Starting phenix.real_space_refine on Thu Mar 13 15:07:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukt_20812/03_2025/6ukt_20812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukt_20812/03_2025/6ukt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2025/6ukt_20812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2025/6ukt_20812.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2025/6ukt_20812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukt_20812/03_2025/6ukt_20812.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 7} 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, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 204 Time building chain proxies: 5.30, per 1000 atoms: 0.59 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 2.19 Time building geometry restraints manager: 2.62 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: 0.750 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.100 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- 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 : 0.007 0.110 9126 Z= 0.439 Angle : 1.034 10.524 12369 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 : 10.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.003 TRP F 114 HIS 0.006 0.002 HIS E 96 PHE 0.029 0.003 PHE E 98 TYR 0.039 0.002 TYR E 107 ARG 0.034 0.001 ARG A 219 *********************** 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 : 1.021 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: 0.3811 time to fit residues: 49.4672 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 : 0.970 ------------------------------------------------------------------------------- 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 100 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.0870 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.059700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049970 restraints weight = 53639.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051350 restraints weight = 32807.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052296 restraints weight = 23473.100| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9126 Z= 0.175 Angle : 0.650 7.122 12369 Z= 0.347 Chirality : 0.041 0.176 1406 Planarity : 0.005 0.073 1623 Dihedral : 6.298 59.456 1304 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.75 % Favored : 88.16 % Rotamer: Outliers : 1.03 % Allowed : 19.04 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.22), residues: 1174 helix: -0.99 (0.24), residues: 395 sheet: -3.66 (0.36), residues: 120 loop : -3.56 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 114 HIS 0.003 0.001 HIS A 62 PHE 0.030 0.001 PHE B 336 TYR 0.016 0.001 TYR A 445 ARG 0.006 0.001 ARG A 23 *********************** 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: 9 poor density : 92 time to evaluate : 0.956 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 23 ARG cc_start: 0.9338 (mtp85) cc_final: 0.9098 (ptp-170) REVERT: A 229 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9033 (t0) REVERT: A 259 MET cc_start: 0.9156 (mtm) cc_final: 0.8875 (mtp) REVERT: A 380 MET cc_start: 0.9049 (ttm) cc_final: 0.8819 (ttm) REVERT: A 439 ASP cc_start: 0.9348 (t0) cc_final: 0.9021 (t0) outliers start: 9 outliers final: 2 residues processed: 99 average time/residue: 0.3683 time to fit residues: 45.1090 Evaluate side-chains 82 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain B residue 259 PHE 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 27 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 102 optimal weight: 0.0570 chunk 85 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- 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 304 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.060110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050390 restraints weight = 54502.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051734 restraints weight = 33824.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052681 restraints weight = 24271.967| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9126 Z= 0.171 Angle : 0.623 6.975 12369 Z= 0.329 Chirality : 0.041 0.220 1406 Planarity : 0.005 0.069 1623 Dihedral : 5.756 54.656 1302 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 2.06 % Allowed : 21.67 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 1174 helix: -0.28 (0.26), residues: 391 sheet: -3.39 (0.36), residues: 127 loop : -3.43 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 114 HIS 0.002 0.000 HIS A 62 PHE 0.019 0.001 PHE B 336 TYR 0.014 0.001 TYR A 445 ARG 0.004 0.000 ARG A 43 *********************** 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 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.145 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 23 ARG cc_start: 0.9236 (mtp85) cc_final: 0.9036 (ptm160) REVERT: A 259 MET cc_start: 0.9164 (mtm) cc_final: 0.8893 (mtp) REVERT: A 401 GLU cc_start: 0.7418 (tt0) cc_final: 0.6691 (tp30) REVERT: A 439 ASP cc_start: 0.9309 (t0) cc_final: 0.8997 (t0) REVERT: B 204 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6936 (pm20) REVERT: B 208 ARG cc_start: 0.8863 (tpp80) cc_final: 0.7926 (tpt170) REVERT: B 354 PHE cc_start: 0.7810 (m-10) cc_final: 0.6699 (m-10) REVERT: D 3 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (mp10) outliers start: 18 outliers final: 6 residues processed: 102 average time/residue: 0.3715 time to fit residues: 48.0169 Evaluate side-chains 88 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 204 GLN Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain D residue 3 GLN 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 17 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN E 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.059939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050056 restraints weight = 53953.