Starting phenix.real_space_refine on Thu Jul 2 02:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx3_48708/07_2026/9mx3_48708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx3_48708/07_2026/9mx3_48708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mx3_48708/07_2026/9mx3_48708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx3_48708/07_2026/9mx3_48708.map" model { file = "/net/cci-nas-00/data/ceres_data/9mx3_48708/07_2026/9mx3_48708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx3_48708/07_2026/9mx3_48708.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 24 5.16 5 C 3606 2.51 5 N 1039 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5929 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5204 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 26, 'TRANS': 614} Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 360 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "B" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.26 Number of scatterers: 5929 At special positions: 0 Unit cell: (95.048, 93.304, 76.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 35 15.00 O 1225 8.00 N 1039 7.00 C 3606 6.00 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: 0.52 Conformation dependent library (CDL) restraints added in 325.5 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 54.6% alpha, 10.3% beta 13 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.844A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 49 through 52 removed outlier: 3.517A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.016A pdb=" N VAL A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.569A pdb=" N TRP A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.611A pdb=" N MET A 157 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 234 through 257 Processing helix chain 'A' and resid 262 through 283 Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 301 through 304 removed outlier: 4.237A pdb=" N SER A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 307 through 336 removed outlier: 3.573A pdb=" N ARG A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.601A pdb=" N VAL A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 364 removed outlier: 4.009A pdb=" N SER A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.844A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.622A pdb=" N GLU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 4.264A pdb=" N ALA A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.338A pdb=" N ASP A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 613 through 633 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 removed outlier: 4.087A pdb=" N THR A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG A 62 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 138 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 140 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 27 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 173 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 228 removed outlier: 5.767A pdb=" N LYS A 222 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 488 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 224 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 490 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 226 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A 370 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA A 444 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 372 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 582 removed outlier: 3.517A pdb=" N LYS A 575 " --> pdb=" O ARG A 595 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 577 " --> pdb=" O THR A 593 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1811 1.34 - 1.46: 1032 1.46 - 1.58: 3152 1.58 - 1.70: 67 1.70 - 1.82: 36 Bond restraints: 6098 Sorted by residual: bond pdb=" N1 C B 18 " pdb=" C6 C B 18 " ideal model delta sigma weight residual 1.367 1.359 0.008 6.00e-03 2.78e+04 1.83e+00 bond pdb=" N9 A B 16 " pdb=" C4 A B 16 " ideal model delta sigma weight residual 1.374 1.366 0.008 6.00e-03 2.78e+04 1.62e+00 bond pdb=" C5 A B 19 " pdb=" C4 A B 19 " ideal model delta sigma weight residual 1.383 1.375 0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CB PHE A 321 " pdb=" CG PHE A 321 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.30e-02 1.89e+03 1.19e+00 ... (remaining 6093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 8300 2.83 - 5.66: 66 5.66 - 8.49: 3 8.49 - 11.31: 2 11.31 - 14.14: 1 Bond angle restraints: 8372 Sorted by residual: angle pdb=" CB MET A 589 " pdb=" CG MET A 589 " pdb=" SD MET A 589 " ideal model delta sigma weight residual 112.70 126.84 -14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C1' C B 10 " pdb=" N1 C B 10 " pdb=" C2 C B 10 " ideal model delta sigma weight residual 118.80 123.48 -4.68 1.10e+00 8.26e-01 1.81e+01 angle pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sigma weight residual 118.80 123.13 -4.33 1.10e+00 8.26e-01 1.55e+01 angle pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C6 C C 8 " ideal model delta sigma weight residual 120.80 116.93 3.87 1.20e+00 6.94e-01 1.04e+01 angle pdb=" C1' U C 16 " pdb=" N1 U C 16 " pdb=" C2 U C 16 " ideal model delta sigma weight residual 117.70 121.38 -3.68 1.20e+00 6.94e-01 9.41e+00 ... (remaining 8367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 3367 19.55 - 39.09: 327 39.09 - 58.64: 95 58.64 - 78.19: 32 78.19 - 97.74: 4 Dihedral angle restraints: 3825 sinusoidal: 1928 harmonic: 1897 Sorted by residual: dihedral pdb=" C2' ADP A 701 " pdb=" C1' ADP A 701 " pdb=" N9 ADP A 