Starting phenix.real_space_refine on Thu May 15 00:18:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1f_39726/05_2025/8z1f_39726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1f_39726/05_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_39726/05_2025/8z1f_39726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1f_39726/05_2025/8z1f_39726.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1f_39726/05_2025/8z1f_39726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1f_39726/05_2025/8z1f_39726.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.24, per 1000 atoms: 0.58 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: 3.85 Conformation dependent library (CDL) restraints added in 893.1 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: 5.85 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: 4.80 Time building geometry restraints manager: 3.87 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: 3.710 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: 0.200 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 38.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP A 357 HIS 0.004 0.001 HIS A 527 PHE 0.007 0.001 PHE A 543 TYR 0.017 0.001 TYR A 354 ARG 0.001 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.21755 ( 195) hydrogen bonds : angle 7.71093 ( 502) metal coordination : bond 0.00204 ( 4) covalent geometry : bond 0.00195 ( 6916) covalent geometry : angle 0.51646 ( 9695) *********************** 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 : 0.897 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: 0.3801 time to fit residues: 60.0641 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 : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 114 HIS A 342 HIS ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.132864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.112630 restraints weight = 79192.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116973 restraints weight = 42575.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.119829 restraints weight = 26623.673| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6920 Z= 0.143 Angle : 0.561 9.062 9695 Z= 0.295 Chirality : 0.045 0.881 1148 Planarity : 0.004 0.046 1002 Dihedral : 18.992 118.236 1718 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.38 % Favored : 93.31 % Rotamer: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.34), residues: 658 helix: 1.25 (0.41), residues: 186 sheet: -0.09 (0.47), residues: 131 loop : -0.80 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 357 HIS 0.006 0.001 HIS A 114 PHE 0.012 0.001 PHE A 521 TYR 0.012 0.001 TYR A 354 ARG 0.006 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 195) hydrogen bonds : angle 5.76677 ( 502) metal coordination : bond 0.00444 ( 4) covalent geometry : bond 0.00299 ( 6916) covalent geometry : angle 0.56114 ( 9695) *********************** 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 127 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.839 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 583 GLN cc_start: 0.7832 (mp10) cc_final: 0.7160 (pp30) REVERT: A 663 TYR cc_start: 0.8692 (t80) cc_final: 0.8125 (t80) REVERT: A 743 VAL cc_start: 0.8786 (m) cc_final: 0.8567 (p) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.3704 time to fit residues: 62.2351 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 : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.134637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.114828 restraints weight = 80016.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.119264 restraints weight = 42523.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.122096 restraints weight = 26349.656| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6920 Z= 0.093 Angle : 0.510 9.073 9695 Z= 0.266 Chirality : 0.044 0.884 1148 Planarity : 0.004 0.048 1002 Dihedral : 18.956 118.682 1718 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.53 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.34), residues: 658 helix: 1.39 (0.42), residues: 186 sheet: -0.03 (0.46), residues: 130 loop : -0.90 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 357 HIS 0.005 0.001 HIS A 527 PHE 0.009 0.001 PHE A 109 TYR 0.010 0.001 TYR A 354 ARG 0.003 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 195) hydrogen bonds : angle 5.39465 ( 502) metal coordination : bond 0.00297 ( 4) covalent geometry : bond 0.00198 ( 6916) covalent geometry : angle 0.51012 ( 9695) *********************** 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 124 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.868 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: A 583 GLN cc_start: 0.7827 (mp10) cc_final: 0.7052 (pp30) REVERT: A 663 TYR cc_start: 0.8576 (t80) cc_final: 0.8006 (t80) REVERT: A 743 VAL cc_start: 0.8794 (m) cc_final: 0.8573 (p) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3629 time to fit residues: 59.5943 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 : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 HIS ** 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 = 0.4262 r_free = 0.4262 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.105961 restraints weight = 81906.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.109857 restraints weight = 43833.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.112587 restraints weight = 27893.961| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6920 Z= 0.190 Angle : 0.632 9.043 9695 Z= 0.334 Chirality : 0.046 0.886 1148 Planarity : 0.004 0.032 1002 Dihedral : 19.513 126.406 1718 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.21 % Favored : 91.