Starting phenix.real_space_refine on Fri Jul 3 05:54:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1f_39726/07_2026/8z1f_39726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1f_39726/07_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_39726/07_2026/8z1f_39726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1f_39726/07_2026/8z1f_39726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z1f_39726/07_2026/8z1f_39726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1f_39726/07_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-dev-6108/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: 2.49, per 1000 atoms: 0.20 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: 1.15 Conformation dependent library (CDL) restraints added in 334.2 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: 2.24 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: 2.72 Time building geometry restraints manager: 1.64 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=" 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 bond pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.18e-01 ... (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=" 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 1.50e+00 4.44e-01 3.68e+01 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 1.50e+00 4.44e-01 3.48e+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 - 0.176: 1146 0.176 - 0.353: 1 0.353 - 0.529: 0 0.529 - 0.706: 0 0.706 - 0.882: 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 2.46 1.58 0.88 2.00e-01 2.50e+01 1.95e+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=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-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: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- 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= 0.107 Angle : 0.517 9.100 9695 Z= 0.330 Chirality : 0.044 0.882 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 0.00195 / 0.11 ( 6916) covalent geometry : angle 0.51651 / 0.33 ( 9695) hydrogen bonds : bond 0.21755 / 24.26 ( 195) hydrogen bonds : angle 7.71093 / 10.16 ( 502) metal coordination : bond 0.00204 / 0.13 ( 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 : 0.387 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: A 583 GLN cc_start: 0.7384 (mp10) cc_final: 0.7038 (pp30) REVERT: A 663 TYR cc_start: 0.8016 (t80) cc_final: 0.7623 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1709 time to fit residues: 27.4737 Evaluate side-chains 107 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 9.9990 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 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.133115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.112979 restraints weight = 78759.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.117232 restraints weight = 42049.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.120019 restraints weight = 26361.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.122110 restraints weight = 18524.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.123492 restraints weight = 13787.744| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6920 Z= 0.207 Angle : 0.617 9.035 9695 Z= 0.337 Chirality : 0.046 0.879 1148 Planarity : 0.005 0.039 1002 Dihedral : 18.981 115.324 1718 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.60 % Favored : 92.10 % Rotamer: Outliers : 0.17 % Allowed : 2.26 % Favored : 97.56 % 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: -0.42 (0.33), residues: 658 helix: 1.01 (0.39), residues: 185 sheet: -0.43 (0.45), residues: 131 loop : -0.91 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 251 TYR 0.009 0.002 TYR A 354 PHE 0.019 0.002 PHE A 543 TRP 0.014 0.001 TRP A 357 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 ( 6916) covalent geometry : angle 0.61709 / 0.34 ( 9695) hydrogen bonds : bond 0.06046 / 6.61 ( 195) hydrogen bonds : angle 6.22787 / 8.19 ( 502) metal coordination : bond 0.00722 / 0.46 ( 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 122 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.306 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 433 TRP cc_start: 0.6389 (m-90) cc_final: 0.6156 (m-90) REVERT: A 583 GLN cc_start: 0.7708 (mp10) cc_final: 0.6970 (pp30) REVERT: A 663 TYR cc_start: 0.8577 (t80) cc_final: 0.8069 (t80) REVERT: A 743 VAL cc_start: 0.8687 (m) cc_final: 0.8480 (p) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1687 time to fit residues: 27.4925 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 : 0.308 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 GLN A 727 GLN A 749 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.110876 restraints weight = 81978.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.115058 restraints weight = 43420.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.117831 restraints weight = 27156.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119705 restraints weight = 18924.