Starting phenix.real_space_refine on Thu Jul 2 06:07:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izp_61038/07_2026/9izp_61038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izp_61038/07_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_61038/07_2026/9izp_61038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_2026/9izp_61038.map" model { file = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_2026/9izp_61038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izp_61038/07_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-dev-6108/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: 1.80, per 1000 atoms: 0.25 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: 0.54 Conformation dependent library (CDL) restraints added in 399.5 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: 0.82 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: 1.18 Time building geometry restraints manager: 0.79 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: 9850 1.14 - 2.29: 569 2.29 - 3.43: 103 3.43 - 4.57: 6 4.57 - 5.71: 2 Bond angle restraints: 10530 Sorted by residual: 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 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT C -8 " pdb=" C4 DT C -8 " pdb=" O4 DT C -8 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+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 - 0.033: 713 0.033 - 0.065: 314 0.065 - 0.098: 120 0.098 - 0.131: 48 0.131 - 0.163: 3 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 2.46 2.29 0.16 2.00e-01 2.50e+01 6.67e-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 2.46 2.31 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" C1' A B -24 " pdb=" O4' A B -24 " pdb=" C2' A B -24 " pdb=" N9 A B -24 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.28e-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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.870 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- 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= 0.385 Angle : 0.600 5.713 10530 Z= 0.474 Chirality : 0.044 0.163 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 0.00525 / 0.38 ( 7510) covalent geometry : angle 0.59972 / 0.47 (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 : 0.267 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: 0.4866 time to fit residues: 57.4810 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 : 0.209 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 498 GLN A 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139065 restraints weight = 8558.108| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.59 r_work: 0.3338 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7510 Z= 0.224 Angle : 0.616 6.552 10530 Z= 0.362 Chirality : 0.044 0.173 1198 Planarity : 0.004 0.042 1005 Dihedral : 21.192 90.754 1937 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.02 % Allowed : 9.01 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.33), residues: 624 helix: 0.72 (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 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 ( 7510) covalent geometry : angle 0.61592 / 0.36 (10530) hydrogen bonds : bond 0.05747 / 3.67 ( 357) hydrogen bonds : angle 4.76947 / 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 85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7912 (mttt) cc_final: 0.7655 (mtpp) REVERT: A 67 ASP cc_start: 0.7025 (m-30) cc_final: 0.6694 (m-30) REVERT: A 155 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6649 (ppp) REVERT: A 242 LYS cc_start: 0.8740 (tptt) cc_final: 0.8459 (tptp) REVERT: A 323 LEU cc_start: 0.8254 (mt) cc_final: 0.7927 (tp) REVERT: A 324 ASP cc_start: 0.7634 (t0) cc_final: 0.7074 (m-30) REVERT: A 385 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7679 (mp10) REVERT: A 413 LYS cc_start: 0.8378 (tttt) cc_final: 0.7930 (ttpp) REVERT: A 471 MET cc_start: 0.6196 (mtm) cc_final: 0.5708 (mtp) REVERT: A 478 PHE cc_start: 0.8764 (m-10) cc_final: 0.8331 (m-10) REVERT: A 512 TYR cc_start: 0.8402 (t80) cc_final: 0.8155 (t80) outliers start: 6 outliers final: 1 residues processed: 81 average time/residue: 0.4732 time to fit residues: 40.4494 Evaluate side-chains 77 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.177889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140750 restraints weight = 8378.323| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.60 