Starting phenix.real_space_refine on Sun Apr 27 10:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw6_48678/04_2025/9mw6_48678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw6_48678/04_2025/9mw6_48678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw6_48678/04_2025/9mw6_48678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw6_48678/04_2025/9mw6_48678.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw6_48678/04_2025/9mw6_48678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw6_48678/04_2025/9mw6_48678.cif" } resolution = 3.4 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= -0.001 sd= 0.011 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 52 5.49 5 S 23 5.16 5 C 3259 2.51 5 N 958 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5473 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4334 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 25, 'TRANS': 509} Chain breaks: 1 Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 573 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna3p': 26} Time building chain proxies: 4.24, per 1000 atoms: 0.77 Number of scatterers: 5473 At special positions: 0 Unit cell: (74.12, 91.56, 106.384, 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 23 16.00 P 52 15.00 O 1181 8.00 N 958 7.00 C 3259 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: 1.46 Conformation dependent library (CDL) restraints added in 648.8 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 48.0% alpha, 11.0% beta 27 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 4.159A pdb=" N LEU A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.711A pdb=" N ALA A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 3.889A 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: 3.811A pdb=" N VAL A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.586A pdb=" N MET A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.835A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.650A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 187 through 200 removed outlier: 4.293A pdb=" N LYS A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.705A pdb=" N GLN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.701A pdb=" N LYS A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.649A pdb=" N TYR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.687A pdb=" N ILE A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.502A pdb=" N GLY A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 494 through 516 removed outlier: 3.766A pdb=" N CYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 4.065A pdb=" N ASP A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.756A pdb=" N LEU A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 632 removed outlier: 3.895A pdb=" N LYS A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.578A pdb=" N VAL A 116 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ARG A 62 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 139 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 64 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 141 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU A 66 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN A 137 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU A 172 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU A 139 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU A 174 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 141 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 28 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 228 removed outlier: 3.580A pdb=" N TYR A 486 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 228 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.602A pdb=" N GLY A 370 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA A 444 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 372 " --> pdb=" O ALA A 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 582 removed outlier: 3.520A pdb=" N ILE A 579 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 591 " --> pdb=" O ILE A 579 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1548 1.34 - 1.46: 1346 1.46 - 1.58: 2654 1.58 - 1.70: 104 1.70 - 1.82: 35 Bond restraints: 5687 Sorted by residual: bond pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA LYS A 