Starting phenix.real_space_refine on Thu Feb 13 12:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukt_20812/02_2025/6ukt_20812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukt_20812/02_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_20812/02_2025/6ukt_20812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukt_20812/02_2025/6ukt_20812.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukt_20812/02_2025/6ukt_20812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukt_20812/02_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-5592/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: 5.42, per 1000 atoms: 0.60 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: 2.56 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: 0.84 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: 2.13 Time building geometry restraints manager: 2.79 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: 0.550 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- 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 : 1.116 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: 0.3823 time to fit residues: 49.7837 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 : 1.059 ------------------------------------------------------------------------------- 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 = 26)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049947 restraints weight = 53639.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051333 restraints weight = 33034.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052280 restraints weight = 23586.094| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 1.268 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: 0.9099 (ptp-170) REVERT: A 229 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9032 (t0) REVERT: A 259 MET cc_start: 0.9157 (mtm) cc_final: 0.8875 (mtp) REVERT: A 380 MET cc_start: 0.9048 (ttm) cc_final: 0.8818 (ttm) REVERT: A 439 ASP cc_start: 0.9349 (t0) cc_final: 0.9022 (t0) outliers start: 9 outliers final: 2 residues processed: 99 average time/residue: 0.3811 time to fit residues: 47.3333 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 : 0.966 ------------------------------------------------------------------------------- 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: 0.4980 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 101 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 E 30 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.059426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049784 restraints weight = 54992.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051113 restraints weight = 34135.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052058 restraints weight = 24500.499| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2000 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= 0.185 Angle : 0.634 7.042 12369 Z= 0.335 Chirality : 0.041 0.231 1406 Planarity : 0.005 0.069 1623 Dihedral : 5.864 55.186 1302 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 2.18 % Allowed : 21.44 % 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 (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: -3.41 (0.23), residues: 1174 helix: -0.29 (0.26), residues: 390 sheet: -3.47 (0.36), residues: 127 loop : -3.43 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 114 HIS 0.002 0.001 HIS A 62 PHE 0.019 0.001 PHE B 336 TYR 0.014 0.001 TYR A 445 ARG 0.005 0.001 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: 19 poor density : 86 time to evaluate : 0.990 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 23 ARG cc_start: 0.9236 (mtp85) cc_final: 0.9031 (ptm160) REVERT: A 229 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8896 (t0) REVERT: A 259 MET cc_start: 0.9183 (mtm) cc_final: 0.8919 (mtp) REVERT: A 380 MET cc_start: 0.9030 (ttm) cc_final: 0.8830 (ttm) REVERT: A 401 GLU cc_start: 0.7573 (tt0) cc_final: 0.6863 (tp30) REVERT: A 439 ASP cc_start: 0.9310 (t0) cc_final: 0.9000 (t0) REVERT: B 190 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9031 (t) REVERT: B 208 ARG cc_start: 0.8851 (tpp80) cc_final: 0.7944 (tpt170) REVERT: B 354 PHE cc_start: 0.7837 (m-10) cc_final: 0.6710 (m-10) REVERT: D 3 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8104 (mp10) outliers start: 19 outliers final: 7 residues processed: 102 average time/residue: 0.3498 time to fit residues: 44.8010 Evaluate side-chains 89 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 B residue 190 THR 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: 1.9990 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 229 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN B 346 ASN D 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.060789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050866 restraints weight = 53875.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052274 restraints weight = 33128.