r_work: 0.3354 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7510 Z= 0.164 Angle : 0.548 10.114 10530 Z= 0.328 Chirality : 0.041 0.158 1198 Planarity : 0.003 0.041 1005 Dihedral : 21.211 91.312 1937 Min Nonbonded Distance : 1.995 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: 0.32 (0.33), residues: 624 helix: 1.01 (0.28), residues: 330 sheet: 0.76 (0.70), residues: 54 loop : -1.00 (0.39), residues: 240 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 0.015 0.002 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 0.00331 / 0.16 ( 7510) covalent geometry : angle 0.54790 / 0.33 (10530) hydrogen bonds : bond 0.05001 / 3.23 ( 357) hydrogen bonds : angle 4.52822 / 3.08 ( 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 94 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7918 (mttt) cc_final: 0.7678 (mtpp) REVERT: A 242 LYS cc_start: 0.8648 (tptt) cc_final: 0.8332 (tptp) REVERT: A 323 LEU cc_start: 0.8317 (mt) cc_final: 0.8033 (tp) REVERT: A 324 ASP cc_start: 0.7657 (t0) cc_final: 0.7155 (m-30) REVERT: A 385 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7766 (mp10) REVERT: A 413 LYS cc_start: 0.8360 (tttt) cc_final: 0.7939 (ttpp) REVERT: A 437 TYR cc_start: 0.7999 (t80) cc_final: 0.7737 (t80) REVERT: A 471 MET cc_start: 0.6275 (mtm) cc_final: 0.5716 (mtp) REVERT: A 526 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: A 588 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8711 (mtmm) REVERT: A 591 GLU cc_start: 0.7627 (tt0) cc_final: 0.7253 (mp0) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.4979 time to fit residues: 47.2978 Evaluate side-chains 81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 50.0000 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.173303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136530 restraints weight = 8614.694| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.67 r_work: 0.3290 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 7510 Z= 0.343 Angle : 0.687 7.334 10530 Z= 0.393 Chirality : 0.049 0.198 1198 Planarity : 0.004 0.041 1005 Dihedral : 21.327 91.063 1937 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.53 % Allowed : 12.41 % Favored : 86.05 % 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: 0.59 (0.72), residues: 54 loop : -1.12 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.028 0.003 TYR A 437 PHE 0.023 0.003 PHE A 252 TRP 0.006 0.002 TRP A 268 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.34 ( 7510) covalent geometry : angle 0.68653 / 0.39 (10530) hydrogen bonds : bond 0.06301 / 4.16 ( 357) hydrogen bonds : angle 4.65204 / 3.18 ( 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 86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8734 (tptt) cc_final: 0.8448 (tptp) REVERT: A 323 LEU cc_start: 0.8392 (mt) cc_final: 0.8113 (tp) REVERT: A 324 ASP cc_start: 0.7704 (t0) cc_final: 0.7207 (m-30) REVERT: A 385 GLN cc_start: 0.8389 (tp-100) cc_final: 0.7966 (mp10) REVERT: A 413 LYS cc_start: 0.8426 (tttt) cc_final: 0.7995 (ttpp) REVERT: A 471 MET cc_start: 0.6336 (mtm) cc_final: 0.5724 (mtp) REVERT: A 490 LEU cc_start: 0.9079 (mt) cc_final: 0.8842 (mt) REVERT: A 526 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6829 (tp30) REVERT: A 588 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8795 (mtmp) REVERT: A 591 GLU cc_start: 0.7733 (tt0) cc_final: 0.7371 (mp0) outliers start: 9 outliers final: 3 residues processed: 82 average time/residue: 0.5304 time to fit residues: 45.8658 Evaluate side-chains 80 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 526 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: 6.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** 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 = 0.4057 r_free = 0.4057 target = 0.177815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140585 restraints weight = 8520.794| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.60 r_work: 0.3358 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2103 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 : 0.538 6.015 10530 Z= 0.322 Chirality : 0.040 0.155 1198 Planarity : 0.003 0.042 1005 Dihedral : 21.310 92.424 1937 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 12.41 % Favored : 85.71 % 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: 0.29 (0.33), residues: 624 helix: 0.99 (0.28), residues: 330 sheet: 