436 " pdb=" CB LYS A 436 " ideal model delta sigma weight residual 1.529 1.551 -0.023 1.64e-02 3.72e+03 1.92e+00 bond pdb=" CB LYS A 436 " pdb=" CG LYS A 436 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CA GLY A 408 " pdb=" C GLY A 408 " ideal model delta sigma weight residual 1.514 1.498 0.016 1.41e-02 5.03e+03 1.28e+00 bond pdb=" C LYS A 87 " pdb=" N VAL A 88 " ideal model delta sigma weight residual 1.332 1.321 0.011 1.36e-02 5.41e+03 6.19e-01 ... (remaining 5682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 7854 2.37 - 4.73: 53 4.73 - 7.10: 2 7.10 - 9.46: 5 9.46 - 11.83: 4 Bond angle restraints: 7918 Sorted by residual: angle pdb=" CA LYS A 436 " pdb=" CB LYS A 436 " pdb=" CG LYS A 436 " ideal model delta sigma weight residual 114.10 123.87 -9.77 2.00e+00 2.50e-01 2.39e+01 angle pdb=" CB LYS A 436 " pdb=" CG LYS A 436 " pdb=" CD LYS A 436 " ideal model delta sigma weight residual 111.30 121.05 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " pdb=" CD LYS A 355 " ideal model delta sigma weight residual 111.30 120.93 -9.63 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CA LYS A 355 " pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 ... (remaining 7913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3056 17.89 - 35.78: 346 35.78 - 53.67: 100 53.67 - 71.56: 50 71.56 - 89.45: 15 Dihedral angle restraints: 3567 sinusoidal: 1987 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ALA A 444 " pdb=" C ALA A 444 " pdb=" N THR A 445 " pdb=" CA THR A 445 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU A 507 " pdb=" CG GLU A 507 " pdb=" CD GLU A 507 " pdb=" OE1 GLU A 507 " ideal model delta sinusoidal sigma weight residual 0.00 89.45 -89.45 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA PHE A 405 " pdb=" C PHE A 405 " pdb=" N VAL A 406 " pdb=" CA VAL A 406 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 756 0.047 - 0.094: 136 0.094 - 0.141: 33 0.141 - 0.188: 0 0.188 - 0.235: 1 Chirality restraints: 926 Sorted by residual: chirality pdb=" CG LEU A 123 " pdb=" CB LEU A 123 " pdb=" CD1 LEU A 123 " pdb=" CD2 LEU A 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE A 454 " pdb=" N ILE A 454 " pdb=" C ILE A 454 " pdb=" CB ILE A 454 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA PRO A 152 " pdb=" N PRO A 152 " pdb=" C PRO A 152 " pdb=" CB PRO A 152 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 923 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 151 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 152 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B 26 " 0.025 2.00e-02 2.50e+03 1.29e-02 3.76e+00 pdb=" N1 C B 26 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C B 26 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C B 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C B 26 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C B 26 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C B 26 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C B 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B 26 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 436 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LYS A 436 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS A 436 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 437 " -0.010 2.00e-02 2.50e+03 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 5385 3.22 - 3.78: 9200 3.78 - 4.34: 11645 4.34 - 4.90: 17176 Nonbonded interactions: 43531 Sorted by model distance: nonbonded pdb=" O PRO A 597 " pdb=" OG SER A 600 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR A 69 " pdb=" OP1 C B 26 " model vdw 2.165 3.040 nonbonded pdb=" O LYS A 24 " pdb=" NH2 ARG A 170 " model vdw 2.256 3.120 nonbonded pdb=" OE1 GLU A 421 " pdb=" ND2 ASN A 423 " model vdw 2.275 3.120 nonbonded pdb=" OH TYR A 538 " pdb=" ND1 HIS A 630 " model vdw 2.275 3.120 ... (remaining 43526 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: 2.250 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.004 0.045 5687 Z= 0.165 Angle : 0.619 11.827 7918 Z= 0.310 Chirality : 0.038 0.235 926 Planarity : 0.004 0.049 820 Dihedral : 17.581 89.445 2537 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.43 % Allowed : 22.31 % Favored : 75.25 % 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: -0.15 (0.38), residues: 531 helix: 1.18 (0.39), residues: 197 sheet: -0.50 (0.62), residues: 80 loop : -0.96 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.004 0.001 HIS A 409 PHE 0.012 0.002 PHE A 530 TYR 0.008 0.001 TYR A 384 ARG 0.003 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.15234 ( 216) hydrogen bonds : angle 5.73045 ( 553) covalent geometry : bond 0.00351 ( 5687) covalent geometry : angle 0.61905 ( 7918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9036 (tp) cc_final: 0.8703 (tp) REVERT: A 43 MET cc_start: 0.9187 (mmm) cc_final: 0.8954 (mmm) REVERT: A 117 MET cc_start: 0.8630 (ptp) cc_final: 0.8038 (ptt) REVERT: A 143 GLU cc_start: 0.7754 (mp0) cc_final: 0.7265 (mp0) REVERT: A 355 LYS cc_start: 0.9605 (tppt) cc_final: 0.9221 (mttt) REVERT: A 448 VAL cc_start: 0.7649 (m) cc_final: 0.7287 (p) REVERT: A 462 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6607 (mmp80) REVERT: A 632 MET cc_start: 0.8723 (ppp) cc_final: 0.8449 (ppp) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.1730 time to fit residues: 12.2852 Evaluate side-chains 54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.0070 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.110066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.081533 restraints weight = 19999.791| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 5.46 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5687 Z= 0.098 Angle : 0.516 6.559 7918 Z= 0.261 Chirality : 0.036 0.135 926 Planarity : 0.004 0.045 820 Dihedral : 15.769 78.302 1415 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.85 % Allowed : 19.07 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.38), residues: 531 helix: 1.30 (0.38), residues: 204 sheet: -0.01 (0.67), residues: 73 loop : -0.87 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 100 HIS 0.002 0.001 HIS A 145 PHE 0.011 0.001 PHE A 400 TYR 0.010 0.001 TYR A 357 ARG 0.003 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 216) hydrogen bonds : angle 4.19965 ( 553) covalent geometry : bond 0.00206 ( 5687) covalent geometry : angle 0.51647 ( 7918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8044 (mmt) cc_final: 0.7784 (mmm) REVERT: A 31 LEU cc_start: 0.9069 (tp) cc_final: 0.8701 (tp) REVERT: A 43 MET cc_start: 0.9147 (mmm) cc_final: 0.8871 (mmm) REVERT: A 117 MET cc_start: 0.8353 (ptp) cc_final: 0.7827 (ptt) REVERT: A 125 ILE cc_start: 0.8151 (mm) cc_final: 0.7939 (tt) REVERT: A 143 GLU cc_start: 0.7789 (mp0) cc_final: 0.7290 (mp0) REVERT: A 355 LYS cc_start: 0.9640 (tppt) cc_final: 0.9283 (mttt) REVERT: A 501 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8890 (m-30) REVERT: A 550 MET cc_start: 0.9131 (tmm) cc_final: 0.8751 (tpp) REVERT: A 632 MET cc_start: 0.8716 (ppp) cc_final: 0.8419 (ppp) outliers start: 19 outliers final: 6 residues processed: 65 average time/residue: 0.1312 time to fit residues: 12.3928 Evaluate side-chains 50 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.0070 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN A 558 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.107130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.078377 restraints weight = 20210.618| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 5.39 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5687 Z= 0.137 Angle : 0.523 6.156 7918 Z= 0.268 Chirality : 0.037 0.138 926 Planarity : 0.004 0.048 820 Dihedral : 15.561 75.787 1395 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.04 % Allowed : 22.31 % Favored : 74.65 % 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: 0.15 (0.38), residues: 531 helix: 1.39 (0.39), residues: 203 sheet: -0.27 (0.74), residues: 59 loop : -0.81 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS A 517 PHE 0.010 0.001 PHE A 530 TYR 0.013 0.001 TYR A 217 ARG 0.002 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 216) hydrogen bonds : angle 4.10231 ( 553) covalent geometry : bond 0.00300 ( 5687) covalent geometry : angle 0.52318 ( 7918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9072 (tp) cc_final: 0.8742 (tp) REVERT: A 43 MET cc_start: 0.9145 (mmm) cc_final: 0.8886 (mmm) REVERT: A 117 MET cc_start: 0.8505 (ptp) cc_final: 0.7925 (ptt) REVERT: A 143 GLU cc_start: 0.7827 (mp0) cc_final: 0.7359 (mp0) REVERT: A 355 LYS cc_start: 0.9639 (tppt) cc_final: 