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.32), residues: 658 helix: 0.13 (0.37), residues: 204 sheet: -0.37 (0.46), residues: 129 loop : -1.30 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 357 HIS 0.006 0.001 HIS A 724 PHE 0.014 0.002 PHE A 521 TYR 0.013 0.002 TYR A 354 ARG 0.007 0.001 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 195) hydrogen bonds : angle 5.45659 ( 502) metal coordination : bond 0.00404 ( 4) covalent geometry : bond 0.00408 ( 6916) covalent geometry : angle 0.63218 ( 9695) *********************** 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 117 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.859 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: 0.5953 (mpp) cc_final: 0.5211 (mmt) REVERT: A 634 LEU cc_start: 0.7300 (tp) cc_final: 0.7077 (tp) REVERT: A 663 TYR cc_start: 0.8563 (t80) cc_final: 0.8148 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3663 time to fit residues: 57.6679 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 : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 327 GLN A 457 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.117248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.097895 restraints weight = 82609.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.101635 restraints weight = 44715.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.104106 restraints weight = 28998.226| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6920 Z= 0.243 Angle : 0.727 9.177 9695 Z= 0.385 Chirality : 0.048 0.895 1148 Planarity : 0.005 0.058 1002 Dihedral : 20.280 130.782 1718 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.51 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.31), residues: 658 helix: -0.43 (0.36), residues: 200 sheet: -1.38 (0.45), residues: 128 loop : -1.80 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 587 HIS 0.013 0.002 HIS A 724 PHE 0.018 0.003 PHE A 637 TYR 0.026 0.003 TYR A 75 ARG 0.007 0.001 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 195) hydrogen bonds : angle 5.87777 ( 502) metal coordination : bond 0.00707 ( 4) covalent geometry : bond 0.00510 ( 6916) covalent geometry : angle 0.72690 ( 9695) *********************** 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 113 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.818 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: 0.5953 (mpp) cc_final: 0.5194 (mmt) REVERT: A 653 LEU cc_start: 0.9357 (mt) cc_final: 0.9141 (mt) REVERT: A 663 TYR cc_start: 0.8581 (t80) cc_final: 0.8231 (t80) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.3656 time to fit residues: 55.4791 Evaluate side-chains 101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 8 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 92 GLN A 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.134002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.116207 restraints weight = 100601.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.119806 restraints weight = 56691.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.122202 restraints weight = 37098.040| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6920 Z= 0.115 Angle : 0.586 9.113 9695 Z= 0.306 Chirality : 0.046 0.896 1148 Planarity : 0.004 0.045 1002 Dihedral : 19.951 130.091 1718 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.81 % Favored : 90.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.32), residues: 658 helix: 0.15 (0.38), residues: 199 sheet: -1.17 (0.46), residues: 125 loop : -1.67 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 587 HIS 0.006 0.001 HIS A 98 PHE 0.007 0.001 PHE A 154 TYR 0.012 0.002 TYR A 354 ARG 0.003 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 195) hydrogen bonds : angle 5.26575 ( 502) metal coordination : bond 0.00445 ( 4) covalent geometry : bond 0.00250 ( 6916) covalent geometry : angle 0.58572 ( 9695) *********************** 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 : 0.821 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 262 MET cc_start: 0.6956 (tmm) cc_final: 0.6575 (ppp) REVERT: A 416 MET cc_start: 0.6147 (mpp) cc_final: 0.5396 (mmt) REVERT: A 653 LEU cc_start: 0.9340 (mt) cc_final: 0.9073 (mt) REVERT: A 663 TYR cc_start: 0.8476 (t80) cc_final: 0.8119 (t80) REVERT: A 685 HIS cc_start: 0.7262 (t-90) cc_final: 0.6986 (t-90) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.4146 time to fit residues: 63.2352 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.124123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.107288 restraints weight = 95183.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.110643 restraints weight = 55088.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.112896 restraints weight = 36622.979| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6920 Z= 0.102 Angle : 0.552 9.166 9695 Z= 0.287 Chirality : 0.045 0.894 1148 Planarity : 0.004 0.047 1002 Dihedral : 19.826 129.003 1718 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.60 % Favored : 91.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.32), residues: 658 helix: 0.38 (0.38), residues: 200 sheet: -1.02 (0.46), residues: 124 loop : -1.58 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 115 HIS 0.005 0.001 HIS A 98 PHE 0.008 0.001 PHE A 316 TYR 0.023 0.002 TYR A 354 ARG 0.004 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 195) hydrogen bonds : angle 5.07576 ( 502) metal coordination : bond 0.00646 ( 4) covalent geometry : bond 0.00224 ( 6916) covalent geometry : angle 0.55162 ( 9695) *********************** 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 115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.867 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 416 MET cc_start: 0.5996 (mpp) cc_final: 0.5266 (mmt) REVERT: A 663 TYR cc_start: 0.8578 (t80) cc_final: 0.8342 (t80) REVERT: A 685 HIS cc_start: 0.7297 (t-90) cc_final: 0.7038 (t-90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3670 time to fit residues: 56.0921 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 : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4168 r_free = 0.4168 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.098744 restraints weight = 84567.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.102618 restraints weight = 45505.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105184 restraints weight = 29177.928| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5129 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= 0.194 Angle : 0.641 9.124 9695 Z= 0.338 Chirality : 0.047 0.893 1148 Planarity : 0.004 0.035 1002 Dihedral : 20.265 131.455 1718 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.73 % Favored : 89.