Starting phenix.real_space_refine on Tue Mar 3 22:18:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukt_20812/03_2026/6ukt_20812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukt_20812/03_2026/6ukt_20812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2026/6ukt_20812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2026/6ukt_20812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2026/6ukt_20812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2026/6ukt_20812.map" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.615 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 2 5.49 5 S 46 5.16 5 C 5613 2.51 5 N 1596 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3834 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 23, 'TRANS': 459} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2128 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 4, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "D" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 899 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 753 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 595 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 8, 'ASP:plan': 7, 'TRP:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 5, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 204 Time building chain proxies: 1.82, per 1000 atoms: 0.20 Number of scatterers: 8979 At special positions: 0 Unit cell: (134.62, 125.08, 90.1, 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 46 16.00 P 2 15.00 O 1722 8.00 N 1596 7.00 C 5613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 37.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 4.075A pdb=" N ASP A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.667A pdb=" N GLN A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.897A pdb=" N ASP A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.609A pdb=" N GLU A 102 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 103 " --> pdb=" O ILE A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.904A pdb=" N LEU A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.585A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 213 through 231 Processing helix chain 'A' and resid 240 through 259 removed outlier: 4.308A pdb=" N MET A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 4.379A pdb=" N ASN A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.125A pdb=" N ASP A 287 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 288 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 320 Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.141A pdb=" N CYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 371 through 381 removed outlier: 4.054A pdb=" N THR A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 5.095A pdb=" N VAL A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 446 through 451 removed outlier: 3.591A pdb=" N SER A 451 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.620A pdb=" N ALA A 479 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 480 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.211A pdb=" N VAL B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.616A pdb=" N ARG B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.675A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.910A pdb=" N ASP B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.907A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.565A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.911A pdb=" N GLY D 56 " --> pdb=" O TRP D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212 removed outlier: 3.922A pdb=" N LEU A 212 " --> pdb=" O ASP A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 40 removed outlier: 4.464A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 223 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 320 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.666A pdb=" N THR B 187 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 197 " --> pdb=" O THR B 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 57 through 58 removed outlier: 6.928A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 96 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.544A pdb=" N SER C 79 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.520A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 34 through 36 323 hydrogen bonds defined for protein. 