Starting phenix.real_space_refine on Mon Dec 30 06:40:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1f_39726/12_2024/8z1f_39726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1f_39726/12_2024/8z1f_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_39726/12_2024/8z1f_39726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1f_39726/12_2024/8z1f_39726.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1f_39726/12_2024/8z1f_39726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1f_39726/12_2024/8z1f_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-5532/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: 8.44, per 1000 atoms: 0.67 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: 4.19 Conformation dependent library (CDL) restraints added in 925.4 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: 6.24 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.731A pdb=" N GLN A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.685A pdb=" N LEU A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.889A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.562A pdb=" N LEU A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.532A pdb=" N ILE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.557A pdb=" N ARG A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.676A pdb=" N ASP A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.924A pdb=" N PHE A 361 " --> pdb=" O TRP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.007A pdb=" N VAL A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.617A pdb=" N GLY A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.571A pdb=" N GLN A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 4.116A pdb=" N TRP A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 670 through 678 removed outlier: 3.579A pdb=" N VAL A 674 " --> pdb=" O CYS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.530A pdb=" N LYS A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 removed outlier: 3.934A pdb=" N ASN A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 762 Processing helix chain 'A' and resid 763 through 772 removed outlier: 3.627A pdb=" N PHE A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.582A pdb=" N ARG A 82 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE A 109 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 84 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 432 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.593A pdb=" N TYR A 173 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 243 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 308 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 245 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 306 " --> pdb=" O CYS A 245 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA A 305 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 340 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 307 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N HIS A 342 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 309 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA4, first strand: chain 'A' and resid 482 through 484 Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA6, first strand: chain 'A' and resid 634 through 638 removed outlier: 3.773A pdb=" N GLU A 636 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 654 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 651 " --> pdb=" O TYR A 663 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 686 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 683 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 722 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 685 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS A 724 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 720 " --> pdb=" O GLY A 744 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.42 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: 3.610 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 43.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.040 ------------------------------------------------------------------------------- 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 6916 Z= 0.123 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 *********************** 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 : 1.008 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: 0.4075 time to fit residues: 64.6626 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 : 0.906 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 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 6916 Z= 0.200 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 *********************** 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 : 1.086 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 80 PHE cc_start: 0.8879 (m-10) cc_final: 0.8598 (m-80) REVERT: A 583 GLN cc_start: 0.7610 (mp10) cc_final: 0.7022 (pp30) REVERT: A 663 TYR cc_start: 0.8398 (t80) cc_final: 0.7965 (t80) REVERT: A 743 VAL