Starting phenix.real_space_refine on Thu Aug 6 00:06:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1f_39726/08_2026/8z1f_39726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1f_39726/08_2026/8z1f_39726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z1f_39726/08_2026/8z1f_39726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1f_39726/08_2026/8z1f_39726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z1f_39726/08_2026/8z1f_39726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1f_39726/08_2026/8z1f_39726.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 67 5.49 5 S 38 5.16 5 C 3948 2.51 5 N 1161 2.21 5 O 1419 1.98 5 H 5934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12569 Number of models: 1 Model: "" Number of chains: 3 Chain: "T" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 2122 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 50} Chain: "A" Number of atoms: 10440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 10440 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 40, 'TRANS': 627} Chain breaks: 4 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.94, per 1000 atoms: 0.15 Number of scatterers: 12569 At special positions: 0 Unit cell: (70.484, 89.946, 128.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 67 15.00 O 1419 8.00 N 1161 7.00 C 3948 6.00 H 5934 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 305.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 548 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 546 " pdb="ZN ZN A 901 " - pdb="ZN ZN A 902 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 724 " 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 37.9% alpha, 11.4% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.731A pdb=" N GLN A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.685A pdb=" N LEU A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.889A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.562A pdb=" N LEU A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.532A pdb=" N ILE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.557A pdb=" N ARG A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.676A pdb=" N ASP A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.924A pdb=" N PHE A 361 " --> pdb=" O TRP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.007A pdb=" N VAL A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.617A pdb=" N GLY A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.571A pdb=" N GLN A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 4.116A pdb=" N TRP A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 670 through 678 removed outlier: 3.579A pdb=" N VAL A 674 " --> pdb=" O CYS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.530A pdb=" N LYS A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 removed outlier: 3.934A pdb=" N ASN A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 762 Processing helix chain 'A' and resid 763 through 772 removed outlier: 3.627A pdb=" N PHE A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.582A pdb=" N ARG A 82 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE A 109 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 84 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 432 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.593A pdb=" N TYR A 173 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 243 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 308 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 245 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 306 " --> pdb=" O CYS A 245 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA A 305 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 340 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 307 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N HIS A 342 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 309 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA4, first strand: chain 'A' and resid 482 through 484 Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA6, first strand: chain 'A' and resid 634 through 638 removed outlier: 3.773A pdb=" N GLU A 636 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 654 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 651 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 686 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 683 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 722 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 685 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS A 724 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 