894 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: 0.84 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2953 1.34 - 1.45: 1450 1.45 - 1.57: 4648 1.57 - 1.69: 7 1.69 - 1.81: 68 Bond restraints: 9126 Sorted by residual: bond pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O1P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O2P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C ASP A 439 " pdb=" N TPO A 440 " ideal model delta sigma weight residual 1.329 1.292 0.037 1.40e-02 5.10e+03 7.17e+00 bond pdb=" CB ARG A 219 " pdb=" CG ARG A 219 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.34e+00 ... (remaining 9121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11773 2.10 - 4.21: 483 4.21 - 6.31: 79 6.31 - 8.42: 26 8.42 - 10.52: 8 Bond angle restraints: 12369 Sorted by residual: angle pdb=" N MET A 467 " pdb=" CA MET A 467 " pdb=" C MET A 467 " ideal model delta sigma weight residual 111.07 117.41 -6.34 1.07e+00 8.73e-01 3.51e+01 angle pdb=" C SER A 402 " pdb=" N VAL A 403 " pdb=" CA VAL A 403 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.21e+01 angle pdb=" N ASN A 453 " pdb=" CA ASN A 453 " pdb=" C ASN A 453 " ideal model delta sigma weight residual 109.81 119.82 -10.01 2.21e+00 2.05e-01 2.05e+01 angle pdb=" C GLU A 444 " pdb=" N TYR A 445 " pdb=" CA TYR A 445 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" N LYS A 462 " pdb=" CA LYS A 462 " pdb=" C LYS A 462 " ideal model delta sigma weight residual 109.81 118.98 -9.17 2.21e+00 2.05e-01 1.72e+01 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4646 17.02 - 34.03: 654 34.03 - 51.05: 144 51.05 - 68.07: 21 68.07 - 85.09: 18 Dihedral angle restraints: 5483 sinusoidal: 2012 harmonic: 3471 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 164.34 -71.34 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 32.43 60.57 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CA LYS A 462 " pdb=" C LYS A 462 " pdb=" N PRO A 463 " pdb=" CA PRO A 463 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 5480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1175 0.076 - 0.151: 203 0.151 - 0.227: 22 0.227 - 0.302: 5 0.302 - 0.378: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB VAL A 330 " pdb=" CA VAL A 330 " pdb=" CG1 VAL A 330 " pdb=" CG2 VAL A 330 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASN A 453 " pdb=" N ASN A 453 " pdb=" C ASN A 453 " pdb=" CB ASN A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1403 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 374 " -0.022 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" CG ASN A 374 " 0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 374 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN A 374 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 357 " -0.056 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO A 358 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 87 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO D 88 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.038 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2117 2.78 - 3.31: 8601 3.31 - 3.84: 14469 3.84 - 4.37: 15140 4.37 - 4.90: 25071 Nonbonded interactions: 65398 Sorted by model distance: nonbonded pdb=" O SER A 335 " pdb=" OG1 THR A 338 " model vdw 2.247 3.040 nonbonded pdb=" O PRO A 213 " pdb=" OG1 THR A 217 " model vdw 2.256 3.040 nonbonded pdb=" O ASN A 26 " pdb=" OG SER A 30 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR C 97 " pdb=" O VAL C 100 " model vdw 2.279 3.040 nonbonded pdb=" O GLU A 15 " pdb=" OG1 THR A 19 " model vdw 2.284 3.040 ... (remaining 65393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.040 Find NCS groups from input model: 0.030 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.008 0.242 9132 Z= 0.449 Angle : 1.034 10.524 12375 Z= 0.565 Chirality : 0.058 0.378 1406 Planarity : 0.007 0.083 1623 Dihedral : 16.893 85.086 3232 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer: Outliers : 0.46 % Allowed : 13.30 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.19), residues: 1174 helix: -2.62 (0.19), residues: 385 sheet: -3.87 (0.37), residues: 120 loop : -3.85 (0.19), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG A 219 TYR 0.039 0.002 TYR E 107 PHE 0.029 0.003 PHE E 98 TRP 0.025 0.003 TRP F 114 HIS 0.006 0.002 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00681 ( 9126) covalent geometry : angle 1.03379 (12369) SS BOND : bond 0.00400 ( 3) SS BOND : angle 1.48262 ( 6) hydrogen bonds : bond 0.16089 ( 323) hydrogen bonds : angle 7.58346 ( 894) Misc. bond : bond 0.17814 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.8022 (t0) cc_final: 0.7811 (t0) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.1519 time to fit residues: 19.4700 Evaluate side-chains 80 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 229 ASN A 273 HIS ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN A 465 ASN A 477 HIS B 204 GLN B 241 ASN B 311 ASN D 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.059179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049583 restraints weight = 54396.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050931 restraints weight = 33562.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.051872 restraints weight = 24147.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052523 restraints weight = 19002.