0.002 TRP A 33 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.39 ( 7510) covalent geometry : angle 0.66673 / 0.53 (10530) hydrogen bonds : bond 0.15475 / 9.73 ( 357) hydrogen bonds : angle 6.06837 / 4.21 ( 951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7742 (mttt) cc_final: 0.7460 (mtpp) REVERT: A 88 ASP cc_start: 0.8337 (m-30) cc_final: 0.8086 (m-30) REVERT: A 242 LYS cc_start: 0.8832 (tptt) cc_final: 0.8592 (tppp) REVERT: A 323 LEU cc_start: 0.8325 (mt) cc_final: 0.8020 (tp) REVERT: A 324 ASP cc_start: 0.7779 (t0) cc_final: 0.7152 (m-30) REVERT: A 413 LYS cc_start: 0.8256 (tttt) cc_final: 0.8022 (ttpp) REVERT: A 447 TYR cc_start: 0.8842 (t80) cc_final: 0.8629 (t80) REVERT: A 471 MET cc_start: 0.6247 (mtm) cc_final: 0.5723 (mtp) REVERT: A 512 TYR cc_start: 0.8236 (t80) cc_final: 0.7990 (t80) REVERT: A 545 LEU cc_start: 0.8002 (tp) cc_final: 0.7735 (tp) REVERT: A 612 PHE cc_start: 0.8328 (m-80) cc_final: 0.8043 (m-10) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.5249 time to fit residues: 61.8768 Evaluate side-chains 77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 255 ASN A 506 ASN A 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139019 restraints weight = 8550.117| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.59 r_work: 0.3336 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7510 Z= 0.221 Angle : 0.630 6.590 10530 Z= 0.366 Chirality : 0.044 0.184 1198 Planarity : 0.004 0.041 1005 Dihedral : 21.191 88.504 1937 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.02 % Allowed : 9.18 % Favored : 89.80 % 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: -0.03 (0.33), residues: 624 helix: 0.71 (0.28), residues: 336 sheet: 0.99 (0.85), residues: 42 loop : -1.18 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 280 TYR 0.021 0.002 TYR A 437 PHE 0.018 0.002 PHE A 382 TRP 0.007 0.002 TRP A 268 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 ( 7510) covalent geometry : angle 0.62976 / 0.37 (10530) hydrogen bonds : bond 0.05840 / 3.72 ( 357) hydrogen bonds : angle 4.77753 / 3.26 ( 951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7913 (mttt) cc_final: 0.7656 (mtpp) REVERT: A 67 ASP cc_start: 0.7020 (m-30) cc_final: 0.6690 (m-30) REVERT: A 155 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: A 242 LYS cc_start: 0.8745 (tptt) cc_final: 0.8464 (tptp) REVERT: A 323 LEU cc_start: 0.8256 (mt) cc_final: 0.7928 (tp) REVERT: A 324 ASP cc_start: 0.7636 (t0) cc_final: 0.7063 (m-30) REVERT: A 385 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7670 (mp10) REVERT: A 413 LYS cc_start: 0.8373 (tttt) cc_final: 0.7928 (ttpp) REVERT: A 471 MET cc_start: 0.6169 (mtm) cc_final: 0.5666 (mtp) REVERT: A 478 PHE cc_start: 0.8766 (m-10) cc_final: 0.8323 (m-10) REVERT: A 512 TYR cc_start: 0.8410 (t80) cc_final: 0.8163 (t80) REVERT: A 537 GLN cc_start: 0.7820 (pm20) cc_final: 0.7589 (pm20) outliers start: 6 outliers final: 1 residues processed: 80 average time/residue: 0.4803 time to fit residues: 40.6286 Evaluate side-chains 76 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141740 restraints weight = 8383.544| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.60 r_work: 0.3367 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7510 Z= 0.148 Angle : 0.544 8.981 10530 Z= 0.326 Chirality : 0.040 0.166 1198 Planarity : 0.003 0.041 1005 Dihedral : 21.192 88.759 1937 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.36 % Allowed : 9.52 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.33), residues: 624 helix: 1.05 (0.29), residues: 330 sheet: 0.99 (0.73), residues: 52 loop : -1.00 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.017 0.002 TYR A 437 PHE 0.015 0.001 PHE A 382 TRP 0.007 0.001 TRP A 33 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 7510) covalent geometry : angle 0.54376 / 0.33 (10530) hydrogen bonds : bond 0.04919 / 3.18 ( 357) hydrogen bonds : angle 4.49402 / 3.06 ( 951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7913 (mttt) cc_final: 0.7670 (mtpp) REVERT: A 242 LYS cc_start: 