Starting phenix.real_space_refine on Thu Sep 18 00:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1f_39726/09_2025/8z1f_39726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1f_39726/09_2025/8z1f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1f_39726/09_2025/8z1f_39726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1f_39726/09_2025/8z1f_39726.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1f_39726/09_2025/8z1f_39726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1f_39726/09_2025/8z1f_39726.cif" } 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-2.0-5805/lib/python3.9/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: 2.37, per 1000 atoms: 0.19 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: 1.05 Conformation dependent library (CDL) restraints added in 349.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.10 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: 2.88 Time building geometry restraints manager: 1.40 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=" 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 bond pdb=" CA ILE A 775 " pdb=" CB ILE A 775 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.15e-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: 5.950 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: 0.070 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.690 Find NCS groups from input model: 0.030 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 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= 0.095 Angle : 0.516 9.100 9695 Z= 0.278 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 aren 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 covalent geometry : bond 0.00195 ( 6916) covalent geometry : angle 0.51646 ( 9695) hydrogen bonds : bond 0.21755 ( 195) hydrogen bonds : angle 7.71093 ( 502) metal coordination : bond 0.00204 ( 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 : 0.332 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: 0.1749 time to fit residues: 27.6721 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 : 0.313 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 92 GLN A 114 HIS A 342 HIS ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.128683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.109087 restraints weight = 81003.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.113240 restraints weight = 42946.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.115917 restraints weight = 26835.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.117984 restraints weight = 18897.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.119124 restraints weight = 14001.789| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6920 Z= 0.197 Angle : 0.639 9.025 9695 Z= 0.335 Chirality : 0.046 0.881 1148 Planarity : 0.004 0.045 1002 Dihedral : 19.245 122.118 1718 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.84 % Favored : 92.86 % Rotamer: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.33), residues: 658 helix: 0.47 (0.39), residues: 193 sheet: -0.22 (0.46), residues: 130 loop : -1.14 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 428 TYR 0.013 0.002 TYR A 354 PHE 0.019 0.002 PHE A 521 TRP 0.018 0.002 TRP A 357 HIS 0.007 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6916) covalent geometry : angle 0.63919 ( 9695) hydrogen bonds : bond 0.05245 ( 195) hydrogen bonds : angle 5.87513 ( 502) metal coordination : bond 0.01186 ( 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 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.301 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: A 583 GLN cc_start: 0.7851 (mp10) cc_final: 0.7011 (pp30) REVERT: A 663 TYR cc_start: 0.8666 (t80) cc_final: 0.8187 (t80) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1855 time to fit residues: 28.8759 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 : 0.309 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.130769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.110715 restraints weight = 81324.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.114891 restraints weight = 43759.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.117746 restraints weight = 27764.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.119609 restraints weight = 19409.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.121032 restraints weight = 14863.445| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2211 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= 0.102 Angle : 0.522 9.051 9695 Z= 0.272 Chirality : 0.044 0.886 1148 Planarity : 0.003 0.031 1002 Dihedral : 19.193 122.065 1718 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % 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 aren not related in a simple way. whole: -0.55 (0.33), residues: 658 helix: 0.87 (0.40), residues: 193 sheet: -0.20 (0.46), residues: 130 loop : -1.17 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.013 0.001 TYR A 354 PHE 0.011 0.001 PHE A 109 TRP 0.004 0.001 TRP A 357 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6916) covalent geometry : angle 0.52191 ( 