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.121102 restraints weight = 14343.049| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6920 Z= 0.156 Angle : 0.550 9.032 9695 Z= 0.299 Chirality : 0.045 0.884 1148 Planarity : 0.004 0.053 1002 Dihedral : 19.186 121.747 1718 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % 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: -0.68 (0.33), residues: 658 helix: 0.95 (0.40), residues: 179 sheet: -0.61 (0.44), residues: 131 loop : -1.13 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.013 0.002 TYR A 354 PHE 0.019 0.002 PHE A 109 TRP 0.010 0.001 TRP A 357 HIS 0.009 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 6916) covalent geometry : angle 0.55048 / 0.30 ( 9695) hydrogen bonds : bond 0.05429 / 6.00 ( 195) hydrogen bonds : angle 5.89472 / 7.75 ( 502) metal coordination : bond 0.00493 / 0.32 ( 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 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.304 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 326 PHE cc_start: 0.8356 (m-10) cc_final: 0.8024 (m-10) REVERT: A 583 GLN cc_start: 0.7811 (mp10) cc_final: 0.7020 (pp30) REVERT: A 663 TYR cc_start: 0.8551 (t80) cc_final: 0.8051 (t80) REVERT: A 743 VAL cc_start: 0.8866 (m) cc_final: 0.8650 (p) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1707 time to fit residues: 27.3337 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 : 0.304 ------------------------------------------------------------------------------- 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: 8.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.125927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.105759 restraints weight = 79737.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.109825 restraints weight = 43309.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.112443 restraints weight = 27570.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.114425 restraints weight = 19725.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.115761 restraints weight = 14885.289| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2599 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= 0.213 Angle : 0.613 9.069 9695 Z= 0.335 Chirality : 0.046 0.885 1148 Planarity : 0.004 0.028 1002 Dihedral : 19.448 123.734 1718 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.27 % Favored : 90.43 % 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: -1.26 (0.32), residues: 658 helix: 0.10 (0.37), residues: 205 sheet: -0.82 (0.44), residues: 129 loop : -1.42 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.012 0.002 TYR A 354 PHE 0.017 0.002 PHE A 243 TRP 0.015 0.002 TRP A 357 HIS 0.007 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 ( 6916) covalent geometry : angle 0.61295 / 0.33 ( 9695) hydrogen bonds : bond 0.05187 / 5.54 ( 195) hydrogen bonds : angle 5.87410 / 7.60 ( 502) metal coordination : bond 0.00610 / 0.40 ( 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 113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.310 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: A 416 MET cc_start: 0.5919 (mpp) cc_final: 0.5182 (mmt) REVERT: A 583 GLN cc_start: 0.7889 (mp10) cc_final: 0.7110 (pp30) REVERT: A 663 TYR cc_start: 0.8575 (t80) cc_final: 0.8167 (t80) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1707 time to fit residues: 26.0000 Evaluate side-chains 107 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.107582 restraints weight = 81542.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.111768 restraints weight = 43275.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.114442 restraints weight = 27173.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.116479 restraints weight = 19223.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.117784 restraints weight = 14365.985| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6920 Z= 0.117 Angle : 0.534 9.045 9695 Z= 0.289 Chirality : 0.045 0.888 1148 Planarity : 0.003 0.037 1002 Dihedral : 19.442 124.125 1718 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.36 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -1.00 (0.32), residues: 658 helix: 0.68 (0.40), residues: 190 sheet: -0.88 (0.44), residues: 130 loop : -1.35 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.013 0.001 TYR A 354 PHE 0.008 0.001 PHE A 521 TRP 0.008 0.001 TRP A 357 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 6916) covalent geometry : angle 0.53448 / 0.29 ( 9695) hydrogen bonds : bond 0.03945 / 4.27 ( 195) hydrogen bonds : angle 5.56350 / 7.25 ( 502) metal coordination : bond 0.00365 / 0.22 ( 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 118 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.406 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.5930 (mpp) cc_final: 0.5179 (mmt) REVERT: A 583 GLN cc_start: 0.7900 (mp10) cc_final: 0.7061 (pp30) REVERT: A 663 TYR cc_start: 0.8579 (t80) cc_final: 0.8205 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1751 time to fit residues: 27.9188 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 : 0.317 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.107856 restraints weight = 80288.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.111987 restraints weight = 42921.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.114774 restraints weight = 27130.