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051434 restraints weight = 33451.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052406 restraints weight = 23916.201| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9126 Z= 0.180 Angle : 0.621 7.932 12369 Z= 0.327 Chirality : 0.041 0.162 1406 Planarity : 0.005 0.067 1623 Dihedral : 5.493 47.292 1302 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 2.29 % Allowed : 22.82 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1174 helix: 0.10 (0.27), residues: 391 sheet: -3.09 (0.38), residues: 127 loop : -3.34 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 114 HIS 0.002 0.001 HIS A 158 PHE 0.009 0.001 PHE A 162 TYR 0.013 0.001 TYR A 445 ARG 0.009 0.001 ARG C 75 *********************** 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 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.701 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 259 MET cc_start: 0.9220 (mtm) cc_final: 0.8953 (mtp) REVERT: A 412 TYR cc_start: 0.8145 (p90) cc_final: 0.7649 (p90) REVERT: A 439 ASP cc_start: 0.9317 (t0) cc_final: 0.8999 (t0) REVERT: B 204 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: B 345 LYS cc_start: 0.9201 (tppp) cc_final: 0.8874 (tppp) REVERT: B 349 LYS cc_start: 0.8935 (ptpp) cc_final: 0.8661 (ptpp) REVERT: E 64 LYS cc_start: 0.9264 (mtpp) cc_final: 0.9055 (ttmm) outliers start: 20 outliers final: 10 residues processed: 100 average time/residue: 0.3896 time to fit residues: 49.1396 Evaluate side-chains 87 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 204 GLN Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 346 ASN 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 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.0030 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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** A 374 ASN ** B 346 ASN ** 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 = 0.3285 r_free = 0.3285 target = 0.060900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051197 restraints weight = 54332.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052522 restraints weight = 34018.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053470 restraints weight = 24709.797| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9126 Z= 0.162 Angle : 0.608 8.946 12369 Z= 0.319 Chirality : 0.041 0.350 1406 Planarity : 0.005 0.067 1623 Dihedral : 5.276 43.031 1302 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 2.06 % Allowed : 23.85 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.24), residues: 1174 helix: 0.47 (0.27), residues: 389 sheet: -2.82 (0.40), residues: 127 loop : -3.22 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 114 HIS 0.003 0.001 HIS A 324 PHE 0.013 0.001 PHE B 336 TYR 0.012 0.001 TYR A 445 ARG 0.005 0.000 ARG A 458 *********************** 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 103 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7544 (mmt90) cc_final: 0.6381 (mmp80) REVERT: A 229 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8840 (t0) REVERT: A 344 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8942 (m170) REVERT: A 439 ASP cc_start: 0.9292 (t0) cc_final: 0.8938 (t0) REVERT: B 171 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7698 (tm-30) REVERT: B 204 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: B 208 ARG cc_start: 0.8810 (tpp80) cc_final: 0.7840 (tpt170) REVERT: B 243 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8773 (mtp) REVERT: C 81 GLN cc_start: 0.9190 (mt0) cc_final: 0.8842 (mt0) REVERT: E 82 MET cc_start: 0.5383 (mmm) cc_final: 0.4927 (mmt) outliers start: 18 outliers final: 9 residues processed: 100 average time/residue: 0.3442 time to fit residues: 43.1534 Evaluate side-chains 91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 229 ASN 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 243 MET Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 259 PHE 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 38 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 75 optimal weight: 0.0270 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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** ** B 346 ASN ** 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 = 0.3303 r_free = 0.3303 target = 0.061510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051728 restraints weight = 53154.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053127 restraints weight = 32850.