720 " --> pdb=" O GLY A 744 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5914 1.03 - 1.23: 39 1.23 - 1.42: 3016 1.42 - 1.62: 3825 1.62 - 1.81: 56 Bond restraints: 12850 Sorted by residual: bond pdb=" N SER A 52 " pdb=" CA SER A 52 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N SER A 52 " pdb=" H SER A 52 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" N9 A T 38 " pdb=" C4 A T 38 " ideal model delta sigma weight residual 1.374 1.381 -0.007 6.00e-03 2.78e+04 1.41e+00 bond pdb=" C4' A T 32 " pdb=" C3' A T 32 " ideal model delta sigma weight residual 1.521 1.532 -0.011 1.00e-02 1.00e+04 1.29e+00 bond pdb=" CB VAL A 752 " pdb=" CG2 VAL A 752 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.29e+00 ... (remaining 12845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.72: 23234 6.72 - 13.45: 2 13.45 - 20.17: 0 20.17 - 26.90: 0 26.90 - 33.62: 3 Bond angle restraints: 23239 Sorted by residual: angle pdb=" O4' A T 32 " pdb=" C1' A T 32 " pdb=" N9 A T 32 " ideal model delta sigma weight residual 108.50 117.34 -8.84 7.00e-01 2.04e+00 1.60e+02 angle pdb=" N9 A T 32 " pdb=" C1' A T 32 " pdb=" H1' A T 32 " ideal model delta sigma weight residual 109.00 75.38 33.62 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C2' A T 32 " pdb=" C1' A T 32 " pdb=" H1' A T 32 " ideal model delta sigma weight residual 109.00 79.75 29.25 3.00e+00 1.11e-01 9.51e+01 angle pdb=" O4' A T 32 " pdb=" C1' A T 32 " pdb=" H1' A T 32 " ideal model delta sigma weight residual 109.00 80.73 28.27 3.00e+00 1.11e-01 8.88e+01 angle pdb=" C2' A T 32 " pdb=" C1' A T 32 " pdb=" N9 A T 32 " ideal model delta sigma weight residual 112.00 121.10 -9.10 1.10e+00 8.26e-01 6.84e+01 ... (remaining 23234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 5584 22.57 - 45.14: 354 45.14 - 67.70: 163 67.70 - 90.27: 25 90.27 - 112.84: 5 Dihedral angle restraints: 6131 sinusoidal: 3887 harmonic: 2244 Sorted by residual: dihedral pdb=" O4' U T 37 " pdb=" C1' U T 37 " pdb=" N1 U T 37 " pdb=" C2 U T 37 " ideal model delta sinusoidal sigma weight residual 200.00 87.16 112.84 1 1.50e+01 4.44e-03 5.92e+01 dihedral pdb=" O4' C T 36 " pdb=" C1' C T 36 " pdb=" N1 C T 36 " pdb=" C2 C T 36 " ideal model delta sinusoidal sigma weight residual -160.00 -75.91 -84.09 1 1.50e+01 4.44e-03 3.83e+01 dihedral pdb=" O4' U T 60 " pdb=" C1' U T 60 " pdb=" N1 U T 60 " pdb=" C2 U T 60 " ideal model delta sinusoidal sigma weight residual -160.00 -88.53 -71.47 1 1.50e+01 4.44e-03 2.91e+01 ... (remaining 6128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 1146 0.179 - 0.358: 1 0.358 - 0.537: 0 0.537 - 0.716: 0 0.716 - 0.895: 1 Chirality restraints: 1148 Sorted by residual: chirality pdb=" C1' A T 32 " pdb=" O4' A T 32 " pdb=" C2' A T 32 " pdb=" N9 A T 32 " both_signs ideal model delta sigma weight residual False 2.47 1.58 0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CB VAL A 752 " pdb=" CA VAL A 752 " pdb=" CG1 VAL A 752 " pdb=" CG2 VAL A 752 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C1' U T 37 " pdb=" O4' U T 37 " pdb=" C2' U T 37 " pdb=" N1 U T 37 " both_signs ideal model delta sigma weight residual False 2.47 2.34 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1145 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 764 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 765 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 480 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A 481 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C T 36 " 0.005 2.00e-02 2.50e+03 7.67e-03 1.62e+00 pdb=" N1 C T 36 " 0.001 2.00e-02 2.50e+03 pdb=" C2 C T 36 " 0.017 2.00e-02 2.50e+03 pdb=" O2 C T 36 " -0.014 2.00e-02 2.50e+03 pdb=" N3 C T 36 " -0.007 2.00e-02 2.50e+03 pdb=" C4 C T 36 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C T 36 " 0.001 2.00e-02 2.50e+03 pdb=" C5 C T 36 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C T 36 " -0.001 2.00e-02 2.50e+03 pdb=" H5 C T 36 " -0.003 2.00e-02 2.50e+03 pdb=" H6 C T 36 " -0.005 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 209 2.09 - 2.72: 19807 2.72 - 3.34: 34386 3.34 - 3.97: 42567 3.97 - 4.60: 65642 Nonbonded interactions: 162611 Sorted by model distance: nonbonded pdb=" OE1 GLU A 372 " pdb=" H GLU A 372 " model vdw 1.460 2.450 nonbonded pdb=" H GLY A 489 " pdb=" O ASN A 498 " model vdw 1.638 2.450 nonbonded pdb=" OG SER A 376 " pdb=" H VAL A 377 " model vdw 1.638 2.450 nonbonded pdb=" O ASP A 106 " pdb=" H VAL A 137 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLU A 172 " pdb=" H GLU A 172 " model vdw 1.666 2.450 ... (remaining 