701 " pdb=" C4 ADP A 701 " ideal model delta sinusoidal sigma weight residual 91.55 -175.50 -92.95 1 2.00e+01 2.50e-03 2.52e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 31.07 -91.07 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" O4' A B 22 " pdb=" C1' A B 22 " pdb=" N9 A B 22 " pdb=" C4 A B 22 " ideal model delta sinusoidal sigma weight residual 70.00 7.73 62.27 1 2.00e+01 2.50e-03 1.28e+01 ... (remaining 3822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 605 0.028 - 0.057: 215 0.057 - 0.085: 95 0.085 - 0.114: 39 0.114 - 0.142: 14 Chirality restraints: 968 Sorted by residual: chirality pdb=" C1' A B 22 " pdb=" O4' A B 22 " pdb=" C2' A B 22 " pdb=" N9 A B 22 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ASN A 423 " pdb=" N ASN A 423 " pdb=" C ASN A 423 " pdb=" CB ASN A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 965 not shown) Planarity restraints: 955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 580 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" CD GLU A 580 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU A 580 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 580 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 344 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 345 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 7 " -0.017 2.00e-02 2.50e+03 1.00e-02 2.26e+00 pdb=" N1 C C 7 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C C 7 " -0.000 2.00e-02 2.50e+03 pdb=" O2 C C 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C C 7 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C C 7 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C C 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C C 7 " -0.000 2.00e-02 2.50e+03 ... (remaining 952 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 712 2.75 - 3.29: 5744 3.29 - 3.82: 9579 3.82 - 4.36: 10809 4.36 - 4.90: 17997 Nonbonded interactions: 44841 Sorted by model distance: nonbonded pdb=" O2' C C 7 " pdb=" O5' C C 8 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 391 " pdb=" O PHE A 398 " model vdw 2.279 3.040 nonbonded pdb=" O ASP A 526 " pdb=" OG SER A 529 " model vdw 2.283 3.040 nonbonded pdb=" O LYS A 355 " pdb=" OG SER A 359 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 108 " model vdw 2.311 3.040 ... (remaining 44836 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 individual isotropic 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: 2.040 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.003 0.032 6098 Z= 0.181 Angle : 0.634 14.143 8372 Z= 0.377 Chirality : 0.040 0.142 968 Planarity : 0.004 0.041 955 Dihedral : 17.065 97.737 2585 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.68 % Allowed : 17.98 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.34), residues: 639 helix: 2.63 (0.30), residues: 306 sheet: 0.58 (0.48), residues: 96 loop : -0.81 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 311 TYR 0.010 0.001 TYR A 160 PHE 0.011 0.001 PHE A 498 TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 ( 6098) covalent geometry : angle 0.63362 / 0.38 ( 8372) hydrogen bonds : bond 0.17529 / 10.74 ( 288) hydrogen bonds : angle 4.92955 / 3.79 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8021 (ptm) REVERT: A 375 GLU cc_start: 0.8216 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 632 MET cc_start: 0.8629 (ttm) cc_final: 0.7875 (tmm) outliers start: 10 outliers final: 3 residues processed: 30 average time/residue: 0.5651 time to fit residues: 17.9076 Evaluate side-chains 25 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.107453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075945 restraints weight = 15434.610| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.13 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6098 Z= 0.136 Angle : 0.580 8.003 8372 Z= 0.299 Chirality : 0.040 0.150 968 Planarity : 0.004 0.040 955 Dihedral : 15.890 97.831 1205 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.87 % Allowed : 14.96 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.34), residues: 639 helix: 2.74 (0.29), residues: 309 sheet: 0.95 (0.48), residues: 103 loop : -0.93 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.011 0.001 TYR A 160 PHE 0.011 0.001 PHE A 141 TRP 0.003 0.001 TRP A 105 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 6098) covalent geometry : angle 0.57959 / 0.30 ( 8372) hydrogen bonds : bond 0.06728 / 4.66 ( 288) hydrogen bonds : angle 4.32887 / 3.24 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 20 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 356 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8537 (tm-30) REVERT: A 632 MET cc_start: 0.8286 (ttm) cc_final: 0.7915 (tmm) outliers start: 23 outliers final: 8 residues processed: 36 average time/residue: 0.4820 time to fit residues: 18.4690 Evaluate side-chains 27 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 550 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.106839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.075170 restraints weight = 15306.118| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.13 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6098 Z= 0.160 Angle : 0.576 9.017 8372 Z= 0.295 Chirality : 0.040 0.140 968 Planarity : 0.004 0.040 955 Dihedral : 15.825 97.986 1199 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.03 % Allowed : 15.29 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.34), residues: 639 helix: 2.75 (0.29), residues: 309 sheet: 0.70 (0.47), residues: 105 loop : -0.98 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.014 