Starting phenix.real_space_refine on Wed Feb 4 09:37:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxn_61869/02_2026/9jxn_61869.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxn_61869/02_2026/9jxn_61869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxn_61869/02_2026/9jxn_61869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxn_61869/02_2026/9jxn_61869.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxn_61869/02_2026/9jxn_61869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxn_61869/02_2026/9jxn_61869.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.072 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6444 2.51 5 N 1596 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9748 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4874 Classifications: {'peptide': 587} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 566} Chain breaks: 2 Chain: "A" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4874 Classifications: {'peptide': 587} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 566} Chain breaks: 2 Time building chain proxies: 2.41, per 1000 atoms: 0.25 Number of scatterers: 9748 At special positions: 0 Unit cell: (104.445, 127.655, 100.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1668 8.00 N 1596 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 441.9 milliseconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 43 through 97 removed outlier: 3.890A pdb=" N VAL B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 168 removed outlier: 3.680A pdb=" N LEU B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.732A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.662A pdb=" N ARG B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.709A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.550A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.723A pdb=" N TYR B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.846A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.742A pdb=" N GLN B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 477 through 503 removed outlier: 3.654A pdb=" N TYR B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 533 Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.987A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 589 through 621 removed outlier: 4.351A pdb=" N VAL B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.669A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 12 through 16 Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 43 through 97 removed outlier: 3.889A pdb=" N VAL A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 168 removed outlier: 3.679A pdb=" N LEU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.733A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.660A pdb=" N ARG A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.709A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.549A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.722A pdb=" N TYR A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.845A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.742A pdb=" N GLN A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.654A pdb=" N TYR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 533 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.986A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 589 through 621 removed outlier: 4.459A pdb=" N VAL A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.668A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1488 1.27 - 1.41: 2872 1.41 - 1.54: 5606 1.54 - 1.68: 8 1.68 - 1.81: 56 Bond restraints: 10030 Sorted by residual: bond pdb=" C GLY A 155 " pdb=" O GLY A 155 " ideal model delta sigma weight residual 1.236 1.138 0.098 1.08e-02 8.57e+03 8.15e+01 bond pdb=" C GLY B 155 " pdb=" O GLY B 155 " ideal model delta sigma weight residual 1.235 1.154 0.081 1.23e-02 6.61e+03 4.32e+01 bond pdb=" C ARG A 157 " pdb=" O ARG A 157 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.19e-02 7.06e+03 4.00e+01 bond pdb=" C ILE A 159 " pdb=" O ILE A 159 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.23e-02 6.61e+03 3.78e+01 bond pdb=" C PHE B 156 " pdb=" O PHE B 156 " ideal model delta sigma weight residual 1.237 1.167 0.069 1.19e-02 7.06e+03 3.40e+01 ... (remaining 10025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 13554 4.39 - 8.79: 47 8.79 - 13.18: 3 13.18 - 17.57: 2 17.57 - 21.97: 2 Bond angle restraints: 13608 Sorted by residual: angle pdb=" C ILE A 591 " pdb=" CA ILE A 591 " pdb=" CB ILE A 591 " ideal model delta sigma weight residual 111.29 89.32 21.97 1.64e+00 3.72e-01 1.79e+02 angle pdb=" C ILE B 591 " pdb=" CA