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053247 restraints weight = 23738.600| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9126 Z= 0.159 Angle : 0.611 7.969 12369 Z= 0.321 Chirality : 0.040 0.166 1406 Planarity : 0.005 0.067 1623 Dihedral : 5.459 48.778 1302 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 2.29 % Allowed : 23.17 % Favored : 74.54 % 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: -3.12 (0.23), residues: 1174 helix: 0.03 (0.26), residues: 391 sheet: -3.11 (0.38), residues: 127 loop : -3.36 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 114 HIS 0.002 0.000 HIS A 62 PHE 0.009 0.001 PHE A 162 TYR 0.013 0.001 TYR A 445 ARG 0.007 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 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.9226 (mtp85) cc_final: 0.8988 (ptm160) REVERT: A 75 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7728 (mmm-85) REVERT: A 259 MET cc_start: 0.9176 (mtm) cc_final: 0.8899 (mtp) REVERT: A 439 ASP cc_start: 0.9313 (t0) cc_final: 0.8996 (t0) REVERT: B 190 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8982 (t) REVERT: B 204 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: B 208 ARG cc_start: 0.8864 (tpp80) cc_final: 0.7871 (tpt170) REVERT: B 345 LYS cc_start: 0.9196 (tppp) cc_final: 0.8875 (tppp) REVERT: B 354 PHE cc_start: 0.7750 (m-10) cc_final: 0.7424 (m-10) REVERT: C 81 GLN cc_start: 0.9214 (mt0) cc_final: 0.8913 (mt0) REVERT: D 3 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: E 64 LYS cc_start: 0.9255 (mtpp) cc_final: 0.9051 (ttmm) REVERT: E 82 MET cc_start: 0.5056 (mmm) cc_final: 0.4638 (mmt) outliers start: 20 outliers final: 9 residues processed: 102 average time/residue: 0.3508 time to fit residues: 44.9452 Evaluate side-chains 89 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 190 THR 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 3 GLN 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: 5.9990 chunk 56 optimal weight: 0.0370 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.057482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047837 restraints weight = 54837.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049147 restraints weight = 34392.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050045 restraints weight = 24983.028| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2403 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= 0.248 Angle : 0.664 8.585 12369 Z= 0.351 Chirality : 0.043 0.348 1406 Planarity : 0.005 0.065 1623 Dihedral : 5.683 41.285 1302 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % Rotamer: Outliers : 1.95 % Allowed : 24.89 % Favored : 73.17 % 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: -2.94 (0.23), residues: 1174 helix: 0.31 (0.27), residues: 395 sheet: -3.18 (0.37), residues: 129 loop : -3.32 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 114 HIS 0.005 0.001 HIS A 324 PHE 0.013 0.002 PHE B 336 TYR 0.018 0.001 TYR D 94 ARG 0.006 0.001 ARG A 43 *********************** 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 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 HIS cc_start: 0.9190 (OUTLIER) cc_final: 0.8865 (m170) REVERT: A 439 ASP cc_start: 0.9298 (t0) cc_final: 0.8978 (t0) REVERT: B 171 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 198 MET cc_start: 0.8255 (mmm) cc_final: 0.8048 (mmt) REVERT: B 208 ARG cc_start: 0.8808 (tpp80) cc_final: 0.7991 (mmt180) REVERT: B 349 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8830 (ptpp) REVERT: C 81 GLN cc_start: 0.9154 (mt0) cc_final: 0.8839 (mt0) REVERT: E 64 LYS cc_start: 0.9321 (mtpp) cc_final: 0.9105 (ttmm) REVERT: E 82 MET cc_start: 0.5746 (mmm) cc_final: 0.4966 (mmm) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.3673 time to fit residues: 43.5401 Evaluate side-chains 89 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 38 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.059378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049522 restraints weight = 54127.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050900 restraints weight = 33506.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051841 restraints weight = 24109.421| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2639 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= 0.177 Angle : 0.636 11.304 12369 Z= 0.331 Chirality : 0.042 0.316 1406 Planarity : 0.005 0.065 1623 Dihedral : 5.367 37.071 1302 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 2.41 % Allowed : 25.00 % 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: -2.70 (0.24), residues: 1174 helix: 0.53 (0.27), residues: 388 sheet: -2.94 (0.39), residues: 129 loop : -3.18 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 114 HIS 0.002 0.001 HIS A 187 PHE 0.010 0.001 PHE A 162 TYR 0.012 0.001 TYR A 445 ARG 0.009 0.001 ARG C 75 *********************** 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 