9695) hydrogen bonds : bond 0.03835 ( 195) hydrogen bonds : angle 5.44254 ( 502) metal coordination : bond 0.00207 ( 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 122 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.343 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 94 LEU cc_start: 0.9105 (mt) cc_final: 0.8825 (mt) REVERT: A 326 PHE cc_start: 0.8321 (m-10) cc_final: 0.7950 (m-10) REVERT: A 511 SER cc_start: 0.7731 (t) cc_final: 0.7447 (m) REVERT: A 538 THR cc_start: 0.8348 (p) cc_final: 0.8100 (p) REVERT: A 583 GLN cc_start: 0.7834 (mp10) cc_final: 0.7036 (pp30) REVERT: A 663 TYR cc_start: 0.8557 (t80) cc_final: 0.8049 (t80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1753 time to fit residues: 28.3715 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 : 0.311 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** 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 = 0.4205 r_free = 0.4205 target = 0.121834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.104967 restraints weight = 98100.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.108302 restraints weight = 55964.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.110505 restraints weight = 37151.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.111940 restraints weight = 27149.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.113045 restraints weight = 21619.395| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6920 Z= 0.234 Angle : 0.706 9.096 9695 Z= 0.374 Chirality : 0.047 0.890 1148 Planarity : 0.005 0.036 1002 Dihedral : 19.898 129.044 1718 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.42 % Favored : 90.12 % 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 aren not related in a simple way. whole: -1.34 (0.32), residues: 658 helix: -0.06 (0.37), residues: 201 sheet: -0.86 (0.46), residues: 128 loop : -1.40 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 428 TYR 0.017 0.003 TYR A 75 PHE 0.014 0.002 PHE A 521 TRP 0.014 0.002 TRP A 587 HIS 0.009 0.002 HIS A 724 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6916) covalent geometry : angle 0.70645 ( 9695) hydrogen bonds : bond 0.05083 ( 195) hydrogen bonds : angle 5.71472 ( 502) metal coordination : bond 0.00455 ( 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 : 0.321 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: A 96 GLN cc_start: 0.9189 (mt0) cc_final: 0.8973 (mt0) REVERT: A 243 PHE cc_start: 0.7489 (m-10) cc_final: 0.7258 (m-80) REVERT: A 416 MET cc_start: 0.5955 (mpp) cc_final: 0.5024 (mmt) REVERT: A 511 SER cc_start: 0.7543 (t) cc_final: 0.7218 (m) REVERT: A 663 TYR cc_start: 0.8737 (t80) cc_final: 0.8362 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1853 time to fit residues: 28.2089 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 : 0.300 ------------------------------------------------------------------------------- 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: 8.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.125965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.108741 restraints weight = 96083.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.112229 restraints weight = 54577.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.114510 restraints weight = 36199.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.115969 restraints weight = 26393.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.117182 restraints weight = 20997.652| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 0.037 6920 Z= 0.105 Angle : 0.554 9.079 9695 Z= 0.289 Chirality : 0.045 0.892 1148 Planarity : 0.004 0.043 1002 Dihedral : 19.545 124.751 1718 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.14 % 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 aren not related in a simple way. whole: -1.07 (0.32), residues: 658 helix: 0.41 (0.38), residues: 203 sheet: -0.65 (0.46), residues: 129 loop : -1.44 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.012 0.001 TYR A 354 PHE 0.007 0.001 PHE A 485 TRP 0.006 0.001 TRP A 433 HIS 0.007 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6916) covalent geometry : angle 0.55426 ( 9695) hydrogen bonds : bond 0.03264 ( 195) hydrogen bonds : angle 5.22674 ( 502) metal coordination : bond 0.00394 ( 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 115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.338 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 96 GLN cc_start: 0.9149 (mt0) cc_final: 0.8857 (mt0) REVERT: A 416 MET cc_start: 0.5924 (mpp) cc_final: 0.5176 (mmt) REVERT: A 663 TYR cc_start: 0.8512 (t80) cc_final: 0.8129 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1972 time to fit residues: 29.8092 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 : 0.307 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4234 r_free = 0.4234 target = 0.123876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107067 restraints weight = 96308.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.110469 restraints weight = 54851.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.112681 restraints weight = 36384.