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.116667 restraints weight = 18934.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.118082 restraints weight = 14337.853| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6920 Z= 0.106 Angle : 0.519 9.071 9695 Z= 0.279 Chirality : 0.045 0.888 1148 Planarity : 0.003 0.034 1002 Dihedral : 19.391 123.550 1718 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.60 % Favored : 91.95 % 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: -0.96 (0.33), residues: 658 helix: 0.80 (0.40), residues: 190 sheet: -0.82 (0.45), residues: 128 loop : -1.40 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.014 0.001 TYR A 181 PHE 0.008 0.001 PHE A 637 TRP 0.006 0.001 TRP A 357 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 6916) covalent geometry : angle 0.51851 / 0.28 ( 9695) hydrogen bonds : bond 0.03605 / 3.89 ( 195) hydrogen bonds : angle 5.43773 / 7.09 ( 502) metal coordination : bond 0.00233 / 0.13 ( 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 116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.312 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 416 MET cc_start: 0.5910 (mpp) cc_final: 0.5162 (mmt) REVERT: A 511 SER cc_start: 0.7680 (t) cc_final: 0.7294 (m) REVERT: A 583 GLN cc_start: 0.7880 (mp10) cc_final: 0.7044 (pp30) REVERT: A 663 TYR cc_start: 0.8551 (t80) cc_final: 0.8109 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1718 time to fit residues: 26.9351 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 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN A 727 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.124283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.107714 restraints weight = 100783.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.111069 restraints weight = 57820.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.113225 restraints weight = 38359.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.114923 restraints weight = 28274.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.116049 restraints weight = 22070.548| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6920 Z= 0.188 Angle : 0.595 9.075 9695 Z= 0.324 Chirality : 0.046 0.888 1148 Planarity : 0.004 0.043 1002 Dihedral : 19.629 125.822 1718 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % 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: -1.26 (0.32), residues: 658 helix: 0.30 (0.38), residues: 197 sheet: -1.01 (0.46), residues: 128 loop : -1.45 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 428 TYR 0.012 0.002 TYR A 463 PHE 0.030 0.002 PHE A 109 TRP 0.012 0.002 TRP A 357 HIS 0.008 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 ( 6916) covalent geometry : angle 0.59545 / 0.32 ( 9695) hydrogen bonds : bond 0.04536 / 4.73 ( 195) hydrogen bonds : angle 5.52891 / 7.14 ( 502) metal coordination : bond 0.00574 / 0.37 ( 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 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.380 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: 0.3842 (mmt) cc_final: 0.3327 (mmt) REVERT: A 416 MET cc_start: 0.6007 (mpp) cc_final: 0.5214 (mmt) REVERT: A 663 TYR cc_start: 0.8748 (t80) cc_final: 0.8362 (t80) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1671 time to fit residues: 27.1482 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 : 0.329 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4234 r_free = 0.4234 target = 0.122863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.103261 restraints weight = 81596.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.107186 restraints weight = 43906.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.109810 restraints weight = 27933.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.111562 restraints weight = 19761.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.112927 restraints weight = 15310.545| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6920 Z= 0.155 Angle : 0.572 9.066 9695 Z= 0.312 Chirality : 0.046 0.890 1148 Planarity : 0.005 0.118 1002 Dihedral : 19.647 127.273 1718 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.37 (0.32), residues: 658 helix: 0.13 (0.38), residues: 203 sheet: -1.02 (0.46), residues: 128 loop : -1.51 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.012 0.002 TYR A 354 PHE 0.011 0.002 PHE A 521 TRP 0.010 0.002 TRP A 357 HIS 0.006 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6916) covalent geometry : angle 0.57198 / 0.31 ( 9695) hydrogen bonds : bond 0.04062 / 4.15 ( 195) hydrogen bonds : angle 5.52089 / 7.14 ( 502) metal coordination : bond 0.00319 / 0.20 ( 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 113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.319 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 113 MET cc_start: 0.3981 (mmt) cc_final: 0.3430 (mmt) REVERT: A 416 MET cc_start: 0.5906 (mpp) cc_final: 0.5142 (mmt) REVERT: A 663 TYR cc_start: 0.8606 (t80) cc_final: 0.8240 (t80) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1619 time to fit residues: 25.1039 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 168 HIS ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.137553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.120415 restraints weight = 99192.