162606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 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 : 0.002 0.037 6920 Z= 0.116 Angle : 0.585 9.100 9695 Z= 0.431 Chirality : 0.050 0.895 1148 Planarity : 0.003 0.040 1002 Dihedral : 18.285 112.840 2989 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.32 % Favored : 94.07 % 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: 0.23 (0.35), residues: 658 helix: 1.56 (0.43), residues: 176 sheet: 0.37 (0.48), residues: 128 loop : -0.64 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 360 TYR 0.017 0.001 TYR A 354 PHE 0.007 0.001 PHE A 543 TRP 0.003 0.001 TRP A 357 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.12 ( 6916) covalent geometry : angle 0.58526 / 0.43 ( 9695) hydrogen bonds : bond 0.21755 / 25.70 ( 195) hydrogen bonds : angle 7.71093 / 10.61 ( 502) metal coordination : bond 0.00204 / 0.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLN cc_start: 0.7384 (mp10) cc_final: 0.7039 (pp30) REVERT: A 663 TYR cc_start: 0.8016 (t80) cc_final: 0.7621 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1469 time to fit residues: 23.6348 Evaluate side-chains 106 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 114 HIS A 248 HIS A 342 HIS A 527 HIS ** A 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.133777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.113551 restraints weight = 78908.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.117970 restraints weight = 42071.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.120932 restraints weight = 26123.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.122963 restraints weight = 18011.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.124386 restraints weight = 13445.078| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6920 Z= 0.201 Angle : 0.606 5.982 9695 Z= 0.326 Chirality : 0.042 0.375 1148 Planarity : 0.004 0.039 1002 Dihedral : 18.911 114.401 1718 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.45 % Favored : 92.25 % Rotamer: Outliers : 0.17 % Allowed : 2.09 % Favored : 97.74 % 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 (0.34), residues: 658 helix: 1.13 (0.40), residues: 184 sheet: -0.10 (0.46), residues: 127 loop : -0.94 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.009 0.001 TYR A 354 PHE 0.017 0.001 PHE A 543 TRP 0.013 0.001 TRP A 357 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 ( 6916) covalent geometry : angle 0.60605 / 0.33 ( 9695) hydrogen bonds : bond 0.06083 / 7.14 ( 195) hydrogen bonds : angle 6.27475 / 8.61 ( 502) metal coordination : bond 0.00638 / 0.60 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9212 (mt0) cc_final: 0.8956 (mt0) REVERT: A 433 TRP cc_start: 0.6362 (m-90) cc_final: 0.6132 (m-90) REVERT: A 527 HIS cc_start: 0.6919 (t-170) cc_final: 0.6043 (t70) REVERT: A 583 GLN cc_start: 0.7706 (mp10) cc_final: 0.6972 (pp30) REVERT: A 663 TYR cc_start: 0.8576 (t80) cc_final: 0.8062 (t80) REVERT: A 743 VAL cc_start: 0.8687 (m) cc_final: 0.8483 (p) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1454 time to fit residues: 23.4766 Evaluate side-chains 105 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 GLN A 749 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.134814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.118166 restraints weight = 96926.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.121969 restraints weight = 54423.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.124493 restraints weight = 35164.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.126303 restraints weight = 24765.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.127364 restraints weight = 18621.256| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6920 Z= 0.117 Angle : 0.510 6.366 9695 Z= 0.274 Chirality : 0.038 0.388 1148 Planarity : 0.004 0.038 1002 Dihedral : 18.999 118.143 1718 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.29 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.51 (0.33), residues: 658 helix: 1.03 (0.40), residues: 187 sheet: -0.59 (0.45), residues: 125 loop : -0.99 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.010 0.001 TYR A 354 PHE 0.013 0.001 PHE A 109 TRP 0.009 0.001 TRP A 357 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 6916) covalent geometry : angle 0.51018 / 0.27 ( 9695) hydrogen bonds : bond 0.05090 / 6.03 ( 195) hydrogen bonds : angle 5.85268 / 8.05 ( 502) metal coordination : bond 0.00203 / 0.