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054084 restraints weight = 23527.922| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9126 Z= 0.160 Angle : 0.611 11.093 12369 Z= 0.318 Chirality : 0.041 0.300 1406 Planarity : 0.005 0.078 1623 Dihedral : 5.102 38.764 1302 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 2.52 % Allowed : 23.05 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.24), residues: 1174 helix: 0.45 (0.27), residues: 391 sheet: -2.66 (0.41), residues: 127 loop : -3.15 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 114 HIS 0.002 0.000 HIS A 62 PHE 0.015 0.001 PHE B 336 TYR 0.012 0.001 TYR A 445 ARG 0.006 0.001 ARG A 458 *********************** 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 108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.123 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 43 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6309 (mmp80) REVERT: A 229 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8633 (t0) REVERT: A 306 MET cc_start: 0.8073 (mmm) cc_final: 0.7523 (mmm) REVERT: A 344 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.8749 (m170) REVERT: A 360 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7236 (ptt-90) REVERT: A 439 ASP cc_start: 0.9249 (t0) cc_final: 0.8904 (t0) REVERT: B 171 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 204 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: B 208 ARG cc_start: 0.8792 (tpp80) cc_final: 0.7823 (tpt170) REVERT: C 81 GLN cc_start: 0.9174 (mt0) cc_final: 0.8945 (mt0) REVERT: D 79 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7757 (m) REVERT: E 82 MET cc_start: 0.5421 (mmm) cc_final: 0.4889 (mmt) outliers start: 22 outliers final: 10 residues processed: 101 average time/residue: 0.3509 time to fit residues: 44.7264 Evaluate side-chains 92 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 229 ASN Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 360 ARG 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 C residue 68 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 79 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 93 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 346 ASN ** 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 = 0.3231 r_free = 0.3231 target = 0.058667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048937 restraints weight = 55644.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050259 restraints weight = 35228.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051184 restraints weight = 25405.884| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9126 Z= 0.227 Angle : 0.658 10.320 12369 Z= 0.343 Chirality : 0.042 0.257 1406 Planarity : 0.005 0.085 1623 Dihedral : 5.267 32.230 1302 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 2.29 % Allowed : 25.00 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 1174 helix: 0.48 (0.27), residues: 398 sheet: -2.87 (0.40), residues: 129 loop : -3.14 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.015 0.001 PHE B 336 TYR 0.016 0.001 TYR D 94 ARG 0.014 0.001 ARG C 75 *********************** 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 99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.163 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 380 MET cc_start: 0.8630 (ptm) cc_final: 0.8242 (ptm) REVERT: A 439 ASP cc_start: 0.9281 (t0) cc_final: 0.8919 (t0) REVERT: A 467 MET cc_start: 0.7936 (mpp) cc_final: 0.7633 (ppp) REVERT: B 171 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 208 ARG cc_start: 0.8806 (tpp80) cc_final: 0.7905 (mmt180) REVERT: B 214 CYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8906 (t) REVERT: C 81 GLN cc_start: 0.9180 (mt0) cc_final: 0.8922 (mt0) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.3224 time to fit residues: 39.5214 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 : 1.033 ------------------------------------------------------------------------------- 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 B residue 204 GLN Chi-restraints excluded: chain B residue 214 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.060403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050505 restraints weight = 55526.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051910 restraints weight = 33966.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052884 restraints weight = 24232.088| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9126 Z= 0.173 Angle : 0.646 11.594 12369 Z= 0.331 Chirality : 0.041 0.247 1406 Planarity : 0.005 0.072 1623 Dihedral : 5.057 29.594 1302 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 1.95 % Allowed : 25.46 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 1174 helix: 0.47 (0.27), residues: 399 sheet: -2.76 (0.40), residues: 130 loop : -3.05 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 114 HIS 0.002 0.001 HIS A 187 PHE 0.018 0.001 PHE B 336 TYR 0.013 0.001 TYR D 94 ARG 0.016 0.001 ARG C 75 *********************** 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 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.928 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: 0.7556 (mmt90) cc_final: 0.6308 (mmp80) REVERT: A 229 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8842 (t0) REVERT: A 380 MET cc_start: 0.8602 (ptm) cc_final: 0.7741 (ptm) REVERT: A 412 TYR cc_start: 0.7842 (p90) cc_final: 0.7081 (p90) REVERT: A 439 ASP cc_start: 0.9254 (t0) cc_final: 0.8885 (t0) REVERT: B 171 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 208 ARG cc_start: 0.8801 (tpp80) cc_final: 0.7890 (mmt180) REVERT: B 214 CYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8871 (t) REVERT: C 81 GLN cc_start: 0.9173 (mt0) cc_final: 0.8931 (mt0) REVERT: E 82 MET cc_start: 0.5209 (mmm) cc_final: 0.4059 (mmm) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.3252 time to fit residues: 40.1641 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 : 0.963 ------------------------------------------------------------------------------- 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 229 ASN 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 244 HIS Chi-restraints excluded: chain B residue 259 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.060615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050804 restraints weight = 55073.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052229 restraints weight = 33772.