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052975 restraints weight = 15929.634| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9132 Z= 0.129 Angle : 0.654 7.002 12375 Z= 0.350 Chirality : 0.041 0.174 1406 Planarity : 0.005 0.073 1623 Dihedral : 6.370 58.803 1304 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.44 % Favored : 87.48 % Rotamer: Outliers : 1.26 % Allowed : 19.15 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.22), residues: 1174 helix: -0.98 (0.24), residues: 395 sheet: -3.70 (0.36), residues: 120 loop : -3.55 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 43 TYR 0.015 0.001 TYR A 445 PHE 0.030 0.001 PHE B 336 TRP 0.017 0.001 TRP F 114 HIS 0.003 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9126) covalent geometry : angle 0.65406 (12369) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.74566 ( 6) hydrogen bonds : bond 0.04095 ( 323) hydrogen bonds : angle 5.77366 ( 894) Misc. bond : bond 0.00061 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.9288 (mtp85) cc_final: 0.8581 (ptp-170) REVERT: A 133 MET cc_start: 0.9697 (mtp) cc_final: 0.9470 (ptp) REVERT: A 221 MET cc_start: 0.8354 (ttt) cc_final: 0.8153 (tpt) REVERT: A 229 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9017 (t0) REVERT: A 259 MET cc_start: 0.9179 (mtm) cc_final: 0.8904 (mtp) REVERT: A 380 MET cc_start: 0.9048 (ttm) cc_final: 0.8795 (ttm) REVERT: A 439 ASP cc_start: 0.9262 (t0) cc_final: 0.8947 (t0) REVERT: D 3 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8138 (mp10) outliers start: 11 outliers final: 3 residues processed: 99 average time/residue: 0.1621 time to fit residues: 19.8256 Evaluate side-chains 83 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 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 229 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.057636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048107 restraints weight = 55710.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049423 restraints weight = 34662.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050328 restraints weight = 25008.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050954 restraints weight = 19778.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051391 restraints weight = 16651.550| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9132 Z= 0.167 Angle : 0.663 6.752 12375 Z= 0.352 Chirality : 0.042 0.236 1406 Planarity : 0.005 0.067 1623 Dihedral : 6.093 54.355 1302 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.14 % Favored : 85.78 % Rotamer: Outliers : 1.95 % Allowed : 21.67 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.23), residues: 1174 helix: -0.36 (0.25), residues: 396 sheet: -3.69 (0.34), residues: 130 loop : -3.48 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 27 TYR 0.014 0.001 TYR B 230 PHE 0.019 0.002 PHE B 336 TRP 0.019 0.002 TRP F 114 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9126) covalent geometry : angle 0.66297 (12369) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.79883 ( 6) hydrogen bonds : bond 0.04032 ( 323) hydrogen bonds : angle 5.57623 ( 894) Misc. bond : bond 0.00015 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9694 (mtp) cc_final: 0.9468 (ptp) REVERT: A 259 MET cc_start: 0.9226 (mtm) cc_final: 0.9007 (mtp) REVERT: A 380 MET cc_start: 0.9092 (ttm) cc_final: 0.8861 (ttm) REVERT: A 439 ASP cc_start: 0.9288 (t0) cc_final: 0.8984 (t0) REVERT: B 171 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 354 PHE cc_start: 0.7772 (m-10) cc_final: 0.6648 (m-10) outliers start: 17 outliers final: 6 residues processed: 97 average time/residue: 0.1383 time to fit residues: 16.9095 Evaluate side-chains 83 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 42 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN B 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049798 restraints weight = 55631.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051157 restraints weight = 34271.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052114 restraints weight = 24560.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052762 restraints weight = 19306.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053224 restraints weight = 16176.081| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9132 Z= 0.117 Angle : 0.620 7.095 12375 Z= 0.325 Chirality : 0.041 0.172 1406 Planarity : 0.004 0.067 1623 Dihedral : 5.618 48.594 1302 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 2.06 % Allowed : 24.31 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.06 (0.23), residues: 1174 helix: 0.15 (0.27), residues: 389 sheet: -3.22 (0.36), residues: 127 loop : -3.33 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 75 TYR 0.013 0.001 TYR A 445 PHE 0.009 0.001 PHE A 162 TRP 0.012 0.001 TRP F 114 HIS 0.002 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9126) covalent geometry : angle 0.61987 (12369) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.78483 ( 6) hydrogen bonds : bond 0.03637 ( 323) hydrogen bonds : angle 5.13731 ( 894) Misc. bond : bond 0.00026 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.9690 (mtp) cc_final: 0.9473 (ptp) REVERT: A 259 MET cc_start: 0.9246 (mtm) cc_final: 0.9015 (mtp) REVERT: A 306 MET cc_start: 0.8188 (mmm) cc_final: 0.7984 (mmm) REVERT: A 439 ASP cc_start: 0.9242 (t0) cc_final: 0.8924 (t0) REVERT: A 467 MET cc_start: 0.8552 (tpp) cc_final: 0.8208 (tpp) REVERT: B 171 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 345 LYS cc_start: 0.9193 (tppp) cc_final: 0.8826 (tppp) REVERT: B 349 LYS cc_start: 0.9051 (ptpp) cc_final: 0.8678 (ptpp) REVERT: E 64 LYS cc_start: 0.9296 (mtpp) cc_final: 0.9078 (ttmm) outliers start: 18 outliers final: 10 residues processed: 102 average time/residue: 0.1473 time to fit residues: 18.9873 Evaluate side-chains 85 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** 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 = 0.3278 r_free = 0.3278 target = 0.060512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050814 restraints weight = 54897.