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8159 (ptt-90) REVERT: A 43 ARG cc_start: 0.7636 (mmt90) cc_final: 0.6445 (mmp80) REVERT: A 143 ARG cc_start: 0.8497 (tpp-160) cc_final: 0.8066 (tpp-160) REVERT: A 325 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8059 (mtp85) REVERT: A 344 HIS cc_start: 0.9241 (OUTLIER) cc_final: 0.8951 (m170) REVERT: A 439 ASP cc_start: 0.9311 (t0) cc_final: 0.8952 (t0) REVERT: B 171 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7719 (tm-30) REVERT: B 198 MET cc_start: 0.8246 (mmm) cc_final: 0.7965 (mmt) REVERT: B 208 ARG cc_start: 0.8812 (tpp80) cc_final: 0.7959 (mmt180) REVERT: B 349 LYS cc_start: 0.9116 (ptpp) cc_final: 0.8573 (ptpp) REVERT: C 81 GLN cc_start: 0.9155 (mt0) cc_final: 0.8936 (mt0) REVERT: E 82 MET cc_start: 0.5408 (mmm) cc_final: 0.4711 (mmt) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 0.3397 time to fit residues: 44.1146 Evaluate side-chains 88 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 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 93 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049053 restraints weight = 54914.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050396 restraints weight = 34148.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051331 restraints weight = 24577.230| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2772 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= 0.199 Angle : 0.650 10.401 12369 Z= 0.339 Chirality : 0.042 0.269 1406 Planarity : 0.005 0.084 1623 Dihedral : 5.340 31.672 1302 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 1.95 % Allowed : 26.61 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.24), residues: 1174 helix: 0.54 (0.27), residues: 389 sheet: -2.96 (0.39), residues: 129 loop : -3.17 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.016 0.001 PHE B 336 TYR 0.013 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 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.049 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 143 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.8062 (tpp-160) REVERT: A 306 MET cc_start: 0.8018 (mmm) cc_final: 0.7449 (mmm) REVERT: A 439 ASP cc_start: 0.9277 (t0) cc_final: 0.8933 (t0) REVERT: B 208 ARG cc_start: 0.8810 (tpp80) cc_final: 0.7988 (mmt180) REVERT: B 214 CYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8887 (t) REVERT: B 349 LYS cc_start: 0.9133 (ptpp) cc_final: 0.8883 (ptpp) REVERT: C 81 GLN cc_start: 0.9138 (mt0) cc_final: 0.8901 (mt0) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.3429 time to fit residues: 39.8118 Evaluate side-chains 91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 259 PHE Chi-restraints excluded: chain B residue 346 ASN 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: 0.7980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 0.0010 chunk 94 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 51 optimal weight: 0.0170 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051789 restraints weight = 54915.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053192 restraints weight = 33736.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054174 restraints weight = 24102.516| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9126 Z= 0.170 Angle : 0.650 11.574 12369 Z= 0.336 Chirality : 0.041 0.255 1406 Planarity : 0.005 0.073 1623 Dihedral : 5.144 37.787 1302 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.52 % Allowed : 26.03 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1174 helix: 0.46 (0.27), residues: 397 sheet: -2.77 (0.39), residues: 130 loop : -3.13 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 131 HIS 0.002 0.000 HIS A 344 PHE 0.012 0.001 PHE B 336 TYR 0.012 0.001 TYR A 445 ARG 0.017 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 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6181 (mmp80) REVERT: A 306 MET cc_start: 0.7926 (mmm) cc_final: 0.7370 (mmm) REVERT: A 439 ASP cc_start: 0.9257 (t0) cc_final: 0.8896 (t0) REVERT: A 467 MET cc_start: 0.7951 (mpp) cc_final: 0.7614 (ppp) REVERT: B 204 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: B 208 ARG cc_start: 0.8801 (tpp80) cc_final: 0.7888 (mmt180) REVERT: B 214 CYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8890 (t) REVERT: B 349 LYS cc_start: 0.9104 (ptpp) cc_final: 0.8655 (ptpp) REVERT: C 81 GLN cc_start: 0.9129 (mt0) cc_final: 0.8907 (mt0) REVERT: D 89 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8404 (tp30) REVERT: D 107 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6482 (tpm170) REVERT: E 82 MET cc_start: 0.5473 (mmm) cc_final: 0.4751 (mmm) outliers start: 22 outliers final: 12 residues processed: 103 average time/residue: 0.3467 time to fit residues: 44.6046 Evaluate side-chains 94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 195 HIS 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 262 THR Chi-restraints excluded: chain B residue 346 ASN 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 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 346 ASN C 73 ASN E 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052365 restraints weight = 55180.