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053196 restraints weight = 23994.285| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9126 Z= 0.176 Angle : 0.650 11.918 12369 Z= 0.331 Chirality : 0.041 0.236 1406 Planarity : 0.005 0.090 1623 Dihedral : 4.991 26.868 1302 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 1.83 % Allowed : 25.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.24), residues: 1174 helix: 0.57 (0.27), residues: 399 sheet: -2.72 (0.40), residues: 131 loop : -2.94 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 114 HIS 0.002 0.001 HIS A 187 PHE 0.018 0.001 PHE B 354 TYR 0.012 0.001 TYR A 445 ARG 0.008 0.000 ARG A 458 *********************** 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 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.999 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: 0.7490 (mmt90) cc_final: 0.6427 (mmp80) REVERT: A 61 LYS cc_start: 0.9347 (ptpp) cc_final: 0.9033 (pttt) REVERT: A 229 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8822 (t0) REVERT: A 380 MET cc_start: 0.8578 (ptm) cc_final: 0.7842 (ptm) REVERT: A 412 TYR cc_start: 0.7868 (p90) cc_final: 0.7356 (p90) REVERT: A 439 ASP cc_start: 0.9198 (t0) cc_final: 0.8844 (t0) REVERT: B 171 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 208 ARG cc_start: 0.8802 (tpp80) cc_final: 0.7896 (mmt180) REVERT: B 349 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8717 (ptpp) REVERT: C 81 GLN cc_start: 0.9177 (mt0) cc_final: 0.8930 (mt0) REVERT: C 88 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8311 (pp20) REVERT: D 107 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6731 (tpm170) REVERT: E 82 MET cc_start: 0.5211 (mmm) cc_final: 0.4458 (mmm) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.3457 time to fit residues: 43.1424 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 229 ASN 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 244 HIS Chi-restraints excluded: chain B residue 259 PHE 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 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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** ** B 346 ASN ** 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 = 0.3316 r_free = 0.3316 target = 0.061919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052177 restraints weight = 54561.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053567 restraints weight = 34104.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054541 restraints weight = 24342.677| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9126 Z= 0.171 Angle : 0.655 12.333 12369 Z= 0.334 Chirality : 0.040 0.235 1406 Planarity : 0.005 0.092 1623 Dihedral : 4.795 24.870 1302 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 1.72 % Allowed : 26.15 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.24), residues: 1174 helix: 0.64 (0.27), residues: 401 sheet: -2.52 (0.41), residues: 131 loop : -2.86 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 114 HIS 0.002 0.001 HIS A 62 PHE 0.019 0.001 PHE B 354 TYR 0.013 0.001 TYR D 94 ARG 0.008 0.000 ARG A 458 ********************** 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 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.021 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 43 ARG cc_start: 0.7265 (mmt90) cc_final: 0.6278 (mmp80) REVERT: A 229 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8737 (t0) REVERT: A 236 LYS cc_start: 0.9344 (tppt) cc_final: 0.8980 (tppt) REVERT: A 380 MET cc_start: 0.8580 (ptm) cc_final: 0.7704 (ptm) REVERT: A 412 TYR cc_start: 0.7724 (p90) cc_final: 0.7018 (p90) REVERT: A 439 ASP cc_start: 0.9123 (t0) cc_final: 0.8774 (t0) REVERT: A 467 MET cc_start: 0.7893 (mpp) cc_final: 0.7407 (ppp) REVERT: B 171 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 208 ARG cc_start: 0.8820 (tpp80) cc_final: 0.7901 (mmt180) REVERT: B 214 CYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8737 (t) REVERT: B 349 LYS cc_start: 0.8956 (ptpp) cc_final: 0.8698 (ptpp) REVERT: C 81 GLN cc_start: 0.9144 (mt0) cc_final: 0.8897 (mt0) REVERT: D 65 LYS cc_start: 0.8817 (ptpt) cc_final: 0.8585 (ptpp) REVERT: D 107 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6531 (tpm170) REVERT: E 82 MET cc_start: 0.5368 (mmm) cc_final: 0.4598 (mmm) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.3320 time to fit residues: 43.1662 Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 229 ASN 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 244 HIS 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 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 321 HIS ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048107 restraints weight = 55470.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049390 restraints weight = 34412.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050284 restraints weight = 24838.435| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9126 Z= 0.301 Angle : 0.742 12.123 12369 Z= 0.384 Chirality : 0.043 0.224 1406 Planarity : 0.006 0.086 1623 Dihedral : 5.417 23.507 1302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 1.95 % Allowed : 26.38 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1174 helix: 0.63 (0.27), residues: 398 sheet: -2.89 (0.40), residues: 128 loop : -2.96 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 114 HIS 0.005 0.001 HIS A 158 PHE 0.019 0.002 PHE E 98 TYR 0.019 0.002 TYR D 94 ARG 0.008 0.001 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.51 seconds wall clock time: 49 minutes 9.38 seconds (2949.38 seconds total)