Starting phenix.real_space_refine on Sat May 10 06:58:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw6_48678/05_2025/9mw6_48678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw6_48678/05_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_48678/05_2025/9mw6_48678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw6_48678/05_2025/9mw6_48678.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw6_48678/05_2025/9mw6_48678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw6_48678/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.69, per 1000 atoms: 0.86 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: 1.45 Conformation dependent library (CDL) restraints added in 674.5 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: 2.18 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: 2.07 Time building geometry restraints manager: 1.62 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: 1.630 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- 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 : 0.590 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: 0.1776 time to fit residues: 12.7783 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 : 0.561 ------------------------------------------------------------------------------- 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 = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.082589 restraints weight = 19924.418| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 5.48 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1075 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= 0.100 Angle : 0.517 6.558 7918 Z= 0.261 Chirality : 0.036 0.135 926 Planarity : 0.004 0.045 820 Dihedral : 15.769 78.308 1415 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.55 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 0.03178 ( 216) hydrogen bonds : angle 4.19875 ( 553) covalent geometry : bond 0.00206 ( 5687) covalent geometry : angle 0.51692 ( 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 : 0.514 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8044 (mmt) cc_final: 0.7783 (mmm) REVERT: A 31 LEU cc_start: 0.9063 (tp) cc_final: 0.8691 (tp) REVERT: A 43 MET cc_start: 0.9145 (mmm) cc_final: 0.8874 (mmm) REVERT: A 117 MET cc_start: 0.8352 (ptp) cc_final: 0.7833 (ptt) REVERT: A 125 ILE cc_start: 0.8156 (mm) cc_final: 0.7942 (tt) REVERT: A 143 GLU cc_start: 0.7770 (mp0) cc_final: 0.7278 (mp0) REVERT: A 355 LYS cc_start: 0.9640 (tppt) cc_final: 0.9283 (mttt) REVERT: A 501 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8889 (m-30) REVERT: A 550 MET cc_start: 0.9121 (tmm) cc_final: 0.8736 (tpp) REVERT: A 632 MET cc_start: 0.8731 (ppp) cc_final: 0.8439 (ppp) outliers start: 19 outliers final: 6 residues processed: 65 average time/residue: 0.1253 time to fit residues: 11.7254 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 : 0.518 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.104529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.075959 restraints weight = 20578.916| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 5.31 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5687 Z= 0.207 Angle : 0.604 6.237 7918 Z= 0.313 Chirality : 0.040 0.144 926 Planarity : 0.004 0.049 820 Dihedral : 15.642 76.351 1395 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.85 % Allowed : 22.11 % Favored : 74.04 % 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: -0.16 (0.38), residues: 531 helix: 1.04 (0.38), residues: 204 sheet: -0.35 (0.68), residues: 69 loop : -0.96 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 100 HIS 0.004 0.001 HIS A 409 PHE 0.014 0.002 PHE A 530 TYR 0.012 0.002 TYR A 560 ARG 0.003 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 216) hydrogen bonds : angle 4.39750 ( 553) covalent geometry : bond 0.00442 ( 5687) covalent geometry : angle 0.60358 ( 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 65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9068 (tp) cc_final: 0.8732 (tp) REVERT: A 43 MET cc_start: 0.9168 (mmm) cc_final: 0.8938 (mmm) REVERT: A 117 MET cc_start: 0.8714 (ptp) cc_final: 0.8092 (ptt) REVERT: A 143 GLU cc_start: 0.7805 (mp0) cc_final: 0.7333 (mp0) REVERT: A 355 LYS cc_start: 0.9643 (tppt) cc_final: 0.9308 (mttt) REVERT: A 384 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 388 ASN cc_start: 0.9474 (t0) cc_final: 0.9083 (m110) REVERT: A 448 VAL cc_start: 0.7791 (m) cc_final: 0.7420 (p) REVERT: A 550 MET cc_start: 0.9122 (tmm) cc_final: 0.8667 (tpp) REVERT: A 632 MET cc_start: 0.8735 (ppp) cc_final: 0.8418 (ppp) outliers start: 19 outliers final: 9 residues processed: 60 average time/residue: 0.1386 time to fit residues: 11.7966 Evaluate side-chains 55 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.107526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.078915 