0.48 (0.69), residues: 54 loop : -0.94 (0.39), residues: 240 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 0.014 0.001 PHE A 382 TRP 0.006 0.001 TRP A 268 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 7510) covalent geometry : angle 0.53756 / 0.32 (10530) hydrogen bonds : bond 0.04649 / 3.00 ( 357) hydrogen bonds : angle 4.41675 / 3.03 ( 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 91 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8615 (tptt) cc_final: 0.8216 (tptp) REVERT: A 323 LEU cc_start: 0.8355 (mt) cc_final: 0.8065 (tp) REVERT: A 324 ASP cc_start: 0.7647 (t0) cc_final: 0.7251 (m-30) REVERT: A 385 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7933 (mp10) REVERT: A 413 LYS cc_start: 0.8379 (tttt) cc_final: 0.7949 (ttpp) REVERT: A 437 TYR cc_start: 0.7982 (t80) cc_final: 0.7635 (t80) REVERT: A 471 MET cc_start: 0.6293 (mtm) cc_final: 0.5635 (mtp) REVERT: A 490 LEU cc_start: 0.9070 (mt) cc_final: 0.8849 (mt) REVERT: A 526 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: A 566 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7785 (mmtt) REVERT: A 571 ASN cc_start: 0.6903 (m110) cc_final: 0.6580 (m-40) REVERT: A 588 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8828 (mtmp) outliers start: 11 outliers final: 2 residues processed: 86 average time/residue: 0.4803 time to fit residues: 43.7124 Evaluate side-chains 83 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET 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: 3.9990 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: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.177264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140447 restraints weight = 8635.636| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.63 r_work: 0.3356 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7510 Z= 0.157 Angle : 0.532 6.402 10530 Z= 0.317 Chirality : 0.040 0.154 1198 Planarity : 0.003 0.041 1005 Dihedral : 21.263 92.007 1937 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.87 % Allowed : 13.78 % Favored : 84.35 % 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: 0.34 (0.33), residues: 624 helix: 1.02 (0.28), residues: 330 sheet: 0.58 (0.69), residues: 54 loop : -0.93 (0.39), residues: 240 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 0.005 0.001 TRP A 33 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 ( 7510) covalent geometry : angle 0.53212 / 0.32 (10530) hydrogen bonds : bond 0.04603 / 3.00 ( 357) hydrogen bonds : angle 4.32591 / 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 93 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8331 (mt) cc_final: 0.8070 (tp) REVERT: A 324 ASP cc_start: 0.7635 (t0) cc_final: 0.7229 (m-30) REVERT: A 385 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7957 (mp10) REVERT: A 413 LYS cc_start: 0.8399 (tttt) cc_final: 0.7952 (ttpp) REVERT: A 437 TYR cc_start: 0.8032 (t80) cc_final: 0.7706 (t80) REVERT: A 455 ASP cc_start: 0.7961 (m-30) cc_final: 0.7587 (m-30) REVERT: A 469 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: A 471 MET cc_start: 0.6176 (mtm) cc_final: 0.5600 (mtp) REVERT: A 490 LEU cc_start: 0.9043 (mt) cc_final: 0.8833 (mt) REVERT: A 526 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6756 (tp30) REVERT: A 566 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7814 (mmtt) REVERT: A 588 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8857 (mtmp) REVERT: A 591 GLU cc_start: 0.7608 (tt0) cc_final: 0.7159 (mp0) REVERT: A 625 ASN cc_start: 0.7660 (m110) cc_final: 0.7342 (t0) outliers start: 11 outliers final: 3 residues processed: 87 average time/residue: 0.4827 time to fit residues: 44.4418 Evaluate side-chains 84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET 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: 10.0000 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.176506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139713 restraints weight = 8553.315| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.59 r_work: 0.3345 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7510 Z= 0.203 Angle : 0.564 6.530 10530 Z= 0.333 Chirality : 0.042 0.165 1198 Planarity : 0.003 0.040 1005 Dihedral : 21.284 92.080 1937 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.87 % Allowed : 14.12 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.33), residues: 624 helix: 0.96 (0.28), residues: 331 sheet: 0.51 (0.70), residues: 54 loop : -0.97 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.022 0.002 TYR A 437 PHE 0.015 0.002 PHE A 382 TRP 0.006 0.002 TRP A 172 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 7510) covalent geometry : angle 0.56416 / 0.33 (10530) hydrogen bonds : bond 0.04869 / 3.18 ( 357) hydrogen bonds : angle 4.33373 / 2.97 ( 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 86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8369 (mt) cc_final: 0.8093 (tp) REVERT: A 324 ASP cc_start: 0.7606 (t0) cc_final: 0.7222 (m-30) REVERT: A 385 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7920 (mp10) REVERT: A 413 LYS cc_start: 0.8422 (tttt) cc_final: 0.7968 (ttpp) REVERT: A 469 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: A 471 MET cc_start: 0.6255 (mtm) cc_final: 0.5717 (mtp) REVERT: A 526 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: A 552 GLU cc_start: 0.7921 (tt0) cc_final: 0.7568 (pm20) REVERT: A 571 ASN cc_start: 0.6929 (m110) cc_final: 0.6595 (m-40) REVERT: A 588 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8894 (mtmp) REVERT: A 591 GLU cc_start: 0.7588 (tt0) cc_final: 0.7129 (mp0) REVERT: A 625 ASN cc_start: 0.7640 (m110) cc_final: 0.7315 (t0) outliers start: 11 outliers final: 2 residues processed: 80 average time/residue: 0.4887 time to fit residues: 41.1577 Evaluate side-chains 76 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.177267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140612 restraints weight = 8614.498| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.59 r_work: 0.3359 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7510 Z= 0.177 Angle : 0.546 6.788 10530 Z= 0.323 Chirality : 0.041 0.161 1198 Planarity : 0.003 0.039 1005 Dihedral : 21.295 92.490 1937 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.53 % Allowed : 14.46 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.30 (0.33), residues: 624 helix: 0.99 (0.28), residues: 331 sheet: 0.45 (0.70), residues: 54 loop : -0.94 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.021 0.002 TYR A 437 PHE 0.027 0.002 PHE A 478 TRP 0.006 0.001 TRP A 268 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 7510) covalent geometry : angle 0.54599 / 0.32 (10530) hydrogen bonds : bond 0.04670 / 3.04 ( 357) hydrogen bonds : angle 4.31217 / 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 86 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7275 (pp-130) cc_final: 0.6917 (ppp) REVERT: A 323 LEU cc_start: 0.8413 (mt) cc_final: 0.8164 (tp) REVERT: A 324 ASP cc_start: 0.7599 (t0) cc_final: 0.7210 (m-30) REVERT: A 385 GLN cc_start: 0.8331 (tp-100) cc_final: 0.7945 (mp10) REVERT: A 413 LYS cc_start: 0.8397 (tttt) cc_final: 0.7961 (ttpp) REVERT: A 437 TYR cc_start: 0.8001 (t80) cc_final: 0.7651 (t80) REVERT: A 455 ASP cc_start: 0.7847 (m-30) cc_final: 0.7528 (m-30) REVERT: A 469 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 471 MET cc_start: 0.6238 (mtm) cc_final: 0.5683 (mtp) REVERT: A 526 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: A 566 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7787 (mmtm) REVERT: A 567 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: A 588 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8915 (mtmp) REVERT: A 625 ASN cc_start: 0.7637 (m110) cc_final: 0.7330 (t0) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.4439 time to fit residues: 38.0497 Evaluate side-chains 81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET 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 Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.177007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140159 restraints weight = 8451.267| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.57 r_work: 0.3351 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7510 Z= 0.198 Angle : 0.569 6.835 10530 Z= 0.335 Chirality : 0.042 0.165 1198 Planarity : 0.003 0.039 1005 Dihedral : 21.302 92.628 1937 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.87 % Allowed : 14.46 % 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: 0.28 (0.33), residues: 624 helix: 0.98 (0.28), residues: 331 sheet: 0.45 (0.70), residues: 54 loop : -0.95 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.022 0.002 TYR A 437 PHE 0.015 0.002 PHE A 382 TRP 0.006 0.001 TRP A 268 