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.123913 restraints weight = 56044.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.126135 restraints weight = 36301.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.127829 restraints weight = 26169.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.128821 restraints weight = 19811.385| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6920 Z= 0.112 Angle : 0.541 9.088 9695 Z= 0.293 Chirality : 0.045 0.891 1148 Planarity : 0.004 0.074 1002 Dihedral : 19.574 127.720 1718 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.51 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.30 (0.32), residues: 658 helix: 0.26 (0.38), residues: 203 sheet: -0.99 (0.46), residues: 128 loop : -1.51 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.012 0.001 TYR A 354 PHE 0.007 0.001 PHE A 521 TRP 0.007 0.001 TRP A 433 HIS 0.003 0.001 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6916) covalent geometry : angle 0.54148 / 0.29 ( 9695) hydrogen bonds : bond 0.03422 / 3.55 ( 195) hydrogen bonds : angle 5.28087 / 6.86 ( 502) metal coordination : bond 0.00574 / 0.36 ( 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 114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.318 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: 0.4008 (mmt) cc_final: 0.3485 (mmt) REVERT: A 416 MET cc_start: 0.5909 (mpp) cc_final: 0.5201 (mmt) REVERT: A 663 TYR cc_start: 0.8278 (t80) cc_final: 0.7976 (t80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1436 time to fit residues: 22.8308 Evaluate side-chains 104 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4258 r_free = 0.4258 target = 0.126056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.109351 restraints weight = 96601.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.112693 restraints weight = 54928.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.114962 restraints weight = 36404.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.116363 restraints weight = 26537.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.117463 restraints weight = 21132.120| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6920 Z= 0.106 Angle : 0.531 9.119 9695 Z= 0.286 Chirality : 0.045 0.890 1148 Planarity : 0.004 0.052 1002 Dihedral : 19.542 127.899 1718 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.36 % Favored : 91.19 % 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: -1.20 (0.32), residues: 658 helix: 0.36 (0.39), residues: 203 sheet: -0.92 (0.46), residues: 125 loop : -1.48 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.010 0.001 TYR A 354 PHE 0.013 0.001 PHE A 637 TRP 0.007 0.001 TRP A 587 HIS 0.009 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 6916) covalent geometry : angle 0.53077 / 0.29 ( 9695) hydrogen bonds : bond 0.03320 / 3.49 ( 195) hydrogen bonds : angle 5.24359 / 6.92 ( 502) metal coordination : bond 0.00452 / 0.28 ( 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 109 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.268 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 113 MET cc_start: 0.3769 (mmt) cc_final: 0.3211 (mmt) REVERT: A 416 MET cc_start: 0.5935 (mpp) cc_final: 0.5182 (mmt) REVERT: A 583 GLN cc_start: 0.7413 (mp10) cc_final: 0.6600 (pp30) REVERT: A 663 TYR cc_start: 0.8566 (t80) cc_final: 0.8190 (t80) REVERT: A 685 HIS cc_start: 0.7288 (t-90) cc_final: 0.6937 (t-90) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1680 time to fit residues: 24.8591 Evaluate side-chains 99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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: 10.0000 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.119151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.102555 restraints weight = 100506.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.105824 restraints weight = 57291.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.107988 restraints weight = 38030.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.109351 restraints weight = 27752.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.110365 restraints weight = 22154.300| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 6920 Z= 0.280 Angle : 0.726 9.090 9695 Z= 0.399 Chirality : 0.049 0.890 1148 Planarity : 0.005 0.045 1002 Dihedral : 20.146 131.250 1718 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.79 % Favored : 88.75 % 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: -2.02 (0.31), residues: 658 helix: -0.62 (0.35), residues: 206 sheet: -1.28 (0.47), residues: 126 loop : -1.81 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 428 TYR 0.019 0.003 TYR A 463 PHE 0.026 0.003 PHE A 739 TRP 0.021 0.003 TRP A 587 HIS 0.014 0.003 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.28 ( 6916) covalent geometry : angle 0.72634 / 0.40 ( 9695) hydrogen bonds : bond 0.05919 / 5.97 ( 195) hydrogen bonds : angle 5.84538 / 7.51 ( 502) metal coordination : bond 0.00760 / 0.50 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.58 seconds wall clock time: 43 minutes 8.31 seconds (2588.31 seconds total)