0.8620 (tptt) cc_final: 0.8299 (tptp) REVERT: A 323 LEU cc_start: 0.8312 (mt) cc_final: 0.8043 (tp) REVERT: A 324 ASP cc_start: 0.7641 (t0) cc_final: 0.7150 (m-30) REVERT: A 372 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: A 385 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7756 (mp10) REVERT: A 413 LYS cc_start: 0.8351 (tttt) cc_final: 0.7933 (ttpp) REVERT: A 437 TYR cc_start: 0.7987 (t80) cc_final: 0.7721 (t80) REVERT: A 455 ASP cc_start: 0.8072 (m-30) cc_final: 0.7659 (m-30) REVERT: A 471 MET cc_start: 0.6256 (mtm) cc_final: 0.5702 (mtp) REVERT: A 526 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: A 537 GLN cc_start: 0.7686 (pm20) cc_final: 0.7463 (pm20) REVERT: A 588 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8708 (mtmm) outliers start: 8 outliers final: 1 residues processed: 88 average time/residue: 0.4676 time to fit residues: 43.4366 Evaluate side-chains 79 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135621 restraints weight = 8603.102| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.61 r_work: 0.3283 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 7510 Z= 0.355 Angle : 0.722 7.394 10530 Z= 0.401 Chirality : 0.051 0.200 1198 Planarity : 0.005 0.043 1005 Dihedral : 21.316 88.200 1937 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.02 % Allowed : 12.24 % Favored : 86.73 % 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: -0.03 (0.33), residues: 624 helix: 0.70 (0.28), residues: 328 sheet: 0.56 (0.71), residues: 54 loop : -1.10 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.028 0.004 TYR A 437 PHE 0.024 0.003 PHE A 252 TRP 0.006 0.002 TRP A 268 HIS 0.004 0.002 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.36 ( 7510) covalent geometry : angle 0.72217 / 0.40 (10530) hydrogen bonds : bond 0.06432 / 4.23 ( 357) hydrogen bonds : angle 4.64187 / 3.17 ( 951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: A 242 LYS cc_start: 0.8722 (tptt) cc_final: 0.8442 (tptp) REVERT: A 323 LEU cc_start: 0.8416 (mt) cc_final: 0.8141 (tp) REVERT: A 324 ASP cc_start: 0.7711 (t0) cc_final: 0.7225 (m-30) REVERT: A 385 GLN cc_start: 0.8388 (tp-100) cc_final: 0.7976 (mp10) REVERT: A 413 LYS cc_start: 0.8414 (tttt) cc_final: 0.7995 (ttpp) REVERT: A 471 MET cc_start: 0.6338 (mtm) cc_final: 0.5748 (mtp) REVERT: A 490 LEU cc_start: 0.9118 (mt) cc_final: 0.8865 (mt) REVERT: A 537 GLN cc_start: 0.7618 (pm20) cc_final: 0.7361 (pm20) REVERT: A 588 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8791 (mtmp) REVERT: A 591 GLU cc_start: 0.7705 (tt0) cc_final: 0.7361 (mp0) outliers start: 6 outliers final: 2 residues processed: 79 average time/residue: 0.4985 time to fit residues: 41.3772 Evaluate side-chains 78 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 541 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.177660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140751 restraints weight = 8542.462| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.59 r_work: 0.3365 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7510 Z= 0.146 Angle : 0.543 5.975 10530 Z= 0.324 Chirality : 0.040 0.160 1198 Planarity : 0.003 0.042 1005 Dihedral : 21.267 89.497 1937 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.87 % Allowed : 12.24 % Favored : 85.88 % 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: 0.33 (0.33), residues: 624 helix: 0.99 (0.28), residues: 331 sheet: 0.48 (0.69), residues: 54 loop : -0.88 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.019 0.002 TYR A 437 PHE 0.020 0.001 PHE A 478 TRP 0.006 0.001 TRP A 268 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 7510) covalent geometry : angle 0.54300 / 0.32 (10530) hydrogen bonds : bond 0.04710 / 3.05 ( 357) hydrogen bonds : angle 4.40968 / 3.02 ( 951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 242 LYS cc_start: 0.8604 (tptt) cc_final: 0.8277 (tptp) REVERT: A 323 LEU cc_start: 0.8360 (mt) cc_final: 0.8073 (tp) REVERT: A 324 ASP cc_start: 0.7677 (t0) cc_final: 0.7241 (m-30) REVERT: A 385 