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053762 restraints weight = 34062.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054722 restraints weight = 24382.652| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3336 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= 0.167 Angle : 0.640 12.067 12369 Z= 0.328 Chirality : 0.041 0.239 1406 Planarity : 0.005 0.090 1623 Dihedral : 4.907 26.749 1302 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 1.61 % Allowed : 26.49 % Favored : 71.90 % 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: -2.50 (0.24), residues: 1174 helix: 0.49 (0.27), residues: 405 sheet: -2.65 (0.40), residues: 131 loop : -3.04 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 131 HIS 0.005 0.001 HIS A 324 PHE 0.011 0.001 PHE B 336 TYR 0.014 0.001 TYR D 94 ARG 0.007 0.001 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 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.004 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: 0.7446 (mmt90) cc_final: 0.6320 (mmp80) REVERT: A 61 LYS cc_start: 0.9354 (ptpp) cc_final: 0.9020 (pttt) REVERT: A 439 ASP cc_start: 0.9194 (t0) cc_final: 0.8855 (t0) REVERT: B 208 ARG cc_start: 0.8801 (tpp80) cc_final: 0.7890 (mmt180) REVERT: B 214 CYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8818 (t) REVERT: C 81 GLN cc_start: 0.9134 (mt0) cc_final: 0.8928 (mt0) REVERT: D 107 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6536 (tpm170) REVERT: E 82 MET cc_start: 0.5455 (mmm) cc_final: 0.4716 (mmm) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.3576 time to fit residues: 42.8549 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 : 1.070 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain B residue 346 ASN 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: 7.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3322 r_free = 0.3322 target = 0.062051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052406 restraints weight = 53434.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053807 restraints weight = 32687.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054774 restraints weight = 23272.698| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9126 Z= 0.176 Angle : 0.656 13.065 12369 Z= 0.334 Chirality : 0.041 0.235 1406 Planarity : 0.005 0.093 1623 Dihedral : 4.827 24.919 1302 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 1.38 % Allowed : 26.95 % 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: -2.41 (0.24), residues: 1174 helix: 0.53 (0.27), residues: 405 sheet: -2.56 (0.41), residues: 131 loop : -2.97 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 131 HIS 0.003 0.001 HIS A 344 PHE 0.009 0.001 PHE A 162 TYR 0.012 0.001 TYR A 445 ARG 0.008 0.001 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 94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.147 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: 0.7387 (mmt90) cc_final: 0.6283 (mmp80) REVERT: A 61 LYS cc_start: 0.9350 (ptpp) cc_final: 0.9021 (pttt) REVERT: A 236 LYS cc_start: 0.9364 (tppt) cc_final: 0.8980 (tppt) REVERT: A 439 ASP cc_start: 0.9167 (t0) cc_final: 0.8814 (t0) REVERT: B 208 ARG cc_start: 0.8821 (tpp80) cc_final: 0.7900 (mmt180) REVERT: B 214 CYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8718 (t) REVERT: B 341 ASP cc_start: 0.9463 (m-30) cc_final: 0.9204 (m-30) REVERT: C 81 GLN cc_start: 0.9117 (mt0) cc_final: 0.8914 (mt0) REVERT: E 82 MET cc_start: 0.5368 (mmm) cc_final: 0.4596 (mmm) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.3371 time to fit residues: 39.3449 Evaluate side-chains 91 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 0.0170 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053404 restraints weight = 54825.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054791 restraints weight = 33942.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055756 restraints weight = 24329.015| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9126 Z= 0.170 Angle : 0.657 13.053 12369 Z= 0.334 Chirality : 0.041 0.230 1406 Planarity : 0.005 0.090 1623 Dihedral : 4.741 23.665 1302 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 1.83 % Allowed : 26.83 % Favored : 71.33 % 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: -2.32 (0.24), residues: 1174 helix: 0.53 (0.27), residues: 407 sheet: -2.50 (0.42), residues: 126 loop : -2.88 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 131 HIS 0.003 0.001 HIS A 344 PHE 0.009 0.001 PHE B 336 TYR 0.015 0.001 TYR A 412 ARG 0.009 0.001 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.79 seconds wall clock time: 46 minutes 58.25 seconds (2818.25 seconds total)