ILE B 591 " pdb=" CB ILE B 591 " ideal model delta sigma weight residual 111.29 90.34 20.95 1.64e+00 3.72e-01 1.63e+02 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 109.34 93.41 15.93 2.08e+00 2.31e-01 5.87e+01 angle pdb=" N ILE B 592 " pdb=" CA ILE B 592 " pdb=" C ILE B 592 " ideal model delta sigma weight residual 109.34 94.11 15.23 2.08e+00 2.31e-01 5.36e+01 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" CB ILE A 592 " ideal model delta sigma weight residual 111.23 123.28 -12.05 1.65e+00 3.67e-01 5.34e+01 ... (remaining 13603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4953 17.41 - 34.81: 661 34.81 - 52.22: 164 52.22 - 69.62: 38 69.62 - 87.03: 14 Dihedral angle restraints: 5830 sinusoidal: 2346 harmonic: 3484 Sorted by residual: dihedral pdb=" C ILE A 591 " pdb=" N ILE A 591 " pdb=" CA ILE A 591 " pdb=" CB ILE A 591 " ideal model delta harmonic sigma weight residual -122.00 -100.25 -21.75 0 2.50e+00 1.60e-01 7.57e+01 dihedral pdb=" C ILE B 591 " pdb=" N ILE B 591 " pdb=" CA ILE B 591 " pdb=" CB ILE B 591 " ideal model delta harmonic sigma weight residual -122.00 -101.61 -20.39 0 2.50e+00 1.60e-01 6.65e+01 dihedral pdb=" N ILE A 159 " pdb=" C ILE A 159 " pdb=" CA ILE A 159 " pdb=" CB ILE A 159 " ideal model delta harmonic sigma weight residual 123.40 135.53 -12.13 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 5827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1394 0.074 - 0.147: 85 0.147 - 0.221: 7 0.221 - 0.294: 1 0.294 - 0.368: 3 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA ILE A 591 " pdb=" N ILE A 591 " pdb=" C ILE A 591 " pdb=" CB ILE A 591 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ILE B 591 " pdb=" N ILE B 591 " pdb=" C ILE B 591 " pdb=" CB ILE B 591 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ILE A 159 " pdb=" N ILE A 159 " pdb=" C ILE A 159 " pdb=" CB ILE A 159 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 1487 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU A 160 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU A 160 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A 161 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 155 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLY B 155 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY B 155 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE B 156 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 157 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C ARG B 157 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG B 157 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B 158 " 0.018 2.00e-02 2.50e+03 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 69 2.47 - 3.08: 7213 3.08 - 3.69: 14917 3.69 - 4.29: 21042 4.29 - 4.90: 35527 Nonbonded interactions: 78768 Sorted by model distance: nonbonded pdb=" O ILE A 591 " pdb=" CG2 ILE A 591 " model vdw 1.863 3.460 nonbonded pdb=" CG2 ILE A 69 " pdb=" CE1 PHE A 185 " model vdw 1.957 3.760 nonbonded pdb=" CG2 ILE B 69 " pdb=" CE1 PHE B 185 " model vdw 1.959 3.760 nonbonded pdb=" CA GLU A 181 " pdb=" OH TYR A 186 " model vdw 2.018 3.470 nonbonded pdb=" CA GLU B 181 " pdb=" OH TYR B 186 " model vdw 2.035 3.470 ... (remaining 78763 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.250 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.005 0.129 10030 Z= 0.292 Angle : 0.752 21.968 13608 Z= 0.453 Chirality : 0.041 0.368 1490 Planarity : 0.004 0.058 1690 Dihedral : 17.001 87.029 3570 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 21.54 % Favored : 78.46 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.26), residues: 1162 helix: 2.53 (0.18), residues: 872 sheet: None (None), residues: 0 loop : -1.03 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 157 TYR 0.016 0.001 TYR A 186 PHE 0.019 0.001 PHE B 156 TRP 0.008 0.001 TRP A 607 HIS 0.006 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00527 (10030) covalent geometry : angle 0.75213 (13608) hydrogen bonds : bond 0.14752 ( 665) hydrogen bonds : angle 5.05891 ( 1971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1007 time to fit residues: 15.1648 Evaluate side-chains 97 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0170 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 476 HIS A 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117491 restraints weight = 12776.927| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.46 r_work: 0.3422 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10030 Z= 0.118 Angle : 0.506 8.240 13608 Z= 0.265 Chirality : 0.037 0.137 1490 Planarity : 0.003 0.038 1690 Dihedral : 3.693 18.643 1288 