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7934 (mp10) REVERT: A 413 LYS cc_start: 0.8382 (tttt) cc_final: 0.7950 (ttpp) REVERT: A 437 TYR cc_start: 0.7974 (t80) cc_final: 0.7623 (t80) REVERT: A 471 MET cc_start: 0.6299 (mtm) cc_final: 0.5652 (mtp) REVERT: A 490 LEU cc_start: 0.9062 (mt) cc_final: 0.8829 (mt) REVERT: A 526 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 537 GLN cc_start: 0.7856 (pm20) cc_final: 0.7637 (pm20) REVERT: A 571 ASN cc_start: 0.6818 (m110) cc_final: 0.6475 (m-40) REVERT: A 588 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8823 (mtmp) outliers start: 11 outliers final: 2 residues processed: 84 average time/residue: 0.4651 time to fit residues: 41.3219 Evaluate side-chains 84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS ** A 156 GLN ** 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 = 0.4050 r_free = 0.4050 target = 0.176896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140091 restraints weight = 8624.472| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.62 r_work: 0.3353 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7510 Z= 0.170 Angle : 0.546 6.141 10530 Z= 0.321 Chirality : 0.041 0.165 1198 Planarity : 0.003 0.040 1005 Dihedral : 21.252 89.305 1937 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.87 % Allowed : 13.27 % Favored : 84.86 % 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: 0.32 (0.33), residues: 624 helix: 1.00 (0.28), residues: 331 sheet: 0.52 (0.69), residues: 54 loop : -0.91 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.020 0.002 TYR A 437 PHE 0.015 0.001 PHE A 382 TRP 0.005 0.001 TRP A 33 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 7510) covalent geometry : angle 0.54608 / 0.32 (10530) hydrogen bonds : bond 0.04760 / 3.10 ( 357) hydrogen bonds : angle 4.33181 / 2.96 ( 951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: A 242 LYS cc_start: 0.8631 (tptt) cc_final: 0.8295 (tptp) REVERT: A 323 LEU cc_start: 0.8347 (mt) cc_final: 0.8073 (tp) REVERT: A 324 ASP cc_start: 0.7666 (t0) cc_final: 0.7243 (m-30) REVERT: A 385 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7919 (mp10) REVERT: A 413 LYS cc_start: 0.8388 (tttt) cc_final: 0.7948 (ttpp) REVERT: A 437 TYR cc_start: 0.8011 (t80) cc_final: 0.7665 (t80) REVERT: A 469 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: A 471 MET cc_start: 0.6203 (mtm) cc_final: 0.5605 (mtp) REVERT: A 490 LEU cc_start: 0.9052 (mt) cc_final: 0.8838 (mt) REVERT: A 526 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: A 537 GLN cc_start: 0.7865 (pm20) cc_final: 0.7648 (pm20) REVERT: A 552 GLU cc_start: 0.7992 (tt0) cc_final: 0.7586 (pm20) REVERT: A 566 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7762 (mmtm) REVERT: A 588 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8839 (mtmp) REVERT: A 625 ASN cc_start: 0.7654 (m110) cc_final: 0.7337 (t0) outliers start: 11 outliers final: 3 residues processed: 88 average time/residue: 0.5029 time to fit residues: 46.6943 Evaluate side-chains 87 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137463 restraints weight = 8542.290| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.60 r_work: 0.3305 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7510 Z= 0.290 Angle : 0.664 6.197 10530 Z= 0.375 Chirality : 0.047 0.186 1198 Planarity : 0.004 0.039 1005 Dihedral : 21.340 89.162 1937 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.21 % Allowed : 13.27 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.12 (0.33), residues: 624 helix: 0.81 (0.28), residues: 329 sheet: 0.45 (0.69), residues: 54 loop : -0.97 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.026 0.003 TYR A 437 PHE 0.029 0.003 PHE A 478 TRP 0.006 0.002 TRP A 268 HIS 0.004 0.002 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.29 ( 7510) covalent geometry : angle 0.66418 / 0.38 (10530) hydrogen bonds : bond 0.05747 / 3.79 ( 357) hydrogen bonds : angle 4.45829 / 3.05 ( 951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: A 242 LYS cc_start: 0.8708 (tptt) cc_final: 0.8396 (tptp) REVERT: A 323 LEU cc_start: 0.8517 (mt) cc_final: 0.8220 (tp) REVERT: A 324 ASP cc_start: 0.7668 (t0) cc_final: 0.7267 (m-30) REVERT: A 385 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7952 (mp10) REVERT: A 413 LYS cc_start: 0.8423 (tttt) cc_final: 0.7989 (ttpp) REVERT: A 469 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: A 471 MET cc_start: 0.6202 (mtm) cc_final: 0.5502 (mtp) REVERT: A 490 LEU cc_start: 0.9089 (mt) cc_final: 0.8865 (mt) REVERT: A 526 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: A 537 GLN cc_start: 0.7876 (pm20) cc_final: 0.7656 (pm20) REVERT: A 566 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8066 (mmtt) REVERT: A 571 ASN cc_start: 0.6840 (m110) cc_final: 0.6494 (m-40) REVERT: A 588 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8864 (mtmp) REVERT: A 591 GLU cc_start: 0.7650 (tt0) cc_final: 0.7314 (mp0) REVERT: A 625 ASN cc_start: 0.7634 (m110) cc_final: 0.7314 (t0) outliers start: 13 outliers final: 3 residues processed: 84 average time/residue: 0.4923 time to fit residues: 43.4887 Evaluate side-chains 80 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 0.0570 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141719 restraints weight = 8632.671| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.65 r_work: 0.3359 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7510 Z= 0.140 Angle : 0.535 6.859 10530 Z= 0.317 Chirality : 0.039 0.142 1198 Planarity : 0.003 0.042 1005 Dihedral : 21.288 90.235 1937 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.36 % Allowed : 13.61 % Favored : 85.03 % 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: 0.36 (0.33), residues: 624 helix: 1.08 (0.28), residues: 331 sheet: 0.40 (0.69), residues: 54 loop : -0.94 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.019 0.002 TYR A 437 PHE 0.013 0.001 PHE A 382 TRP 0.006 0.001 TRP A 268 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 7510) covalent geometry : angle 0.53472 / 0.32 (10530) hydrogen bonds : bond 0.04491 / 2.91 ( 357) hydrogen bonds : angle 4.30537 / 2.96 ( 951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7336 (pp-130) cc_final: 0.6978 (ppp) REVERT: A 217 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8298 (mt-10) REVERT: A 323 LEU cc_start: 0.8436 (mt) cc_final: 0.8161 (tp) REVERT: A 324 ASP cc_start: 0.7657 (t0) cc_final: 0.7225 (m-30) REVERT: A 385 GLN cc_start: 0.8344 (tp-100) cc_final: 0.7960 (mp10) REVERT: A 413 LYS cc_start: 0.8427 (tttt) cc_final: 0.7970 (ttpp) REVERT: A 437 TYR cc_start: 0.7997 (t80) cc_final: 0.7664 (t80) REVERT: A 455 ASP cc_start: 0.7873 (m-30) cc_final: 0.7538 (m-30) REVERT: A 471 MET cc_start: 0.6207 (mtm) cc_final: 0.5651 (mtp) REVERT: A 490 LEU cc_start: 0.9065 (mt) cc_final: 0.8864 (mt) REVERT: A 526 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: A 537 GLN cc_start: 0.7845 (pm20) cc_final: 0.7624 (pm20) REVERT: A 571 ASN cc_start: 0.6902 (m110) cc_final: 0.6553 (m-40) REVERT: A 588 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8940 (mtmp) REVERT: A 625 ASN cc_start: 0.7616 (m110) cc_final: 0.7311 (t0) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.5500 time to fit residues: 52.3348 Evaluate side-chains 84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139513 restraints weight = 8447.996| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.54 r_work: 0.3347 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7510 Z= 0.221 Angle : 0.602 6.893 10530 Z= 0.347 Chirality : 0.043 0.171 1198 Planarity : 0.004 0.040 1005 Dihedral : 21.293 89.864 1937 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.36 % Allowed : 14.80 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.33), residues: 624 helix: 0.96 (0.28), residues: 331 sheet: 0.38 (0.70), residues: 54 loop : -0.98 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.023 0.002 TYR A 437 PHE 0.026 0.002 PHE A 478 TRP 0.006 0.002 TRP A 268 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 ( 7510) covalent geometry : angle 0.60156 / 0.35 (10530) hydrogen bonds : bond 