0.9313 (mttt) REVERT: A 632 MET cc_start: 0.8715 (ppp) cc_final: 0.8390 (ppp) outliers start: 15 outliers final: 10 residues processed: 57 average time/residue: 0.1407 time to fit residues: 11.6063 Evaluate side-chains 51 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.110787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.082485 restraints weight = 20132.382| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 5.50 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.002 0.042 5687 Z= 0.100 Angle : 0.506 7.726 7918 Z= 0.254 Chirality : 0.036 0.135 926 Planarity : 0.004 0.047 820 Dihedral : 15.555 75.535 1395 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.84 % Allowed : 22.72 % Favored : 74.44 % 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: 0.29 (0.39), residues: 531 helix: 1.37 (0.39), residues: 209 sheet: -0.17 (0.74), residues: 59 loop : -0.66 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 PHE 0.008 0.001 PHE A 358 TYR 0.006 0.001 TYR A 217 ARG 0.003 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 216) hydrogen bonds : angle 3.84261 ( 553) covalent geometry : bond 0.00219 ( 5687) covalent geometry : angle 0.50649 ( 7918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9044 (tp) cc_final: 0.8671 (tp) REVERT: A 43 MET cc_start: 0.9148 (mmm) cc_final: 0.8880 (mmm) REVERT: A 117 MET cc_start: 0.8345 (ptp) cc_final: 0.7802 (ptt) REVERT: A 143 GLU cc_start: 0.7783 (mp0) cc_final: 0.7299 (mp0) REVERT: A 355 LYS cc_start: 0.9630 (tppt) cc_final: 0.9296 (mttt) REVERT: A 384 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7750 (t80) REVERT: A 388 ASN cc_start: 0.9400 (t0) cc_final: 0.8944 (m110) REVERT: A 501 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8947 (m-30) REVERT: A 632 MET cc_start: 0.8733 (ppp) cc_final: 0.8403 (ppp) outliers start: 14 outliers final: 7 residues processed: 57 average time/residue: 0.1556 time to fit residues: 12.4732 Evaluate side-chains 51 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.0060 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.105267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076754 restraints weight = 20642.628| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 5.39 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5687 Z= 0.197 Angle : 0.588 7.060 7918 Z= 0.302 Chirality : 0.039 0.143 926 Planarity : 0.004 0.050 820 Dihedral : 15.627 76.180 1395 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.04 % Allowed : 23.94 % Favored : 73.02 % 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: -0.07 (0.38), residues: 531 helix: 1.03 (0.38), residues: 213 sheet: -0.72 (0.66), residues: 67 loop : -0.75 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 100 HIS 0.004 0.001 HIS A 517 PHE 0.014 0.002 PHE A 530 TYR 0.011 0.001 TYR A 560 ARG 0.006 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 216) hydrogen bonds : angle 4.13286 ( 553) covalent geometry : bond 0.00422 ( 5687) covalent geometry : angle 0.58833 ( 7918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9064 (tp) cc_final: 0.8736 (tp) REVERT: A 117 MET cc_start: 0.8623 (ptp) cc_final: 0.8004 (ptt) REVERT: A 143 GLU cc_start: 0.7838 (mp0) cc_final: 0.7370 (mp0) REVERT: A 355 LYS cc_start: 0.9643 (tppt) cc_final: 0.9305 (mttt) REVERT: A 384 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7819 (t80) REVERT: A 388 ASN cc_start: 0.9466 (t0) cc_final: 0.9077 (m110) REVERT: A 632 MET cc_start: 0.8710 (ppp) cc_final: 0.8309 (ppp) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.1551 time to fit residues: 11.8277 Evaluate side-chains 51 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.108257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.080210 restraints weight = 20169.756| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 5.30 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5687 Z= 0.110 Angle : 0.536 7.864 7918 Z= 0.266 Chirality : 0.036 0.137 926 Planarity : 0.004 0.047 820 Dihedral : 15.586 75.711 1395 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.04 % Allowed : 24.34 % Favored : 72.62 % 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: -0.02 (0.38), residues: 531 helix: 1.12 (0.39), residues: 210 sheet: -0.55 (0.66), residues: 67 loop : -0.79 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 PHE 