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052183 restraints weight = 34183.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053127 restraints weight = 24425.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053788 restraints weight = 19134.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054266 restraints weight = 15992.071| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9132 Z= 0.114 Angle : 0.620 8.709 12375 Z= 0.326 Chirality : 0.041 0.364 1406 Planarity : 0.005 0.078 1623 Dihedral : 5.358 44.345 1302 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 2.06 % Allowed : 25.69 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.86 (0.23), residues: 1174 helix: 0.32 (0.27), residues: 389 sheet: -2.97 (0.38), residues: 127 loop : -3.24 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 27 TYR 0.012 0.001 TYR A 445 PHE 0.013 0.001 PHE B 336 TRP 0.010 0.001 TRP F 114 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9126) covalent geometry : angle 0.61970 (12369) SS BOND : bond 0.00515 ( 3) SS BOND : angle 0.39338 ( 6) hydrogen bonds : bond 0.03473 ( 323) hydrogen bonds : angle 4.96589 ( 894) Misc. bond : bond 0.00020 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7277 (mmt90) cc_final: 0.6336 (mmp80) REVERT: A 259 MET cc_start: 0.9278 (mtm) cc_final: 0.9006 (mtp) REVERT: A 344 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8780 (m170) REVERT: A 412 TYR cc_start: 0.8053 (p90) cc_final: 0.7808 (p90) REVERT: A 439 ASP cc_start: 0.9217 (t0) cc_final: 0.8876 (t0) REVERT: A 467 MET cc_start: 0.8444 (tpp) cc_final: 0.8146 (mpp) REVERT: B 171 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 198 MET cc_start: 0.8102 (mmm) cc_final: 0.7859 (mmt) REVERT: B 204 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: B 349 LYS cc_start: 0.9046 (ptpp) cc_final: 0.8709 (ptpp) REVERT: B 354 PHE cc_start: 0.7748 (m-80) cc_final: 0.7270 (m-80) REVERT: D 45 ARG cc_start: 0.8857 (mmt-90) cc_final: 0.8338 (mmt-90) REVERT: E 82 MET cc_start: 0.5343 (mmm) cc_final: 0.4631 (mmm) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 0.1418 time to fit residues: 17.5025 Evaluate side-chains 90 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047531 restraints weight = 55716.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048840 restraints weight = 34850.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049729 restraints weight = 25251.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.050357 restraints weight = 20047.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050788 restraints weight = 16922.345| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 : 0.004 0.048 9132 Z= 0.177 Angle : 0.674 9.538 12375 Z= 0.354 Chirality : 0.043 0.287 1406 Planarity : 0.006 0.105 1623 Dihedral : 5.643 37.146 1302 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 2.41 % Allowed : 26.72 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.24), residues: 1174 helix: 0.40 (0.27), residues: 389 sheet: -3.27 (0.37), residues: 126 loop : -3.23 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.015 0.001 TYR E 111 PHE 0.014 0.002 PHE B 336 TRP 0.020 0.002 TRP F 114 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9126) covalent geometry : angle 0.67410 (12369) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.41225 ( 6) hydrogen bonds : bond 0.03824 ( 323) hydrogen bonds : angle 5.19425 ( 894) Misc. bond : bond 0.00014 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.9252 (t0) cc_final: 0.8904 (t0) REVERT: A 458 ARG cc_start: 0.7256 (mmm160) cc_final: 0.7007 (mmm160) REVERT: A 467 MET cc_start: 0.8508 (tpp) cc_final: 0.8262 (tpp) REVERT: B 171 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 198 MET cc_start: 0.8291 (mmm) cc_final: 0.8010 (mmt) REVERT: B 208 ARG cc_start: 0.8801 (tpp80) cc_final: 0.7999 (mmt180) REVERT: B 214 CYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8878 (t) REVERT: B 345 LYS cc_start: 0.9263 (tppp) cc_final: 0.8865 (tppp) REVERT: B 349 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8694 (ptpp) REVERT: D 94 TYR cc_start: 0.8466 (m-10) cc_final: 0.8258 (m-10) REVERT: E 82 MET cc_start: 0.5420 (mmm) cc_final: 0.4433 (mmm) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 0.1374 time to fit residues: 16.1965 Evaluate side-chains 92 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** 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 = 0.3275 r_free = 0.3275 target = 0.060187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050489 restraints weight = 54318.