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 7510) covalent geometry : angle 0.56933 / 0.33 (10530) hydrogen bonds : bond 0.04828 / 3.14 ( 357) hydrogen bonds : angle 4.33454 / 2.97 ( 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 88 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8440 (mt) cc_final: 0.8186 (tp) REVERT: A 324 ASP cc_start: 0.7636 (t0) cc_final: 0.7204 (m-30) REVERT: A 385 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7945 (mp10) REVERT: A 413 LYS cc_start: 0.8414 (tttt) cc_final: 0.7969 (ttpp) REVERT: A 455 ASP cc_start: 0.7855 (m-30) cc_final: 0.7557 (m-30) REVERT: A 471 MET cc_start: 0.6245 (mtm) cc_final: 0.5718 (mtp) REVERT: A 526 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: A 567 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: A 570 GLU cc_start: 0.7257 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 588 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8912 (mtmp) REVERT: A 596 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7573 (tmtt) REVERT: A 625 ASN cc_start: 0.7615 (m110) cc_final: 0.7304 (t0) outliers start: 11 outliers final: 4 residues processed: 83 average time/residue: 0.5248 time to fit residues: 45.9829 Evaluate side-chains 81 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142054 restraints weight = 8477.031| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.57 r_work: 0.3377 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 7510 Z= 0.160 Angle : 0.552 7.203 10530 Z= 0.327 Chirality : 0.041 0.153 1198 Planarity : 0.003 0.040 1005 Dihedral : 21.292 92.990 1937 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.19 % Allowed : 14.97 % 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: 0.35 (0.33), residues: 624 helix: 1.04 (0.28), residues: 331 sheet: 0.49 (0.70), residues: 54 loop : -0.92 (0.40), 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 0.030 0.002 PHE A 478 TRP 0.006 0.001 TRP A 268 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 7510) covalent geometry : angle 0.55239 / 0.33 (10530) hydrogen bonds : bond 0.04557 / 2.95 ( 357) hydrogen bonds : angle 4.32404 / 2.96 ( 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 85 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7261 (pp-130) cc_final: 0.6897 (ppp) REVERT: A 323 LEU cc_start: 0.8427 (mt) cc_final: 0.8173 (tp) REVERT: A 324 ASP cc_start: 0.7603 (t0) cc_final: 0.7177 (m-30) REVERT: A 385 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7963 (mp10) REVERT: A 413 LYS cc_start: 0.8398 (tttt) cc_final: 0.7962 (ttpp) REVERT: A 437 TYR cc_start: 0.7992 (t80) cc_final: 0.7661 (t80) REVERT: A 455 ASP cc_start: 0.7744 (m-30) cc_final: 0.7481 (m-30) REVERT: A 469 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: A 471 MET cc_start: 0.6214 (mtm) cc_final: 0.5697 (mtp) REVERT: A 526 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6826 (tp30) REVERT: A 566 LYS cc_start: 0.8402 (mmtt) cc_final: 0.7617 (mmtt) REVERT: A 567 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 588 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8906 (mtmp) REVERT: A 596 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7604 (tmtt) REVERT: A 625 ASN cc_start: 0.7607 (m110) cc_final: 0.7308 (t0) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.4759 time to fit residues: 40.7891 Evaluate side-chains 84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 596 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141896 restraints weight = 8536.694| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.58 r_work: 0.3372 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7510 Z= 0.167 Angle : 0.550 6.941 10530 Z= 0.326 Chirality : 0.041 0.151 1198 Planarity : 0.003 0.039 1005 Dihedral : 21.272 93.045 1937 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 0.41 (0.33), residues: 624 helix: 1.10 (0.28), residues: 331 sheet: 0.62 (0.72), residues: 54 loop : -0.95 (0.40), 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 0.014 0.001 PHE A 382 TRP 0.006 0.001 TRP A 268 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 7510) covalent geometry : angle 0.55002 / 0.33 (10530) hydrogen bonds : bond 0.04583 / 2.97 ( 357) hydrogen bonds : angle 4.31028 / 2.95 ( 951) =============================================================================== Job complete usr+sys time: 2241.55 seconds wall clock time: 38 minutes 57.70 seconds (2337.70 seconds total)