0.001 TYR A 160 PHE 0.012 0.001 PHE A 405 TRP 0.004 0.001 TRP A 105 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6098) covalent geometry : angle 0.57618 / 0.30 ( 8372) hydrogen bonds : bond 0.06395 / 4.47 ( 288) hydrogen bonds : angle 4.24559 / 3.19 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 22 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: A 375 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: A 539 MET cc_start: 0.9328 (mmm) cc_final: 0.8397 (mtm) REVERT: A 632 MET cc_start: 0.8246 (ttm) cc_final: 0.7888 (tmm) outliers start: 24 outliers final: 10 residues processed: 40 average time/residue: 0.4614 time to fit residues: 19.7117 Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.108458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076977 restraints weight = 15207.123| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.10 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6098 Z= 0.107 Angle : 0.542 10.113 8372 Z= 0.275 Chirality : 0.039 0.143 968 Planarity : 0.003 0.040 955 Dihedral : 15.741 97.463 1199 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.20 % Allowed : 15.46 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.34), residues: 639 helix: 2.76 (0.29), residues: 309 sheet: 0.91 (0.49), residues: 97 loop : -0.89 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.007 0.001 TYR A 160 PHE 0.008 0.001 PHE A 141 TRP 0.003 0.000 TRP A 105 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 6098) covalent geometry : angle 0.54246 / 0.27 ( 8372) hydrogen bonds : bond 0.05515 / 4.01 ( 288) hydrogen bonds : angle 3.97246 / 3.01 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 22 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 356 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: A 375 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 539 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8405 (mtm) outliers start: 25 outliers final: 10 residues processed: 39 average time/residue: 0.3408 time to fit residues: 14.3104 Evaluate side-chains 31 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 52 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.108399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076899 restraints weight = 15561.810| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 4.15 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6098 Z= 0.111 Angle : 0.559 10.917 8372 Z= 0.275 Chirality : 0.039 0.142 968 Planarity : 0.003 0.040 955 Dihedral : 15.689 97.732 1199 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.70 % Allowed : 16.81 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.34), residues: 639 helix: 2.75 (0.29), residues: 309 sheet: 0.89 (0.49), residues: 97 loop : -0.87 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 478 TYR 0.009 0.001 TYR A 160 PHE 0.008 0.001 PHE A 498 TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 6098) covalent geometry : angle 0.55901 / 0.27 ( 8372) hydrogen bonds : bond 0.05449 / 3.97 ( 288) hydrogen bonds : angle 3.88203 / 2.94 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 20 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9252 (pp) REVERT: A 356 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: A 539 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8414 (mtm) outliers start: 22 outliers final: 12 residues processed: 38 average time/residue: 0.4511 time to fit residues: 18.3159 Evaluate side-chains 34 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.108287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077142 restraints weight = 15599.081| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 4.15 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6098 Z= 0.114 Angle : 0.580 11.766 8372 Z= 0.279 Chirality : 0.039 0.141 968 Planarity : 0.003 0.040 955 Dihedral : 15.660 97.909 1199 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.69 % Allowed : 17.82 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.33), residues: 639 helix: 2.77 (0.29), residues: 309 sheet: 0.91 (0.49), residues: 97 loop : -0.86 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 311 TYR 0.009 0.001 TYR A 160 PHE 0.008 0.001 PHE A 498 TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6098) covalent geometry : angle 0.58018 / 0.28 ( 8372) hydrogen bonds : bond 0.05437 / 3.96 ( 288) hydrogen bonds : angle 3.86592 / 2.93 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9250 (pp) REVERT: A 356 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: A 375 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: A 539 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8397 (mtm) outliers start: 16 outliers final: 13 residues processed: 32 average time/residue: 0.4559 time to fit residues: 15.5336 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.108302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.077035 restraints weight = 15468.754| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.14 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6098 Z= 0.127 Angle : 0.607 12.477 8372 Z= 0.298 Chirality : 0.039 0.140 968 Planarity : 0.003 0.040 955 Dihedral : 15.640 98.035 1198 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.53 % Allowed : 17.48 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.34), residues: 639 helix: 2.61 (0.29), residues: 315 sheet: 0.97 (0.48), residues: 104 loop : -0.95 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 311 TYR 0.009 0.001 TYR A 160 PHE 0.009 0.001 PHE A 498 TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 6098) covalent geometry : angle 0.60731 / 0.30 ( 8372) hydrogen