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051845 restraints weight = 33514.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052797 restraints weight = 24017.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053460 restraints weight = 18876.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053928 restraints weight = 15787.679| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9132 Z= 0.117 Angle : 0.640 11.079 12375 Z= 0.332 Chirality : 0.041 0.275 1406 Planarity : 0.005 0.092 1623 Dihedral : 5.247 34.304 1302 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 2.29 % Allowed : 27.41 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1174 helix: 0.52 (0.27), residues: 388 sheet: -3.02 (0.39), residues: 124 loop : -3.14 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 27 TYR 0.012 0.001 TYR A 445 PHE 0.010 0.001 PHE A 162 TRP 0.008 0.001 TRP B 211 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9126) covalent geometry : angle 0.63962 (12369) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.52948 ( 6) hydrogen bonds : bond 0.03411 ( 323) hydrogen bonds : angle 4.89121 ( 894) Misc. bond : bond 0.00017 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7541 (mmt90) cc_final: 0.6357 (mmp80) REVERT: A 344 HIS cc_start: 0.9129 (OUTLIER) cc_final: 0.8765 (m170) REVERT: A 439 ASP cc_start: 0.9220 (t0) cc_final: 0.8848 (t0) REVERT: A 458 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6925 (mmm160) REVERT: A 467 MET cc_start: 0.8445 (tpp) cc_final: 0.8089 (mpp) REVERT: B 171 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 198 MET cc_start: 0.8273 (mmm) cc_final: 0.7981 (mmt) REVERT: B 208 ARG cc_start: 0.8796 (tpp80) cc_final: 0.7892 (mmt180) REVERT: B 349 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8714 (ptpp) REVERT: D 107 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6655 (tpm170) REVERT: E 82 MET cc_start: 0.5313 (mmm) cc_final: 0.4240 (mmm) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 0.1540 time to fit residues: 19.6775 Evaluate side-chains 90 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** 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 = 0.3318 r_free = 0.3318 target = 0.061786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052134 restraints weight = 53202.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053534 restraints weight = 32545.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054506 restraints weight = 23161.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055192 restraints weight = 18077.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055678 restraints weight = 15032.560| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9132 Z= 0.111 Angle : 0.629 11.323 12375 Z= 0.324 Chirality : 0.041 0.244 1406 Planarity : 0.005 0.086 1623 Dihedral : 4.932 31.630 1302 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.99 % Favored : 88.93 % Rotamer: Outliers : 2.64 % Allowed : 27.06 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.24), residues: 1174 helix: 0.63 (0.27), residues: 390 sheet: -2.77 (0.39), residues: 130 loop : -3.04 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.013 0.001 TYR A 412 PHE 0.009 0.001 PHE A 162 TRP 0.008 0.001 TRP B 131 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9126) covalent geometry : angle 0.62864 (12369) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.41715 ( 6) hydrogen bonds : bond 0.03233 ( 323) hydrogen bonds : angle 4.72573 ( 894) Misc. bond : bond 0.00016 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7361 (mmt90) cc_final: 0.6434 (mmp80) REVERT: A 306 MET cc_start: 0.8108 (mmm) cc_final: 0.7829 (mmm) REVERT: A 439 ASP cc_start: 0.9106 (t0) cc_final: 0.8739 (t0) REVERT: A 458 ARG cc_start: 0.7192 (mmm160) cc_final: 0.6926 (mmm160) REVERT: B 171 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 204 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: B 214 CYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8788 (t) REVERT: B 349 LYS cc_start: 0.9060 (ptpp) cc_final: 0.8569 (pttm) REVERT: C 81 GLN cc_start: 0.9098 (mt0) cc_final: 0.8876 (mm-40) REVERT: D 107 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6685 (tpm170) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 0.1399 time to fit residues: 17.8148 Evaluate side-chains 93 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.0070 chunk 109 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051697 restraints weight = 53856.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053104 restraints weight = 32907.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054056 restraints weight = 23386.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054735 restraints weight = 18244.