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9268 (mt0) cc_final: 0.9067 (mt0) REVERT: A 527 HIS cc_start: 0.6487 (t-170) cc_final: 0.6108 (t70) REVERT: A 583 GLN cc_start: 0.7807 (mp10) cc_final: 0.7032 (pp30) REVERT: A 663 TYR cc_start: 0.8631 (t80) cc_final: 0.8083 (t80) REVERT: A 743 VAL cc_start: 0.8839 (m) cc_final: 0.8633 (p) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1454 time to fit residues: 23.9104 Evaluate side-chains 108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.108486 restraints weight = 83052.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.112522 restraints weight = 44070.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.115166 restraints weight = 28018.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.117149 restraints weight = 19995.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.118487 restraints weight = 15045.078| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6920 Z= 0.218 Angle : 0.614 6.203 9695 Z= 0.332 Chirality : 0.040 0.360 1148 Planarity : 0.004 0.030 1002 Dihedral : 19.242 121.403 1718 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.12 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -1.11 (0.32), residues: 658 helix: 0.30 (0.38), residues: 203 sheet: -0.78 (0.43), residues: 131 loop : -1.36 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 428 TYR 0.012 0.002 TYR A 354 PHE 0.019 0.002 PHE A 521 TRP 0.014 0.002 TRP A 357 HIS 0.007 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 ( 6916) covalent geometry : angle 0.61368 / 0.33 ( 9695) hydrogen bonds : bond 0.05409 / 6.09 ( 195) hydrogen bonds : angle 5.89651 / 7.93 ( 502) metal coordination : bond 0.01040 / 0.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 PHE cc_start: 0.8397 (m-10) cc_final: 0.8048 (m-10) REVERT: A 416 MET cc_start: 0.5905 (mpp) cc_final: 0.5158 (mmt) REVERT: A 527 HIS cc_start: 0.7237 (t-170) cc_final: 0.6982 (t70) REVERT: A 583 GLN cc_start: 0.7879 (mp10) cc_final: 0.7104 (pp30) REVERT: A 663 TYR cc_start: 0.8608 (t80) cc_final: 0.8189 (t80) REVERT: A 743 VAL cc_start: 0.8950 (m) cc_final: 0.8740 (p) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1769 time to fit residues: 27.5138 Evaluate side-chains 108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.127087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.107691 restraints weight = 82839.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.111724 restraints weight = 44283.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.114469 restraints weight = 28109.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.116314 restraints weight = 19690.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.117692 restraints weight = 14994.204| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6920 Z= 0.163 Angle : 0.565 6.455 9695 Z= 0.303 Chirality : 0.039 0.366 1148 Planarity : 0.005 0.108 1002 Dihedral : 19.367 124.273 1718 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.36 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -1.23 (0.32), residues: 658 helix: 0.20 (0.38), residues: 203 sheet: -0.86 (0.44), residues: 130 loop : -1.42 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 623 TYR 0.014 0.002 TYR A 354 PHE 0.018 0.002 PHE A 109 TRP 0.011 0.001 TRP A 357 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 6916) covalent geometry : angle 0.56484 / 0.30 ( 9695) hydrogen bonds : bond 0.04569 / 5.13 ( 195) hydrogen bonds : angle 5.67862 / 7.69 ( 502) metal coordination : bond 0.00276 / 0.23 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.5917 (mpp) cc_final: 0.5163 (mmt) REVERT: A 583 GLN cc_start: 0.7891 (mp10) cc_final: 0.7071 (pp30) REVERT: A 663 TYR cc_start: 0.8585 (t80) cc_final: 0.8165 (t80) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1693 time to fit residues: 25.8202 Evaluate side-chains 105 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.128756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.112317 restraints weight = 96510.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.115563 restraints weight = 54413.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.117921 restraints weight = 37043.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.119503 restraints weight = 26397.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120741 restraints weight = 20539.693| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6920 Z= 0.109 Angle : 0.524 7.070 9695 Z= 0.280 Chirality : 0.039 0.362 1148 Planarity : 0.004 0.076 1002 Dihedral : 19.335 125.491 1718 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.97 (0.33), residues: 658 helix: 0.62 (0.40), residues: 196 sheet: -0.79 (0.45), residues: 128 loop : -1.34 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.013 0.001 TYR A 354 PHE 0.007 0.001 PHE A 521 TRP 0.006 0.001 TRP A 357 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6916) covalent geometry : angle 0.52377 / 0.28 ( 9695) hydrogen bonds : bond 0.03971 / 4.49 ( 195) hydrogen bonds : angle 5.47449 / 7.37 ( 502) metal coordination : bond 0.00255 / 0.