bonds : bond 0.05697 / 4.17 ( 288) hydrogen bonds : angle 3.87238 / 2.92 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 24 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9252 (pp) REVERT: A 356 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: A 375 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 539 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8435 (mtm) outliers start: 21 outliers final: 12 residues processed: 40 average time/residue: 0.4841 time to fit residues: 20.5975 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.108933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.077373 restraints weight = 15196.712| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.13 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6098 Z= 0.119 Angle : 0.583 13.097 8372 Z= 0.284 Chirality : 0.039 0.140 968 Planarity : 0.003 0.040 955 Dihedral : 15.605 98.037 1198 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.69 % Allowed : 18.66 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.34), residues: 639 helix: 2.65 (0.29), residues: 315 sheet: 0.97 (0.48), residues: 104 loop : -0.95 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.009 0.001 TYR A 160 PHE 0.009 0.001 PHE A 498 TRP 0.003 0.000 TRP A 105 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6098) covalent geometry : angle 0.58329 / 0.28 ( 8372) hydrogen bonds : bond 0.05473 / 3.99 ( 288) hydrogen bonds : angle 3.84311 / 2.90 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9236 (pp) REVERT: A 356 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: A 375 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: A 539 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8419 (mtm) outliers start: 16 outliers final: 10 residues processed: 32 average time/residue: 0.4853 time to fit residues: 16.5868 Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.109700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078080 restraints weight = 15315.540| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.18 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6098 Z= 0.109 Angle : 0.581 13.645 8372 Z= 0.281 Chirality : 0.039 0.139 968 Planarity : 0.003 0.040 955 Dihedral : 15.541 97.913 1198 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.69 % Allowed : 18.66 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.34), residues: 639 helix: 2.70 (0.29), residues: 315 sheet: 0.98 (0.49), residues: 104 loop : -0.92 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 311 TYR 0.007 0.001 TYR A 14 PHE 0.007 0.001 PHE A 65 TRP 0.002 0.000 TRP A 105 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6098) covalent geometry : angle 0.58114 / 0.28 ( 8372) hydrogen bonds : bond 0.05177 / 3.81 ( 288) hydrogen bonds : angle 3.64353 / 2.74 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9213 (pp) REVERT: A 356 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: A 375 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 539 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8336 (mtm) outliers start: 16 outliers final: 11 residues processed: 34 average time/residue: 0.3779 time to fit residues: 13.8061 Evaluate side-chains 34 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.106514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074620 restraints weight = 15361.951| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.14 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6098 Z= 0.210 Angle : 0.624 13.725 8372 Z= 0.314 Chirality : 0.041 0.143 968 Planarity : 0.004 0.038 955 Dihedral : 15.607 98.924 1198 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.69 % Allowed : 18.66 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.33), residues: 639 helix: 2.83 (0.29), residues: 303 sheet: 0.78 (0.48), residues: 107 loop : -0.98 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 462 TYR 0.019 0.002 TYR A 160 PHE 0.018 0.002 PHE A 498 TRP 0.008 0.001 TRP A 105 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 6098) covalent geometry : angle 0.62436 / 0.31 ( 8372) hydrogen bonds : bond 0.06445 / 4.46 ( 288) hydrogen bonds : angle 4.00347 / 2.97 ( 813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9235 (pp) REVERT: A 356 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: A 375 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: A 539 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8533 (mtm) outliers start: 16 outliers final: 10 residues processed: 33 average time/residue: 0.4964 time to fit residues: 17.4954 Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.107696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075779 restraints weight = 15495.889| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.17 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6098 Z= 0.137 Angle : 0.595 13.427 8372 Z= 0.292 Chirality : 0.039 0.139 968 Planarity : 0.003 0.039 955 Dihedral : 15.554 98.291 1198 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.69 % Allowed : 18.66 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.34), residues: 639 helix: 2.78 (0.29), residues: 309 sheet: 0.77 (0.48), residues: 107 loop : -1.14 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.011 0.001 TYR A 160 PHE 0.011 0.001 PHE A 498 TRP 0.004 0.001 TRP A 105 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6098) covalent geometry : angle 0.59507 / 0.29 ( 8372) hydrogen bonds : bond 0.05714 / 4.06 ( 288) hydrogen bonds : angle 3.82750 / 2.85 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1421.02 seconds wall clock time: 25 minutes 11.63 seconds (1511.63 seconds total)