0.05030 / 3.29 ( 357) hydrogen bonds : angle 4.36514 / 2.99 ( 951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8440 (mt) cc_final: 0.8194 (tp) REVERT: A 324 ASP cc_start: 0.7590 (t0) cc_final: 0.7182 (m-30) REVERT: A 385 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7905 (mp10) REVERT: A 413 LYS cc_start: 0.8401 (tttt) cc_final: 0.7951 (ttpp) REVERT: A 455 ASP cc_start: 0.7838 (m-30) cc_final: 0.7531 (m-30) REVERT: A 469 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: A 471 MET cc_start: 0.6222 (mtm) cc_final: 0.5683 (mtp) REVERT: A 526 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: A 537 GLN cc_start: 0.7830 (pm20) cc_final: 0.7611 (pm20) REVERT: A 571 ASN cc_start: 0.6859 (m110) cc_final: 0.6478 (m-40) REVERT: A 588 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8901 (mtmp) REVERT: A 591 GLU cc_start: 0.7606 (tt0) cc_final: 0.7223 (mp0) REVERT: A 625 ASN cc_start: 0.7587 (m110) cc_final: 0.7276 (t0) outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 0.5794 time to fit residues: 49.6530 Evaluate side-chains 79 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.178286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141577 restraints weight = 8483.446| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.61 r_work: 0.3354 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7510 Z= 0.161 Angle : 0.563 7.162 10530 Z= 0.331 Chirality : 0.041 0.158 1198 Planarity : 0.003 0.040 1005 Dihedral : 21.263 90.362 1937 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.02 % Allowed : 15.31 % Favored : 83.67 % 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: 0.32 (0.33), residues: 624 helix: 1.03 (0.28), residues: 331 sheet: 0.34 (0.69), residues: 54 loop : -0.94 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.020 0.002 TYR A 437 PHE 0.014 0.001 PHE A 382 TRP 0.006 0.001 TRP A 268 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 7510) covalent geometry : angle 0.56314 / 0.33 (10530) hydrogen bonds : bond 0.04622 / 2.99 ( 357) hydrogen bonds : angle 4.33516 / 2.97 ( 951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7313 (pp-130) cc_final: 0.6955 (ppp) REVERT: A 323 LEU cc_start: 0.8449 (mt) cc_final: 0.8183 (tp) REVERT: A 324 ASP cc_start: 0.7653 (t0) cc_final: 0.7214 (m-30) REVERT: A 385 GLN cc_start: 0.8326 (tp-100) cc_final: 0.7956 (mp10) REVERT: A 413 LYS cc_start: 0.8409 (tttt) cc_final: 0.7972 (ttpp) REVERT: A 437 TYR cc_start: 0.8016 (t80) cc_final: 0.7676 (t80) REVERT: A 455 ASP cc_start: 0.7783 (m-30) cc_final: 0.7484 (m-30) REVERT: A 471 MET cc_start: 0.6217 (mtm) cc_final: 0.5671 (mtp) REVERT: A 571 ASN cc_start: 0.6912 (m110) cc_final: 0.6590 (m-40) REVERT: A 588 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8916 (mtmp) REVERT: A 625 ASN cc_start: 0.7612 (m110) cc_final: 0.7312 (t0) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.5147 time to fit residues: 42.6174 Evaluate side-chains 77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139106 restraints weight = 8528.291| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.54 r_work: 0.3330 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 7510 Z= 0.252 Angle : 0.633 6.897 10530 Z= 0.362 Chirality : 0.046 0.177 1198 Planarity : 0.004 0.039 1005 Dihedral : 21.300 90.144 1937 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.36 % Allowed : 15.48 % Favored : 83.16 % 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: 0.20 (0.33), residues: 624 helix: 0.93 (0.28), residues: 331 sheet: 0.32 (0.69), residues: 54 loop : -0.99 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.025 0.003 TYR A 437 PHE 0.030 0.002 PHE A 478 TRP 0.007 0.002 TRP A 268 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 ( 7510) covalent geometry : angle 0.63256 / 0.36 (10530) hydrogen bonds : bond 0.05372 / 3.53 ( 357) hydrogen bonds : angle 4.42149 / 3.03 ( 951) =============================================================================== Job complete usr+sys time: 2239.08 seconds wall clock time: 38 minutes 53.24 seconds (2333.24 seconds total)