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.32), residues: 658 helix: -0.11 (0.37), residues: 200 sheet: -1.31 (0.46), residues: 125 loop : -1.69 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 587 HIS 0.008 0.001 HIS A 724 PHE 0.013 0.002 PHE A 725 TYR 0.021 0.002 TYR A 354 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 195) hydrogen bonds : angle 5.38110 ( 502) metal coordination : bond 0.00362 ( 4) covalent geometry : bond 0.00406 ( 6916) covalent geometry : angle 0.64100 ( 9695) *********************** 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 111 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.859 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: 0.6020 (mpp) cc_final: 0.5283 (mmt) REVERT: A 663 TYR cc_start: 0.8653 (t80) cc_final: 0.8231 (t80) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3658 time to fit residues: 55.3429 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.120692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.104439 restraints weight = 97934.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.107739 restraints weight = 55318.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.109860 restraints weight = 36661.079| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6920 Z= 0.127 Angle : 0.584 9.129 9695 Z= 0.304 Chirality : 0.046 0.895 1148 Planarity : 0.004 0.036 1002 Dihedral : 20.187 133.381 1718 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 11.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.32), residues: 658 helix: 0.05 (0.38), residues: 198 sheet: -1.34 (0.46), residues: 125 loop : -1.70 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 115 HIS 0.005 0.001 HIS A 98 PHE 0.007 0.001 PHE A 521 TYR 0.024 0.002 TYR A 354 ARG 0.003 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 195) hydrogen bonds : angle 5.22690 ( 502) metal coordination : bond 0.00365 ( 4) covalent geometry : bond 0.00271 ( 6916) covalent geometry : angle 0.58410 ( 9695) *********************** 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 116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.890 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 172 GLU cc_start: 0.6985 (pm20) cc_final: 0.6768 (pm20) REVERT: A 416 MET cc_start: 0.6011 (mpp) cc_final: 0.5308 (mmt) REVERT: A 626 SER cc_start: 0.9395 (m) cc_final: 0.9150 (p) REVERT: A 663 TYR cc_start: 0.8537 (t80) cc_final: 0.8182 (t80) REVERT: A 685 HIS cc_start: 0.7221 (t-90) cc_final: 0.6980 (t-90) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3566 time to fit residues: 55.8885 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 : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 8 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.123989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.107219 restraints weight = 94746.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.110558 restraints weight = 54423.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.112824 restraints weight = 36399.799| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6920 Z= 0.095 Angle : 0.559 9.187 9695 Z= 0.288 Chirality : 0.046 0.893 1148 Planarity : 0.004 0.038 1002 Dihedral : 19.981 132.484 1718 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.75 % Favored : 91.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.32), residues: 658 helix: 0.43 (0.40), residues: 190 sheet: -1.22 (0.46), residues: 125 loop : -1.58 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 115 HIS 0.006 0.001 HIS A 114 PHE 0.009 0.001 PHE A 637 TYR 0.021 0.001 TYR A 354 ARG 0.003 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 195) hydrogen bonds : angle 4.97200 ( 502) metal coordination : bond 0.00808 ( 4) covalent geometry : bond 0.00206 ( 6916) covalent geometry : angle 0.55935 ( 9695) ********************** 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 116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.893 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: 0.9160 (mt0) cc_final: 0.8940 (mt0) REVERT: A 416 MET cc_start: 0.6091 (mpp) cc_final: 0.5376 (mmt) REVERT: A 480 TYR cc_start: 0.8963 (m-80) cc_final: 0.8662 (m-10) REVERT: A 583 GLN cc_start: 0.8943 (mm110) cc_final: 0.8191 (mp10) REVERT: A 626 SER cc_start: 0.9388 (m) cc_final: 0.9149 (p) REVERT: A 663 TYR cc_start: 0.8592 (t80) cc_final: 0.8290 (t80) REVERT: A 685 HIS cc_start: 0.7295 (t-90) cc_final: 0.7056 (t-90) REVERT: A 715 MET cc_start: 0.2073 (tpp) cc_final: 0.1692 (tpp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3605 time to fit residues: 56.5496 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 : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 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 = 0.4143 r_free = 0.4143 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100800 restraints weight = 99947.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.104031 restraints weight = 57259.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.106049 restraints weight = 38038.102| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6920 Z= 0.210 Angle : 0.668 9.127 9695 Z= 0.354 Chirality : 0.047 0.892 1148 Planarity : 0.005 0.035 1002 Dihedral : 20.526 136.200 1718 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.94 % Favored : 88.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.32), residues: 658 helix: -0.32 (0.37), residues: 199 sheet: -1.54 (0.46), residues: 125 loop : -1.71 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 587 HIS 0.010 0.002 HIS A 724 PHE 0.017 0.002 PHE A 725 TYR 0.021 0.002 TYR A 329 ARG 0.005 0.001 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 195) hydrogen bonds : angle 5.41060 ( 502) metal coordination : bond 0.00734 ( 4) covalent geometry : bond 0.00435 ( 6916) covalent geometry : angle 0.66828 ( 9695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4670.92 seconds wall clock time: 81 minutes 43.44 seconds (4903.44 seconds total)