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.15 % Allowed : 21.15 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.26), residues: 1162 helix: 2.41 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.008 0.001 TYR B 73 PHE 0.019 0.001 PHE B 511 TRP 0.013 0.001 TRP A 266 HIS 0.002 0.000 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00264 (10030) covalent geometry : angle 0.50613 (13608) hydrogen bonds : bond 0.04229 ( 665) hydrogen bonds : angle 3.75141 ( 1971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.327 Fit side-chains REVERT: B 48 LYS cc_start: 0.8877 (mttm) cc_final: 0.8652 (mtmt) REVERT: B 129 LYS cc_start: 0.8369 (tptp) cc_final: 0.7977 (mptt) REVERT: B 208 ASP cc_start: 0.8314 (t70) cc_final: 0.7596 (t0) REVERT: B 383 THR cc_start: 0.8823 (m) cc_final: 0.8505 (p) REVERT: B 408 MET cc_start: 0.7572 (mtp) cc_final: 0.7290 (mtm) REVERT: A 129 LYS cc_start: 0.8359 (tptp) cc_final: 0.8001 (mptt) REVERT: A 208 ASP cc_start: 0.8301 (t70) cc_final: 0.7586 (t0) REVERT: A 383 THR cc_start: 0.8827 (m) cc_final: 0.8505 (p) REVERT: A 408 MET cc_start: 0.7595 (mtp) cc_final: 0.7302 (mtm) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.0931 time to fit residues: 14.9871 Evaluate side-chains 108 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 89 optimal weight: 0.0470 chunk 100 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116685 restraints weight = 12825.114| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.56 r_work: 0.3379 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10030 Z= 0.113 Angle : 0.471 8.039 13608 Z= 0.244 Chirality : 0.036 0.111 1490 Planarity : 0.003 0.029 1690 Dihedral : 3.642 18.568 1288 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.79 % Allowed : 20.19 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.25), residues: 1162 helix: 2.42 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -1.12 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.009 0.001 TYR A 345 PHE 0.011 0.001 PHE A 416 TRP 0.010 0.001 TRP B 395 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00253 (10030) covalent geometry : angle 0.47107 (13608) hydrogen bonds : bond 0.03837 ( 665) hydrogen bonds : angle 3.54199 ( 1971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.274 Fit side-chains REVERT: B 129 LYS cc_start: 0.8315 (tptp) cc_final: 0.8087 (mptt) REVERT: B 208 ASP cc_start: 0.8314 (t70) cc_final: 0.7567 (t0) REVERT: B 311 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8579 (mp) REVERT: B 383 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 549 GLU cc_start: 0.8785 (tt0) cc_final: 0.8165 (tp30) REVERT: A 129 LYS cc_start: 0.8351 (tptp) cc_final: 0.8108 (mptt) REVERT: A 208 ASP cc_start: 0.8304 (t70) cc_final: 0.7562 (t0) REVERT: A 311 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 383 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8476 (p) outliers start: 29 outliers final: 14 residues processed: 131 average time/residue: 0.0971 time to fit residues: 18.3457 Evaluate side-chains 118 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 591 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN B 499 HIS A 399 GLN A 499 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115858 restraints weight = 13066.919| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.59 r_work: 0.3371 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10030 Z= 0.109 Angle : 0.467 8.400 13608 Z= 0.242 Chirality : 0.036 0.115 1490 Planarity : 0.003 0.030 1690 Dihedral : 3.600 18.749 1288 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.94 % Allowed : 18.94 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.25), residues: 1162 helix: 2.45 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -1.05 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.012 0.001 TYR B 352 PHE 0.012 0.001 PHE B 336 TRP 0.010 0.001 TRP B 395 HIS 0.002 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00249 (10030) covalent geometry : angle 0.46689 (13608) hydrogen bonds : bond 0.03609 ( 665) hydrogen bonds : angle 3.43821 ( 1971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.390 Fit side-chains REVERT: B 92 GLN cc_start: 0.8398 (mp10) cc_final: 0.8181 (mp10) REVERT: B 383 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 408 MET cc_start: 0.7529 (mtp) cc_final: 0.7129 (mtm) REVERT: B 444 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.6910 (p) REVERT: B 529 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: B 549 GLU cc_start: 0.8776 (tt0) cc_final: 0.8182 (tp30) REVERT: A 92 GLN cc_start: 0.8409 (mp10) cc_final: 0.8195 (mp10) REVERT: A 129 LYS cc_start: 0.8331 (tptp) cc_final: 0.8106 (mptt) REVERT: A 383 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8424 (p) REVERT: A 408 MET cc_start: 0.7511 (mtp) cc_final: 0.7122 (mtm) REVERT: A 444 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6923 (p) REVERT: A 529 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7864 (m-30) outliers start: 41 outliers final: 18 residues processed: 140 average time/residue: 0.0911 time to fit residues: 18.7327 Evaluate side-chains 126 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 529 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 113 optimal weight: 0.0870 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.152548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113015 restraints weight = 13098.147| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.50 r_work: 0.3360 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10030 Z= 0.118 Angle : 0.474 8.710 13608 Z= 0.247 Chirality : 0.036 0.115 1490 Planarity : 0.003 0.031 1690 Dihedral : 3.636 19.107 1288 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.75 % Allowed : 19.71 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.25), residues: 1162 helix: 2.40 (0.17), residues: 886 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 211 TYR 0.009 0.001 TYR A 352 PHE 0.011 0.001 PHE A 610 TRP 0.009 0.001 TRP A 607 HIS 0.002 0.000 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00275 (10030) covalent geometry : angle 0.47437 (13608) hydrogen bonds : bond 0.03624 ( 665) hydrogen bonds : angle 3.43287 ( 1971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.422 Fit side-chains REVERT: B 92 GLN cc_start: 0.8361 (mp10) cc_final: 0.8069 (mp10) REVERT: B 383 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 408 MET cc_start: 0.7517 (mtp) cc_final: 0.7132 (mtm) REVERT: B 444 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.6883 (p) REVERT: B 549 GLU cc_start: 0.8782 (tt0) cc_final: 0.8183 (tp30) REVERT: A 48 LYS cc_start: 0.8914 (mttp) cc_final: 0.8556 (mtmt) REVERT: A 55 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 92 GLN cc_start: 0.8351 (mp10) cc_final: 0.8060 (mp10) REVERT: A 129 LYS cc_start: 0.8337 (tptp) cc_final: 0.8104 (mptt) REVERT: A 383 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8408 (p) REVERT: A 408 MET cc_start: 0.7512 (mtp) cc_final: 0.7127 (mtm) REVERT: A 444 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.6907 (p) outliers start: 39 outliers final: 23 residues processed: 139 average time/residue: 0.0895 time to fit residues: 18.4242 Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 551 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.151136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111305 restraints weight = 13189.181| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.71 r_work: 0.3321 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10030 Z= 0.137 Angle : 0.494 8.944 13608 Z= 0.257 Chirality : 0.037 0.116 1490 Planarity : 0.003 0.033 1690 Dihedral : 3.725 20.128 1288 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.46 % Allowed : 20.29 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.25), residues: 1162 helix: 2.33 (0.17), residues: 886 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.010 0.001 TYR A 73 PHE 0.013 0.001 PHE A 610 TRP 0.010 0.001 TRP B 573 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00325 (10030) covalent geometry : angle 0.49405 (13608) hydrogen bonds : bond 0.03794 ( 665) hydrogen bonds : angle 3.46405 ( 1971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.369 Fit side-chains REVERT: B 339 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8601 (pt) REVERT: B 372 PHE cc_start: 0.7386 (m-80) cc_final: 0.7087 (m-80) REVERT: B 383 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 408 MET cc_start: 0.7420 (mtp) cc_final: 0.7107 (mtm) REVERT: B 444 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7076 (p) REVERT: B 549 GLU cc_start: 0.8873 (tt0) cc_final: 0.8256 (tp30) REVERT: A 55 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 129 LYS cc_start: 0.8343 (tptp) cc_final: 0.8070 (mptt) REVERT: A 339 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8631 (pt) REVERT: A 372 PHE cc_start: 0.7392 (m-80) cc_final: 0.7094 (m-80) REVERT: A 383 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8520 (p) REVERT: A 408 MET cc_start: 0.7400 (mtp) cc_final: 0.7089 (mtm) REVERT: A 444 THR cc_start: 0.7453 (OUTLIER) cc_final: 0.7090 (p) REVERT: A 574 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8578 (p) outliers start: 36 outliers final: 22 residues processed: 137 average time/residue: 0.0931 time to fit residues: 18.6844 Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 574 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112534 restraints weight = 13071.960| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.58 r_work: 0.3323 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10030 Z= 0.130 Angle : 0.484 8.631 13608 Z= 0.252 Chirality : 0.036 0.114 1490 Planarity : 0.003 0.033 1690 Dihedral : 3.732 20.779 1288 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.46 % Allowed : 20.10 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.25), residues: 1162 helix: 2.37 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.009 0.001 TYR B 73 PHE 0.012 0.001 PHE B 610 TRP 0.010 0.001 TRP A 607 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00308 (10030) covalent geometry : angle 0.48440 (13608) hydrogen bonds : bond 0.03711 ( 665) hydrogen bonds : angle 3.45214 ( 1971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.400 Fit side-chains REVERT: B 339 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8607 (pt) REVERT: B 372 PHE cc_start: 0.7375 (m-80) cc_final: 0.7089 (m-80) REVERT: B 383 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8510 (p) REVERT: B 408 MET cc_start: 0.7433 (mtp) cc_final: 0.7140 (mtm) REVERT: B 444 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7102 (p) REVERT: B 549 GLU cc_start: 0.8855 (tt0) cc_final: 0.8250 (tp30) REVERT: B 574 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 55 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: A 129 LYS cc_start: 0.8325 (tptp) cc_final: 0.8053 (mptt) REVERT: A 339 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8613 (pt) REVERT: A 372 PHE cc_start: 0.7383 (m-80) cc_final: 0.7084 (m-80) REVERT: A 383 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 408 MET cc_start: 0.7413 (mtp) cc_final: 0.7128 (mtm) REVERT: A 444 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7133 (p) outliers start: 36 outliers final: 24 residues processed: 135 average time/residue: 0.0935 time to fit residues: 18.4695 Evaluate side-chains 136 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 551 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.151904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110849 restraints weight = 13223.857| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.59 r_work: 0.3316 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10030 Z= 0.136 Angle : 0.494 9.429 13608 Z= 0.256 Chirality : 0.037 0.115 1490 Planarity : 0.003 0.033 1690 Dihedral : 3.761 21.126 1288 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.17 % Allowed : 20.77 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1162 helix: 2.36 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 371 TYR 0.011 0.001 TYR A 352 PHE 0.013 0.001 PHE A 610 TRP 0.011 0.001 TRP A 607 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00322 (10030) covalent geometry : angle 0.49357 (13608) hydrogen bonds : bond 0.03761 ( 665) hydrogen bonds : angle 3.46492 ( 1971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.397 Fit side-chains REVERT: B 339 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8562 (pt) REVERT: B 372 PHE cc_start: 0.7404 (m-80) cc_final: 0.7111 (m-80) REVERT: B 383 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 408 MET cc_start: 0.7400 (mtp) cc_final: 0.7053 (mtm) REVERT: B 444 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7159 (p) REVERT: B 549 GLU cc_start: 0.8859 (tt0) cc_final: 0.8263 (tp30) REVERT: B 574 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 23 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: A 55 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: A 129 LYS cc_start: 0.8347 (tptp) cc_final: 0.8075 (mptt) REVERT: A 339 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8602 (pt) REVERT: A 372 PHE cc_start: 0.7432 (m-80) cc_final: 0.7130 (m-80) REVERT: A 383 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 408 MET cc_start: 0.7433 (mtp) cc_final: 0.7156 (mtm) REVERT: A 444 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7182 (p) REVERT: A 574 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8574 (p) outliers start: 33 outliers final: 19 residues processed: 130 average time/residue: 0.1031 time to fit residues: 19.5015 Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 574 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.149701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110807 restraints weight = 13146.835| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.50 r_work: 0.3304 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10030 Z= 0.150 Angle : 0.506 9.380 13608 Z= 0.262 Chirality : 0.037 0.117 1490 