0.008 0.001 PHE A 358 TYR 0.005 0.001 TYR A 357 ARG 0.007 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 216) hydrogen bonds : angle 3.80684 ( 553) covalent geometry : bond 0.00253 ( 5687) covalent geometry : angle 0.53623 ( 7918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9065 (tp) cc_final: 0.8698 (tp) REVERT: A 43 MET cc_start: 0.9086 (mmm) cc_final: 0.8735 (mmm) REVERT: A 117 MET cc_start: 0.8419 (ptp) cc_final: 0.7852 (ptt) REVERT: A 143 GLU cc_start: 0.7798 (mp0) cc_final: 0.7307 (mp0) REVERT: A 355 LYS cc_start: 0.9635 (tppt) cc_final: 0.9303 (mttt) REVERT: A 384 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7775 (t80) REVERT: A 387 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9012 (tp) REVERT: A 388 ASN cc_start: 0.9425 (t0) cc_final: 0.8941 (m110) REVERT: A 632 MET cc_start: 0.8707 (ppp) cc_final: 0.8271 (ppp) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 0.1382 time to fit residues: 10.7950 Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.104521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.076376 restraints weight = 20481.218| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 5.30 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5687 Z= 0.190 Angle : 0.611 8.089 7918 Z= 0.308 Chirality : 0.039 0.143 926 Planarity : 0.004 0.049 820 Dihedral : 15.671 76.355 1395 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.65 % Allowed : 24.54 % Favored : 71.81 % 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: -0.41 (0.38), residues: 531 helix: 0.90 (0.38), residues: 213 sheet: -0.61 (0.69), residues: 66 loop : -1.18 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 100 HIS 0.003 0.001 HIS A 517 PHE 0.013 0.002 PHE A 530 TYR 0.015 0.002 TYR A 217 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 216) hydrogen bonds : angle 4.13129 ( 553) covalent geometry : bond 0.00412 ( 5687) covalent geometry : angle 0.61128 ( 7918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9069 (tp) cc_final: 0.8711 (tp) REVERT: A 43 MET cc_start: 0.9109 (mmm) cc_final: 0.8863 (mmm) REVERT: A 117 MET cc_start: 0.8662 (ptp) cc_final: 0.8060 (ptt) REVERT: A 143 GLU cc_start: 0.7851 (mp0) cc_final: 0.7366 (mp0) REVERT: A 209 LEU cc_start: 0.8632 (mm) cc_final: 0.7990 (tp) REVERT: A 355 LYS cc_start: 0.9630 (tppt) cc_final: 0.9314 (mttt) REVERT: A 384 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 388 ASN cc_start: 0.9488 (t0) cc_final: 0.9034 (m110) REVERT: A 632 MET cc_start: 0.8668 (ppp) cc_final: 0.8228 (ppp) outliers start: 18 outliers final: 12 residues processed: 55 average time/residue: 0.1809 time to fit residues: 14.3514 Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.0070 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.108865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.080383 restraints weight = 19920.034| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 5.45 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5687 Z= 0.102 Angle : 0.540 8.549 7918 Z= 0.265 Chirality : 0.036 0.144 926 Planarity : 0.004 0.046 820 Dihedral : 15.602 75.639 1395 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.03 % Allowed : 26.17 % Favored : 71.81 % 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: -0.08 (0.38), residues: 531 helix: 1.13 (0.39), residues: 210 sheet: -0.49 (0.72), residues: 57 loop : -0.92 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 PHE 0.008 0.001 PHE A 358 TYR 0.005 0.001 TYR A 228 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 216) hydrogen bonds : angle 3.77287 ( 553) covalent geometry : bond 0.00227 ( 5687) covalent geometry : angle 0.54004 ( 7918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9047 (tp) cc_final: 0.8631 (tp) REVERT: A 43 MET cc_start: 0.9098 (mmm) cc_final: 0.8826 (mmm) REVERT: A 117 MET cc_start: 0.8350 (ptp) cc_final: 0.7834 (ptt) REVERT: A 143 GLU cc_start: 0.7752 (mp0) cc_final: 0.7321 (mp0) REVERT: A 209 LEU cc_start: 0.8574 (mm) cc_final: 0.7918 (tp) REVERT: A 355 LYS cc_start: 0.9621 (tppt) cc_final: 0.9349 (mttt) REVERT: A 384 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 388 ASN cc_start: 0.9440 (t0) cc_final: 0.8944 (m110) REVERT: A 632 MET cc_start: 0.8659 (ppp) cc_final: 0.8205 (ppp) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.1440 time to fit residues: 