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.114235 restraints weight = 26773.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.115201 restraints weight = 20889.185| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6920 Z= 0.140 Angle : 0.565 9.125 9695 Z= 0.296 Chirality : 0.045 0.892 1148 Planarity : 0.004 0.044 1002 Dihedral : 19.699 125.787 1718 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.97 % Favored : 90.58 % 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 aren not related in a simple way. whole: -1.27 (0.32), residues: 658 helix: 0.22 (0.37), residues: 207 sheet: -0.79 (0.46), residues: 129 loop : -1.55 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.010 0.001 TYR A 463 PHE 0.010 0.001 PHE A 637 TRP 0.007 0.001 TRP A 587 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6916) covalent geometry : angle 0.56492 ( 9695) hydrogen bonds : bond 0.03522 ( 195) hydrogen bonds : angle 5.24210 ( 502) metal coordination : bond 0.00254 ( 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 : 0.340 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: 0.5940 (mpp) cc_final: 0.5207 (mmt) REVERT: A 583 GLN cc_start: 0.8044 (mp10) cc_final: 0.7842 (mp10) REVERT: A 663 TYR cc_start: 0.8553 (t80) cc_final: 0.8139 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1776 time to fit residues: 27.4912 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 : 0.313 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.121644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.104936 restraints weight = 97327.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.108077 restraints weight = 55590.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.110325 restraints weight = 38214.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.111864 restraints weight = 27683.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.112872 restraints weight = 21814.518| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4579 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= 0.155 Angle : 0.597 9.099 9695 Z= 0.314 Chirality : 0.046 0.892 1148 Planarity : 0.004 0.031 1002 Dihedral : 19.926 128.593 1718 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.27 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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 aren not related in a simple way. whole: -1.49 (0.32), residues: 658 helix: -0.01 (0.37), residues: 207 sheet: -0.88 (0.47), residues: 126 loop : -1.67 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.017 0.002 TYR A 329 PHE 0.011 0.002 PHE A 739 TRP 0.007 0.001 TRP A 587 HIS 0.010 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6916) covalent geometry : angle 0.59678 ( 9695) hydrogen bonds : bond 0.03563 ( 195) hydrogen bonds : angle 5.31376 ( 502) metal coordination : bond 0.00311 ( 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 120 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.412 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: 0.6017 (mpp) cc_final: 0.5322 (mmt) REVERT: A 663 TYR cc_start: 0.8556 (t80) cc_final: 0.8189 (t80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1922 time to fit residues: 30.5661 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 : 0.309 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.132638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.115232 restraints weight = 100738.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.118798 restraints weight = 57087.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.121032 restraints weight = 37395.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.122676 restraints weight = 27342.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.123522 restraints weight = 21116.700| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6920 Z= 0.150 Angle : 0.596 9.120 9695 Z= 0.314 Chirality : 0.046 0.893 1148 Planarity : 0.004 0.064 1002 Dihedral : 19.988 130.185 1718 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.27 % Favored : 90.27 % 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 aren not related in a simple way. whole: -1.57 (0.32), residues: 658 helix: -0.12 (0.37), residues: 206 sheet: -1.02 (0.46), residues: 126 loop : -1.64 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 623 TYR 0.024 0.002 TYR A 354 PHE 0.010 0.001 PHE A 521 TRP 0.005 0.001 TRP A 587 HIS 0.008 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6916) covalent geometry : angle 0.59641 ( 9695) hydrogen bonds : bond 0.03505 ( 195) hydrogen bonds : angle 5.26890 ( 502) metal coordination : bond 0.00277 ( 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: symmetry clash REVERT: A 416 MET cc_start: 0.6179 (mpp) cc_final: 0.5488 (mmt) REVERT: A 663 TYR cc_start: 0.8578 (t80) cc_final: 0.8212 (t80) REVERT: A 685 HIS cc_start: 0.7302 (t-90) cc_final: 0.6980 (t-90) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1828 time to fit residues: 27.6574 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 : 0.333 ------------------------------------------------------------------------------- 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: 3.