restraints weight = 20669.877| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 5.39 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1418 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= 0.109 Angle : 0.519 7.535 7918 Z= 0.261 Chirality : 0.036 0.137 926 Planarity : 0.004 0.047 820 Dihedral : 15.577 75.818 1395 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.43 % Allowed : 23.73 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.39), residues: 531 helix: 1.15 (0.38), residues: 209 sheet: -0.41 (0.76), residues: 57 loop : -0.67 (0.40), residues: 265 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 530 TYR 0.006 0.001 TYR A 217 ARG 0.002 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 216) hydrogen bonds : angle 3.99365 ( 553) covalent geometry : bond 0.00239 ( 5687) covalent geometry : angle 0.51929 ( 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: 12 poor density : 46 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9087 (tp) cc_final: 0.8723 (tp) REVERT: A 43 MET cc_start: 0.9166 (mmm) cc_final: 0.8902 (mmm) REVERT: A 117 MET cc_start: 0.8527 (ptp) cc_final: 0.7950 (ptt) REVERT: A 143 GLU cc_start: 0.7792 (mp0) cc_final: 0.7314 (mp0) REVERT: A 355 LYS cc_start: 0.9622 (tppt) cc_final: 0.9297 (mttt) REVERT: A 384 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7788 (t80) REVERT: A 387 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9003 (tp) REVERT: A 388 ASN cc_start: 0.9453 (t0) cc_final: 0.9039 (m110) REVERT: A 550 MET cc_start: 0.9030 (tmm) cc_final: 0.8822 (tpp) REVERT: A 632 MET cc_start: 0.8708 (ppp) cc_final: 0.8371 (ppp) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.1330 time to fit residues: 11.1186 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 : 0.563 ------------------------------------------------------------------------------- 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 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.0170 chunk 2 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.109643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.080367 restraints weight = 20106.146| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 5.49 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5687 Z= 0.096 Angle : 0.498 6.889 7918 Z= 0.250 Chirality : 0.036 0.136 926 Planarity : 0.004 0.046 820 Dihedral : 15.542 75.429 1395 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.84 % Allowed : 24.54 % 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: 0.18 (0.39), residues: 531 helix: 1.23 (0.39), residues: 209 sheet: -0.33 (0.74), residues: 57 loop : -0.64 (0.40), residues: 265 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 498 TYR 0.005 0.001 TYR A 357 ARG 0.003 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 216) hydrogen bonds : angle 3.79875 ( 553) covalent geometry : bond 0.00208 ( 5687) covalent geometry : angle 0.49833 ( 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 57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9049 (tp) cc_final: 0.8681 (tp) REVERT: A 43 MET cc_start: 0.9151 (mmm) cc_final: 0.8890 (mmm) REVERT: A 53 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.9143 (tpm170) REVERT: A 143 GLU cc_start: 0.7798 (mp0) cc_final: 0.7322 (mp0) REVERT: A 355 LYS cc_start: 0.9633 (tppt) cc_final: 0.9303 (mttt) REVERT: A 632 MET cc_start: 0.8744 (ppp) cc_final: 0.8400 (ppp) outliers start: 14 outliers final: 10 residues processed: 54 average time/residue: 0.1454 time to fit residues: 10.8744 Evaluate side-chains 50 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 53 ARG 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 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 598 ILE 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: 2.9990 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.108455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.080449 restraints weight = 20142.554| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 5.32 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1895 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= 0.103 Angle : 0.505 7.475 7918 Z= 0.252 Chirality : 0.036 0.136 926 Planarity : 0.004 0.046 820 Dihedral : 15.548 75.523 1395 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.43 % Allowed : 24.75 % Favored : 72.82 % 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: 0.14 (0.39), residues: 531 helix: 1.25 (0.39), residues: 210 sheet: -0.39 (0.65), residues: 69 loop : -0.72 (0.41), residues: 252 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 0.020 0.001 PHE A 56 TYR 0.015 0.001 TYR A 217 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 216) hydrogen bonds : angle 3.74033 ( 553) covalent geometry : bond 0.00228 ( 5687) covalent geometry : angle 0.50457 ( 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 