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055221 restraints weight = 15144.278| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9132 Z= 0.120 Angle : 0.664 12.099 12375 Z= 0.341 Chirality : 0.041 0.237 1406 Planarity : 0.005 0.086 1623 Dihedral : 4.954 29.457 1302 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 1.83 % Allowed : 27.98 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.24), residues: 1174 helix: 0.66 (0.27), residues: 392 sheet: -2.63 (0.40), residues: 131 loop : -2.96 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 325 TYR 0.018 0.001 TYR A 412 PHE 0.019 0.001 PHE B 354 TRP 0.009 0.001 TRP F 114 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9126) covalent geometry : angle 0.66441 (12369) SS BOND : bond 0.00209 ( 3) SS BOND : angle 0.57271 ( 6) hydrogen bonds : bond 0.03258 ( 323) hydrogen bonds : angle 4.74438 ( 894) Misc. bond : bond 0.00011 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7379 (mmt90) cc_final: 0.6400 (mmp80) REVERT: A 439 ASP cc_start: 0.9106 (t0) cc_final: 0.8754 (t0) REVERT: A 458 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6910 (mmm160) REVERT: B 171 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 198 MET cc_start: 0.8646 (mmt) cc_final: 0.8377 (mmt) REVERT: B 204 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: B 214 CYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8797 (t) REVERT: B 349 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8695 (pttm) REVERT: C 81 GLN cc_start: 0.9122 (mt0) cc_final: 0.8887 (mm-40) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 0.1325 time to fit residues: 16.3123 Evaluate side-chains 91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.060044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050435 restraints weight = 54614.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051798 restraints weight = 33761.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052714 restraints weight = 24229.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053382 restraints weight = 19094.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053846 restraints weight = 15945.331| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9132 Z= 0.136 Angle : 0.677 12.455 12375 Z= 0.346 Chirality : 0.041 0.234 1406 Planarity : 0.005 0.078 1623 Dihedral : 4.987 27.306 1302 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 1.72 % Allowed : 28.44 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.24), residues: 1174 helix: 0.67 (0.27), residues: 399 sheet: -2.72 (0.40), residues: 126 loop : -2.99 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 43 TYR 0.017 0.001 TYR D 94 PHE 0.018 0.001 PHE B 354 TRP 0.012 0.001 TRP F 114 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9126) covalent geometry : angle 0.67702 (12369) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.55453 ( 6) hydrogen bonds : bond 0.03276 ( 323) hydrogen bonds : angle 4.78417 ( 894) Misc. bond : bond 0.00015 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9353 (tppt) cc_final: 0.8988 (tppt) REVERT: A 439 ASP cc_start: 0.9068 (t0) cc_final: 0.8697 (t0) REVERT: A 458 ARG cc_start: 0.7255 (mmm160) cc_final: 0.6979 (mmm160) REVERT: B 171 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 208 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8000 (mmt180) REVERT: B 214 CYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8829 (t) REVERT: B 349 LYS cc_start: 0.9113 (ptpp) cc_final: 0.8701 (pttm) REVERT: C 81 GLN cc_start: 0.9177 (mt0) cc_final: 0.8963 (mm-40) REVERT: D 89 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: D 107 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6598 (tpm170) REVERT: E 82 MET cc_start: 0.5202 (mmm) cc_final: 0.4490 (mmm) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1445 time to fit residues: 16.9874 Evaluate side-chains 93 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 0.0020 chunk 107 optimal weight: 7.9990 chunk 84 optimal weight: 0.2980 chunk 46 optimal weight: 0.0060 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.062722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053037 restraints weight = 53351.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054460 restraints weight = 32570.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055443 restraints weight = 23141.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056137 restraints weight = 18013.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056620 restraints weight = 14936.186| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9132 Z= 0.116 Angle : 0.676 12.473 12375 Z= 0.343 Chirality : 0.041 0.232 1406 Planarity : 0.005 0.095 1623 Dihedral : 4.810 26.176 1302 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 2.18 % Allowed : 27.98 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.24), residues: 1174 helix: 0.71 (0.27), residues: 397 sheet: -2.42 (0.42), residues: 126 loop : -2.84 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.018 0.001 TYR E 111 PHE 0.021 0.001 PHE B 354 TRP 0.006 0.001 TRP B 131 HIS 0.002 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9126) covalent geometry : angle 0.67618 (12369) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.48114 ( 6) hydrogen bonds : bond 0.03112 ( 323) hydrogen bonds : angle 4.62196 ( 894) Misc. bond : bond 0.00018 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.57 seconds wall clock time: 23 minutes 30.43 seconds (1410.43 seconds total)