10.2089 Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.106569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078847 restraints weight = 19950.857| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 5.27 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5687 Z= 0.117 Angle : 0.568 11.340 7918 Z= 0.273 Chirality : 0.037 0.178 926 Planarity : 0.004 0.048 820 Dihedral : 15.595 75.682 1395 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.23 % Allowed : 26.37 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.38), residues: 531 helix: 1.13 (0.39), residues: 212 sheet: -0.50 (0.72), residues: 57 loop : -0.95 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 100 HIS 0.002 0.001 HIS A 409 PHE 0.009 0.001 PHE A 530 TYR 0.017 0.001 TYR A 217 ARG 0.001 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 216) hydrogen bonds : angle 3.80513 ( 553) covalent geometry : bond 0.00259 ( 5687) covalent geometry : angle 0.56834 ( 7918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9056 (tp) cc_final: 0.8655 (tp) REVERT: A 117 MET cc_start: 0.8381 (ptp) cc_final: 0.7824 (ptt) REVERT: A 143 GLU cc_start: 0.7802 (mp0) cc_final: 0.7350 (mp0) REVERT: A 209 LEU cc_start: 0.8619 (mm) cc_final: 0.7943 (tp) REVERT: A 355 LYS cc_start: 0.9624 (tppt) cc_final: 0.9348 (mttt) REVERT: A 384 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 388 ASN cc_start: 0.9424 (t0) cc_final: 0.8902 (m110) REVERT: A 632 MET cc_start: 0.8641 (ppp) cc_final: 0.8181 (ppp) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.1442 time to fit residues: 10.0769 Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 11 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.109473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.081530 restraints weight = 20264.611| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 5.48 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5687 Z= 0.097 Angle : 0.570 11.812 7918 Z= 0.268 Chirality : 0.036 0.158 926 Planarity : 0.004 0.047 820 Dihedral : 15.590 75.442 1395 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.03 % Allowed : 26.77 % Favored : 71.20 % 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: 0.03 (0.39), residues: 531 helix: 1.23 (0.39), residues: 210 sheet: -0.23 (0.71), residues: 59 loop : -0.91 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 100 HIS 0.001 0.000 HIS A 83 PHE 0.009 0.001 PHE A 39 TYR 0.004 0.001 TYR A 14 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.02656 ( 216) hydrogen bonds : angle 3.67304 ( 553) covalent geometry : bond 0.00217 ( 5687) covalent geometry : angle 0.56951 ( 7918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9014 (tp) cc_final: 0.8609 (tp) REVERT: A 43 MET cc_start: 0.8757 (mmm) cc_final: 0.8386 (mmm) REVERT: A 117 MET cc_start: 0.8047 (ptp) cc_final: 0.7452 (ptt) REVERT: A 143 GLU cc_start: 0.7748 (mp0) cc_final: 0.7335 (mp0) REVERT: A 209 LEU cc_start: 0.8560 (mm) cc_final: 0.7890 (tp) REVERT: A 355 LYS cc_start: 0.9603 (tppt) cc_final: 0.9343 (mttt) REVERT: A 632 MET cc_start: 0.8667 (ppp) cc_final: 0.8190 (ppp) outliers start: 10 outliers final: 10 residues processed: 51 average time/residue: 0.1536 time to fit residues: 10.9510 Evaluate side-chains 52 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.108007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.080311 restraints weight = 20168.319| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 5.34 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5687 Z= 0.103 Angle : 0.588 12.957 7918 Z= 0.272 Chirality : 0.036 0.184 926 Planarity : 0.004 0.048 820 Dihedral : 15.595 75.517 1395 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.83 % Allowed : 26.98 % Favored : 71.20 % 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: 0.05 (0.39), residues: 531 helix: 1.25 (0.39), residues: 210 sheet: -0.21 (0.71), residues: 59 loop : -0.91 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 409 PHE 0.008 0.001 PHE A 530 TYR 0.018 0.001 TYR A 217 ARG 0.001 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 216) hydrogen bonds : angle 3.65523 ( 553) covalent geometry : bond 0.00230 ( 5687) covalent geometry : angle 0.58796 ( 7918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2714.27 seconds wall clock time: 47 minutes 30.23 seconds (2850.23 seconds total)