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9046 (tp) cc_final: 0.8676 (tp) REVERT: A 53 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.9093 (tpm170) REVERT: A 143 GLU cc_start: 0.7750 (mp0) cc_final: 0.7293 (mp0) REVERT: A 355 LYS cc_start: 0.9643 (tppt) cc_final: 0.9303 (mttt) REVERT: A 632 MET cc_start: 0.8697 (ppp) cc_final: 0.8339 (ppp) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.1499 time to fit residues: 10.6583 Evaluate side-chains 49 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.103767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.075761 restraints weight = 20429.773| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 5.22 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5687 Z= 0.223 Angle : 0.666 10.980 7918 Z= 0.334 Chirality : 0.040 0.197 926 Planarity : 0.005 0.050 820 Dihedral : 15.727 76.521 1395 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.65 % Allowed : 24.14 % Favored : 72.21 % 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: -0.46 (0.38), residues: 531 helix: 0.80 (0.37), residues: 213 sheet: -0.67 (0.66), residues: 68 loop : -1.15 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 100 HIS 0.004 0.001 HIS A 517 PHE 0.026 0.002 PHE A 56 TYR 0.012 0.002 TYR A 560 ARG 0.003 0.001 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.05346 ( 216) hydrogen bonds : angle 4.24939 ( 553) covalent geometry : bond 0.00480 ( 5687) covalent geometry : angle 0.66592 ( 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 61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9074 (tp) cc_final: 0.8716 (tp) REVERT: A 43 MET cc_start: 0.9066 (mmm) cc_final: 0.8721 (mmm) REVERT: A 53 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9023 (tpm170) REVERT: A 143 GLU cc_start: 0.7966 (mp0) cc_final: 0.7377 (mp0) REVERT: A 209 LEU cc_start: 0.8668 (mm) cc_final: 0.8014 (tp) REVERT: A 355 LYS cc_start: 0.9633 (tppt) cc_final: 0.9322 (mttt) REVERT: A 384 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 448 VAL cc_start: 0.7807 (m) cc_final: 0.7436 (p) REVERT: A 632 MET cc_start: 0.8632 (ppp) cc_final: 0.8189 (ppp) outliers start: 18 outliers final: 10 residues processed: 57 average time/residue: 0.2012 time to fit residues: 16.2390 Evaluate side-chains 52 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 360 ASN 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 Chi-restraints excluded: chain A residue 598 ILE 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: 0.8980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.0030 chunk 31 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5108 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.107376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079866 restraints weight = 19939.680| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 5.25 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2121 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= 0.100 Angle : 0.545 9.319 7918 Z= 0.266 Chirality : 0.036 0.146 926 Planarity : 0.004 0.046 820 Dihedral : 15.607 75.642 1395 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.83 % Allowed : 25.56 % 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: -0.03 (0.38), residues: 531 helix: 1.27 (0.39), residues: 204 sheet: -0.49 (0.73), residues: 57 loop : -0.92 (0.39), residues: 270 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 0.018 0.001 PHE A 56 TYR 0.004 0.001 TYR A 228 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 216) hydrogen bonds : angle 3.80809 ( 553) covalent geometry : bond 0.00221 ( 5687) covalent geometry : angle 0.54480 ( 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 52 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.570 Fit side-chains REVERT: A 31 LEU cc_start: 0.9076 (tp) cc_final: 0.8683 (tp) REVERT: A 43 MET cc_start: 0.9118 (mmm) cc_final: 0.8773 (mmm) REVERT: A 53 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.9059 (tpm170) REVERT: A 143 GLU cc_start: 0.7861 (mp0) cc_final: 0.7357 (mp0) REVERT: A 209 LEU cc_start: 0.8580 (mm) cc_final: 0.7938 (tp) REVERT: A 355 LYS cc_start: 0.9618 (tppt) cc_final: 0.9342 (mttt) REVERT: A 632 MET cc_start: 0.8631 (ppp) cc_final: 0.8169 (ppp) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1619 time to fit residues: 10.9321 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 : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG 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 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.107892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080285 restraints weight = 19832.143| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 5.27 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 5687 Z= 0.104 Angle : 0.583 12.508 7918 Z= 0.276 Chirality : 0.037 0.158 926 Planarity : 0.004 0.047 820 Dihedral : 15.582 75.488 1395 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.23 % Allowed : 25.35 % Favored : 72.41 % 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: 1.13 (0.38), residues: 210 sheet: -0.29 (0.74), residues: 57 loop : -0.76 (0.40), residues: 264 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 0.018 0.001 PHE A 56 TYR 0.009 0.001 TYR A 217 ARG 0.001 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 216) hydrogen bonds : angle 3.75885 ( 553) covalent geometry : bond 0.00237 ( 5687) covalent geometry : angle 0.58282 ( 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 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9048 (tp) cc_final: 0.8650 (tp) REVERT: A 43 MET cc_start: 0.9118 (mmm) cc_final: 0.8808 (mmm) REVERT: A 53 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.9020 (tpm170) REVERT: A 120 GLN cc_start: 0.8653 (tp40) cc_final: 0.8444 (tp-100) REVERT: A 143 GLU cc_start: 0.7844 (mp0) cc_final: 0.7408 (mp0) REVERT: A 209 LEU cc_start: 0.8571 (mm) cc_final: 0.7906 (tp) REVERT: A 355 LYS cc_start: 0.9630 (tppt) cc_final: 0.9350 (mttt) REVERT: A 632 MET cc_start: 0.8617 (ppp) cc_final: 0.8147 (ppp) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.1607 time to fit residues: 11.7797 Evaluate side-chains 52 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 134 SER 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 539 MET Chi-restraints excluded: chain A residue 556 LEU 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: 8.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.0010 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 overall best weight: 0.2922 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.109932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.081976 restraints weight = 20411.753| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 5.58 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2481 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= 0.097 Angle : 0.569 11.161 7918 Z= 0.270 Chirality : 0.036 0.146 926 Planarity : 0.004 0.047 820 Dihedral : 15.578 75.382 1395 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.22 % Allowed : 26.17 % 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: 0.16 (0.39), residues: 531 helix: 1.31 (0.39), residues: 205 sheet: -0.08 (0.72), residues: 59 loop : -0.79 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 145 PHE 0.016 0.001 PHE A 56 TYR 0.004 0.001 TYR A 153 ARG 0.001 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.02668 ( 216) hydrogen bonds : angle 3.65771 ( 553) covalent geometry : bond 0.00221 ( 5687) covalent geometry : angle 0.56905 ( 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 50 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.540 Fit side-chains REVERT: A 31 LEU cc_start: 0.9022 (tp) cc_final: 0.8618 (tp) REVERT: A 43 MET cc_start: 0.9160 (mmm) cc_final: 0.8845 (mmm) REVERT: A 53 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.9089 (tpm170) REVERT: A 120 GLN cc_start: 0.8553 (tp40) cc_final: 0.8308 (tp-100) REVERT: A 143 GLU cc_start: 0.7774 (mp0) cc_final: 0.7341 (mp0) REVERT: A 209 LEU cc_start: 0.8541 (mm) cc_final: 0.7882 (tp) REVERT: A 355 LYS cc_start: 0.9596 (tppt) cc_final: 0.9322 (mttt) REVERT: A 632 MET cc_start: 0.8657 (ppp) cc_final: 0.8180 (ppp) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.1499 time to fit residues: 10.1105 Evaluate side-chains 49 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG 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 539 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 0.0570 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 54 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.6456 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.109420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.081459 restraints weight = 20178.026| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 5.55 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5687 Z= 0.101 Angle : 0.587 12.319 7918 Z= 0.273 Chirality : 0.037 0.173 926 Planarity : 0.004 0.048 820 Dihedral : 15.592 75.421 1395 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.03 % Allowed : 25.35 % 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: 0.12 (0.39), residues: 531 helix: 1.10 (0.39), residues: 211 sheet: -0.05 (0.72), residues: 59 loop : -0.71 (0.41), residues: 261 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 0.016 0.001 PHE A 56 TYR 0.009 0.001 TYR A 217 ARG 0.002 0.000 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 216) hydrogen bonds : angle 3.66656 ( 553) covalent geometry : bond 0.00232 ( 5687) covalent geometry : angle 0.58720 ( 7918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.00 seconds wall clock time: 46 minutes 59.50 seconds (2819.50 seconds total)