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.133406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.115985 restraints weight = 100115.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.119570 restraints weight = 56778.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.121786 restraints weight = 37177.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.123497 restraints weight = 27235.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.124336 restraints weight = 20921.178| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6920 Z= 0.120 Angle : 0.565 9.142 9695 Z= 0.297 Chirality : 0.045 0.893 1148 Planarity : 0.004 0.034 1002 Dihedral : 19.971 131.497 1718 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.12 % Favored : 90.43 % 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 aren not related in a simple way. whole: -1.47 (0.32), residues: 658 helix: 0.03 (0.37), residues: 207 sheet: -1.09 (0.47), residues: 125 loop : -1.57 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.023 0.002 TYR A 354 PHE 0.008 0.001 PHE A 725 TRP 0.007 0.001 TRP A 357 HIS 0.007 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6916) covalent geometry : angle 0.56480 ( 9695) hydrogen bonds : bond 0.03198 ( 195) hydrogen bonds : angle 5.13530 ( 502) metal coordination : bond 0.00371 ( 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 117 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.317 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: 0.6162 (mpp) cc_final: 0.5475 (mmt) REVERT: A 663 TYR cc_start: 0.8541 (t80) cc_final: 0.8206 (t80) REVERT: A 685 HIS cc_start: 0.7321 (t-90) cc_final: 0.7032 (t-90) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1780 time to fit residues: 27.8499 Evaluate side-chains 100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN A 583 GLN ** A 727 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 = 0.4148 r_free = 0.4148 target = 0.117778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101572 restraints weight = 99835.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.104681 restraints weight = 56558.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.106979 restraints weight = 38627.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.108346 restraints weight = 27648.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.109508 restraints weight = 21972.245| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5674 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= 0.206 Angle : 0.654 9.119 9695 Z= 0.349 Chirality : 0.047 0.894 1148 Planarity : 0.005 0.034 1002 Dihedral : 20.501 135.880 1718 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.49 % Favored : 88.91 % 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 aren not related in a simple way. whole: -1.83 (0.32), residues: 658 helix: -0.43 (0.36), residues: 206 sheet: -1.26 (0.47), residues: 126 loop : -1.68 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 431 TYR 0.027 0.002 TYR A 354 PHE 0.017 0.002 PHE A 521 TRP 0.009 0.001 TRP A 587 HIS 0.009 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6916) covalent geometry : angle 0.65406 ( 9695) hydrogen bonds : bond 0.04165 ( 195) hydrogen bonds : angle 5.45792 ( 502) metal coordination : bond 0.00409 ( 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 113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.372 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: 0.6060 (mpp) cc_final: 0.5439 (mmt) REVERT: A 663 TYR cc_start: 0.8636 (t80) cc_final: 0.8343 (t80) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1783 time to fit residues: 26.9371 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 : 0.360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.119057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.102677 restraints weight = 99823.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105955 restraints weight = 56880.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.108283 restraints weight = 37723.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.109662 restraints weight = 27284.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.110835 restraints weight = 21813.315| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6920 Z= 0.148 Angle : 0.601 9.127 9695 Z= 0.318 Chirality : 0.046 0.896 1148 Planarity : 0.004 0.035 1002 Dihedral : 20.460 137.576 1718 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.03 % Favored : 89.51 % 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 aren not related in a simple way. whole: -1.87 (0.32), residues: 658 helix: -0.41 (0.36), residues: 211 sheet: -1.34 (0.46), residues: 126 loop : -1.72 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.024 0.002 TYR A 354 PHE 0.009 0.002 PHE A 521 TRP 0.011 0.001 TRP A 115 HIS 0.009 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6916) covalent geometry : angle 0.60110 ( 9695) hydrogen bonds : bond 0.03489 ( 195) hydrogen bonds : angle 5.35563 ( 502) metal coordination : bond 0.00322 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.98 seconds wall clock time: 44 minutes 52.92 seconds (2692.92 seconds total)