Planarity : 0.003 0.033 1690 Dihedral : 3.813 21.653 1288 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.88 % Allowed : 21.35 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.25), residues: 1162 helix: 2.31 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 371 TYR 0.010 0.001 TYR B 352 PHE 0.013 0.001 PHE A 610 TRP 0.011 0.001 TRP A 607 HIS 0.003 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00359 (10030) covalent geometry : angle 0.50579 (13608) hydrogen bonds : bond 0.03876 ( 665) hydrogen bonds : angle 3.49902 ( 1971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.382 Fit side-chains REVERT: B 339 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8524 (pt) REVERT: B 372 PHE cc_start: 0.7462 (m-80) cc_final: 0.7157 (m-80) REVERT: B 383 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8532 (p) REVERT: B 408 MET cc_start: 0.7422 (mtp) cc_final: 0.7075 (mtm) REVERT: B 549 GLU cc_start: 0.8863 (tt0) cc_final: 0.8270 (tp30) REVERT: A 23 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: A 55 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 129 LYS cc_start: 0.8361 (tptp) cc_final: 0.8083 (mptt) REVERT: A 339 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8577 (pt) REVERT: A 372 PHE cc_start: 0.7475 (m-80) cc_final: 0.7177 (m-80) REVERT: A 383 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8528 (p) REVERT: A 408 MET cc_start: 0.7425 (mtp) cc_final: 0.7084 (mtm) REVERT: A 444 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7178 (p) REVERT: A 574 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8593 (p) outliers start: 30 outliers final: 21 residues processed: 126 average time/residue: 0.0900 time to fit residues: 16.5102 Evaluate side-chains 133 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114080 restraints weight = 13033.267| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.57 r_work: 0.3353 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10030 Z= 0.107 Angle : 0.477 9.627 13608 Z= 0.246 Chirality : 0.036 0.115 1490 Planarity : 0.003 0.034 1690 Dihedral : 3.698 21.106 1288 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.69 % Allowed : 21.73 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.25), residues: 1162 helix: 2.45 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 371 TYR 0.008 0.001 TYR B 73 PHE 0.010 0.001 PHE B 336 TRP 0.012 0.001 TRP B 573 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00241 (10030) covalent geometry : angle 0.47719 (13608) hydrogen bonds : bond 0.03474 ( 665) hydrogen bonds : angle 3.41063 ( 1971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.404 Fit side-chains REVERT: B 92 GLN cc_start: 0.8570 (mp10) cc_final: 0.8305 (mp10) REVERT: B 339 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8627 (pt) REVERT: B 372 PHE cc_start: 0.7291 (m-80) cc_final: 0.7053 (m-80) REVERT: B 383 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8434 (p) REVERT: B 408 MET cc_start: 0.7448 (mtp) cc_final: 0.7093 (mtm) REVERT: B 549 GLU cc_start: 0.8827 (tt0) cc_final: 0.8266 (tp30) REVERT: B 574 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 23 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: A 55 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 92 GLN cc_start: 0.8558 (mp10) cc_final: 0.8295 (mp10) REVERT: A 339 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8622 (pt) REVERT: A 372 PHE cc_start: 0.7353 (m-80) cc_final: 0.7113 (m-80) REVERT: A 408 MET cc_start: 0.7423 (mtp) cc_final: 0.7080 (mtm) REVERT: A 574 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8592 (p) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.0862 time to fit residues: 18.0250 Evaluate side-chains 138 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111115 restraints weight = 13101.034| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.63 r_work: 0.3325 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10030 Z= 0.131 Angle : 0.494 9.775 13608 Z= 0.255 Chirality : 0.037 0.135 1490 Planarity : 0.003 0.034 1690 Dihedral : 3.738 21.210 1288 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.88 % Allowed : 22.21 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.25), residues: 1162 helix: 2.41 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.009 0.001 TYR B 73 PHE 0.012 0.001 PHE B 610 TRP 0.018 0.001 TRP A 514 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00309 (10030) covalent geometry : angle 0.49422 (13608) hydrogen bonds : bond 0.03681 ( 665) hydrogen bonds : angle 3.44843 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.82 seconds wall clock time: 35 minutes 35.71 seconds (2135.71 seconds total)