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.5898 (mpp) cc_final: 0.5145 (mmt) REVERT: A 511 SER cc_start: 0.7702 (t) cc_final: 0.7276 (m) REVERT: A 583 GLN cc_start: 0.7915 (mp10) cc_final: 0.7093 (pp30) REVERT: A 663 TYR cc_start: 0.8608 (t80) cc_final: 0.8239 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1674 time to fit residues: 26.4276 Evaluate side-chains 109 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN ** A 727 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 = 0.4319 r_free = 0.4319 target = 0.136722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.119087 restraints weight = 101841.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.122670 restraints weight = 57956.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.125054 restraints weight = 37690.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.126784 restraints weight = 27176.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.127935 restraints weight = 20749.882| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6920 Z= 0.171 Angle : 0.575 6.375 9695 Z= 0.308 Chirality : 0.039 0.361 1148 Planarity : 0.004 0.047 1002 Dihedral : 19.528 127.564 1718 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -1.25 (0.32), residues: 658 helix: 0.35 (0.39), residues: 195 sheet: -1.00 (0.46), residues: 128 loop : -1.46 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.025 0.002 TYR A 181 PHE 0.013 0.002 PHE A 739 TRP 0.010 0.002 TRP A 357 HIS 0.007 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 ( 6916) covalent geometry : angle 0.57485 / 0.31 ( 9695) hydrogen bonds : bond 0.04422 / 4.92 ( 195) hydrogen bonds : angle 5.53664 / 7.42 ( 502) metal coordination : bond 0.00738 / 0.72 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6036 (mpp) cc_final: 0.5263 (mmt) REVERT: A 663 TYR cc_start: 0.8582 (t80) cc_final: 0.8205 (t80) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1498 time to fit residues: 23.5638 Evaluate side-chains 103 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.122500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.102811 restraints weight = 79612.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.106772 restraints weight = 42235.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.109466 restraints weight = 26698.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.111209 restraints weight = 18809.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.112563 restraints weight = 14513.358| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6920 Z= 0.152 Angle : 0.569 6.304 9695 Z= 0.305 Chirality : 0.040 0.357 1148 Planarity : 0.004 0.039 1002 Dihedral : 19.685 130.970 1718 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.27 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -1.43 (0.32), residues: 658 helix: 0.19 (0.38), residues: 200 sheet: -1.13 (0.46), residues: 128 loop : -1.57 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 428 TYR 0.015 0.002 TYR A 354 PHE 0.025 0.002 PHE A 243 TRP 0.012 0.002 TRP A 587 HIS 0.017 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 6916) covalent geometry : angle 0.56867 / 0.31 ( 9695) hydrogen bonds : bond 0.03903 / 4.36 ( 195) hydrogen bonds : angle 5.57528 / 7.46 ( 502) metal coordination : bond 0.00369 / 0.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4400 (mmt) cc_final: 0.3785 (mmt) REVERT: A 416 MET cc_start: 0.5924 (mpp) cc_final: 0.5166 (mmt) REVERT: A 583 GLN cc_start: 0.7705 (mp10) cc_final: 0.6889 (pp30) REVERT: A 663 TYR cc_start: 0.8551 (t80) cc_final: 0.8186 (t80) REVERT: A 715 MET cc_start: 0.1670 (tpp) cc_final: 0.1450 (tpp) REVERT: A 750 MET cc_start: 0.7680 (tmm) cc_final: 0.7087 (tmm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1444 time to fit residues: 22.0991 Evaluate side-chains 102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.124746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.104759 restraints weight = 79630.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.108785 restraints weight = 42767.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.111520 restraints weight = 27270.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.113311 restraints weight = 19350.