cc_start: 0.8627 (m) cc_final: 0.8375 (p) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.3928 time to fit residues: 65.9233 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 : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 727 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6916 Z= 0.313 Angle : 0.688 9.099 9695 Z= 0.365 Chirality : 0.047 0.886 1148 Planarity : 0.004 0.042 1002 Dihedral : 19.743 128.563 1718 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.66 % Favored : 90.88 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.29 (0.32), residues: 658 helix: -0.16 (0.37), residues: 202 sheet: -0.66 (0.45), residues: 129 loop : -1.33 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 357 HIS 0.007 0.002 HIS A 724 PHE 0.026 0.002 PHE A 109 TYR 0.016 0.002 TYR A 354 ARG 0.013 0.001 ARG A 623 *********************** 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 114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.991 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: 0.5946 (mpp) cc_final: 0.5205 (mmt) REVERT: A 663 TYR cc_start: 0.8456 (t80) cc_final: 0.8137 (t80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3863 time to fit residues: 60.0981 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 : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6916 Z= 0.180 Angle : 0.567 9.053 9695 Z= 0.297 Chirality : 0.045 0.890 1148 Planarity : 0.004 0.029 1002 Dihedral : 19.535 124.329 1718 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.04 (0.32), residues: 658 helix: 0.34 (0.38), residues: 198 sheet: -0.62 (0.46), residues: 128 loop : -1.34 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 587 HIS 0.005 0.001 HIS A 98 PHE 0.009 0.001 PHE A 85 TYR 0.013 0.002 TYR A 354 ARG 0.003 0.000 ARG A 428 *********************** 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 114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.948 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: 0.5919 (mpp) cc_final: 0.5194 (mmt) REVERT: A 663 TYR cc_start: 0.8418 (t80) cc_final: 0.8053 (t80) REVERT: A 715 MET cc_start: 0.1643 (tpp) cc_final: 0.1410 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3647 time to fit residues: 56.4692 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 : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 457 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6916 Z= 0.263 Angle : 0.627 9.113 9695 Z= 0.330 Chirality : 0.046 0.893 1148 Planarity : 0.004 0.034 1002 Dihedral : 19.870 126.626 1718 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -1.46 (0.32), residues: 658 helix: 0.04 (0.37), residues: 200 sheet: -1.02 (0.46), residues: 128 loop : -1.56 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 587 HIS 0.008 0.002 HIS A 98 PHE 0.012 0.002 PHE A 739 TYR 0.016 0.002 TYR A 75 ARG 0.005 0.000 ARG A 428 *********************** 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 114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.976 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: 0.6023 (mpp) cc_final: 0.5311 (mmt) REVERT: A 663 TYR cc_start: 0.8506 (t80) cc_final: 0.8249 (t80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3733 time to fit residues: 57.9311 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 : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6916 Z= 0.176 Angle : 0.574 9.107 9695 Z= 0.300 Chirality : 0.046 0.893 1148 Planarity : 0.004 0.042 1002 Dihedral : 19.768 127.390 1718 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.21 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.39 (0.32), residues: 658 helix: 0.08 (0.37), residues: 206 sheet: -0.86 (0.48), residues: 119 loop : -1.58 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 587 HIS 0.007 0.001 HIS A 98 PHE 0.008 0.001 PHE A 485 TYR 0.009 0.001 TYR A 463 ARG 0.005 0.000 ARG A 430 *********************** 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 117 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.5991 (mpp) cc_final: 0.5302 (mmt) REVERT: A 634 LEU cc_start: 0.7290 (tp) cc_final: 0.7086 (tp) REVERT: A 637 PHE cc_start: 0.7269 (t80) cc_final: 0.6879 (t80) REVERT: A 663 TYR cc_start: 0.8438 (t80) cc_final: 0.8095 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4030 time to fit residues: 62.5707 Evaluate side-chains 102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6916 Z= 0.267 Angle : 0.649 9.114 9695 Z= 0.344 Chirality : 0.047 0.894 1148 Planarity : 0.004 0.032 1002 Dihedral : 20.238 131.268 1718 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.79 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -1.76 (0.32), residues: 658 helix: -0.38 (0.36), residues: 206 sheet: -1.15 (0.48), residues: 119 loop : -1.66 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 587 HIS 0.008 0.002 HIS A 724 PHE 0.013 0.002 PHE A 521 TYR 0.014 0.002 TYR A 463 ARG 0.004 0.001 ARG A 428 *********************** 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 : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.6029 (mpp) cc_final: 0.5343 (mmt) REVERT: A 634 LEU cc_start: 0.7354 (tp) cc_final: 0.7129 (tp) REVERT: A 637 PHE cc_start: 0.7279 (t80) cc_final: 0.6999 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3855 time to fit residues: 60.0188 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 : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 457 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6916 Z= 0.209 Angle : 0.608 9.113 9695 Z= 0.319 Chirality : 0.046 0.896 1148 Planarity : 0.004 0.036 1002 Dihedral : 20.228 133.396 1718 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 13.85 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: -1.70 (0.32), residues: 658 helix: -0.11 (0.37), residues: 198 sheet: -1.20 (0.48), residues: 119 loop : -1.72 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 587 HIS 0.009 0.001 HIS A 98 PHE 0.009 0.002 PHE A 739 TYR 0.017 0.002 TYR A 329 ARG 0.003 0.000 ARG A 534 *********************** 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 120 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.909 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: 0.6047 (mpp) cc_final: 0.5342 (mmt) REVERT: A 663 TYR cc_start: 0.8322 (t80) cc_final: 0.7981 (t80) REVERT: A 685 HIS cc_start: 0.7305 (t-90) cc_final: 0.7015 (t-90) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3830 time to fit residues: 62.1136 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 : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6916 Z= 0.226 Angle : 0.618 9.152 9695 Z= 0.326 Chirality : 0.046 0.896 1148 Planarity : 0.004 0.037 1002 Dihedral : 20.453 135.175 1718 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.49 % Favored : 89.06 % 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: -1.85 (0.32), residues: 658 helix: -0.46 (0.36), residues: 205 sheet: -1.27 (0.48), residues: 119 loop : -1.68 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 587 HIS 0.008 0.001 HIS A 98 PHE 0.011 0.002 PHE A 521 TYR 0.016 0.002 TYR A 329 ARG 0.005 0.000 ARG A 630 *********************** 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 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.975 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 329 TYR cc_start: 0.8527 (t80) cc_final: 0.8315 (t80) REVERT: A 416 MET cc_start: 0.6093 (mpp) cc_final: 0.5414 (mmt) REVERT: A 663 TYR cc_start: 0.8387 (t80) cc_final: 0.8059 (t80) REVERT: A 685 HIS cc_start: 0.7301 (t-90) cc_final: 0.6999 (t-90) REVERT: A 750 MET cc_start: 0.7796 (tmm) cc_final: 0.7132 (tmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.4089 time to fit residues: 64.7129 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6916 Z= 0.144 Angle : 0.566 9.166 9695 Z= 0.294 Chirality : 0.046 0.895 1148 Planarity : 0.004 0.035 1002 Dihedral : 20.213 134.934 1718 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.21 % Favored : 91.19 % 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 (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: -1.66 (0.32), residues: 658 helix: -0.01 (0.38), residues: 200 sheet: -1.41 (0.47), residues: 120 loop : -1.65 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.006 0.001 HIS A 98 PHE 0.008 0.001 PHE A 757 TYR 0.018 0.002 TYR A 329 ARG 0.004 0.000 ARG A 534 ********************** 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 121 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.921 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 329 TYR cc_start: 0.8389 (t80) cc_final: 0.8187 (t80) REVERT: A 416 MET cc_start: 0.6082 (mpp) cc_final: 0.5483 (mmt) REVERT: A 626 SER cc_start: 0.9287 (m) cc_final: 0.9054 (p) REVERT: A 663 TYR cc_start: 0.8268 (t80) cc_final: 0.7925 (t80) REVERT: A 685 HIS cc_start: 0.7235 (t-90) cc_final: 0.7004 (t-90) REVERT: A 715 MET cc_start: 0.2287 (tpp) cc_final: 0.1847 (tpp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.4010 time to fit residues: 64.3021 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 : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.121164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.104421 restraints weight = 95233.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.107817 restraints weight = 54714.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.110121 restraints weight = 36324.027| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6916 Z= 0.150 Angle : 0.559 9.183 9695 Z= 0.291 Chirality : 0.045 0.893 1148 Planarity : 0.004 0.031 1002 Dihedral : 20.164 134.753 1718 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.97 % Favored : 90.43 % 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: -1.56 (0.32), residues: 658 helix: 0.05 (0.38), residues: 201 sheet: -1.21 (0.47), residues: 125 loop : -1.63 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 357 HIS 0.006 0.001 HIS A 98 PHE 0.008 0.001 PHE A 725 TYR 0.017 0.002 TYR A 329 ARG 0.002 0.000 ARG A 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3625.07 seconds wall clock time: 65 minutes 30.80 seconds (3930.80 seconds total)