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.114754 restraints weight = 15005.768| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6920 Z= 0.105 Angle : 0.537 6.367 9695 Z= 0.285 Chirality : 0.039 0.360 1148 Planarity : 0.005 0.068 1002 Dihedral : 19.575 130.953 1718 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.36 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.29 (0.32), residues: 658 helix: 0.35 (0.39), residues: 196 sheet: -1.11 (0.45), residues: 127 loop : -1.48 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.012 0.001 TYR A 354 PHE 0.007 0.001 PHE A 725 TRP 0.007 0.001 TRP A 587 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 6916) covalent geometry : angle 0.53679 / 0.29 ( 9695) hydrogen bonds : bond 0.03585 / 3.98 ( 195) hydrogen bonds : angle 5.36316 / 7.28 ( 502) metal coordination : bond 0.00738 / 0.51 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4207 (mmt) cc_final: 0.3689 (mmt) REVERT: A 243 PHE cc_start: 0.7019 (m-80) cc_final: 0.6476 (m-80) REVERT: A 416 MET cc_start: 0.5901 (mpp) cc_final: 0.5142 (mmt) REVERT: A 663 TYR cc_start: 0.8503 (t80) cc_final: 0.8141 (t80) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1592 time to fit residues: 24.0956 Evaluate side-chains 102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 457 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 = 0.4267 r_free = 0.4267 target = 0.125832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105460 restraints weight = 78730.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.109564 restraints weight = 42582.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.112310 restraints weight = 27250.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.114111 restraints weight = 19369.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.115445 restraints weight = 15123.124| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6920 Z= 0.094 Angle : 0.516 6.160 9695 Z= 0.272 Chirality : 0.039 0.361 1148 Planarity : 0.004 0.045 1002 Dihedral : 19.470 130.735 1718 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.14 % Favored : 92.40 % 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: -1.16 (0.32), residues: 658 helix: 0.42 (0.39), residues: 202 sheet: -0.97 (0.46), residues: 127 loop : -1.43 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 430 TYR 0.010 0.001 TYR A 354 PHE 0.007 0.001 PHE A 725 TRP 0.007 0.001 TRP A 587 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 6916) covalent geometry : angle 0.51592 / 0.27 ( 9695) hydrogen bonds : bond 0.03266 / 3.68 ( 195) hydrogen bonds : angle 5.17284 / 7.05 ( 502) metal coordination : bond 0.00653 / 0.45 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4161 (mmt) cc_final: 0.3645 (mmt) REVERT: A 416 MET cc_start: 0.5925 (mpp) cc_final: 0.5175 (mmt) REVERT: A 663 TYR cc_start: 0.8530 (t80) cc_final: 0.8152 (t80) REVERT: A 685 HIS cc_start: 0.7158 (t-90) cc_final: 0.6841 (t-90) REVERT: A 715 MET cc_start: 0.1224 (tpp) cc_final: 0.1000 (tpp) REVERT: A 750 MET cc_start: 0.7918 (tmm) cc_final: 0.7383 (tmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1724 time to fit residues: 25.4296 Evaluate side-chains 102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 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 = 0.4203 r_free = 0.4203 target = 0.120377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.101003 restraints weight = 82441.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.104804 restraints weight = 44478.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.107461 restraints weight = 28608.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.109179 restraints weight = 20342.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.110474 restraints weight = 15781.420| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6920 Z= 0.218 Angle : 0.643 6.242 9695 Z= 0.345 Chirality : 0.041 0.358 1148 Planarity : 0.005 0.051 1002 Dihedral : 19.882 132.850 1718 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.49 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -1.70 (0.32), residues: 658 helix: -0.24 (0.37), residues: 206 sheet: -1.25 (0.47), residues: 127 loop : -1.63 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 428 TYR 0.015 0.002 TYR A 463 PHE 0.020 0.002 PHE A 739 TRP 0.016 0.002 TRP A 587 HIS 0.010 0.002 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 ( 6916) covalent geometry : angle 0.64265 / 0.34 ( 9695) hydrogen bonds : bond 0.04962 / 5.38 ( 195) hydrogen bonds : angle 5.58049 / 7.49 ( 502) metal coordination : bond 0.00548 / 0.52 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2372.71 seconds wall clock time: 41 minutes 12.93 seconds (2472.93 seconds total)