Starting phenix.real_space_refine on Sun Jul 27 01:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukt_20812/07_2025/6ukt_20812.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukt_20812/07_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_20812/07_2025/6ukt_20812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukt_20812/07_2025/6ukt_20812.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukt_20812/07_2025/6ukt_20812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukt_20812/07_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-5711/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: 5.46, per 1000 atoms: 0.61 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 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: 0.85 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: 2.14 Time building geometry restraints manager: 2.74 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: 1.130 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.490 Find NCS groups from input model: 0.110 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 9132 Z= 0.449 Angle : 1.034 10.524 12375 Z= 0.565 Chirality : 0.058 0.378 1406 Planarity : 0.007 0.083 1623 Dihedral : 16.893 85.086 3232 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.29 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 Details of bonding type rmsd hydrogen bonds : bond 0.16089 ( 323) hydrogen bonds : angle 7.58346 ( 894) SS BOND : bond 0.00400 ( 3) SS BOND : angle 1.48262 ( 6) covalent geometry : bond 0.00681 ( 9126) covalent geometry : angle 1.03379 (12369) Misc. bond : bond 0.17814 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.086 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: 0.3707 time to fit residues: 48.0877 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 : 1.054 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 465 ASN A 477 HIS B 204 GLN B 241 ASN B 311 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.050621 restraints weight = 53544.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051983 restraints weight = 32993.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.052947 restraints weight = 23681.628| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9132 Z= 0.120 Angle : 0.644 6.951 12375 Z= 0.344 Chirality : 0.041 0.175 1406 Planarity : 0.005 0.074 1623 Dihedral : 6.249 59.431 1304 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.67 % Favored : 88.25 % Rotamer: Outliers : 0.92 % Allowed : 18.81 % Favored : 80.28 % 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: -1.00 (0.24), residues: 395 sheet: -3.63 (0.36), residues: 120 loop : -3.56 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 114 HIS 0.003 0.001 HIS A 62 PHE 0.029 0.001 PHE B 336 TYR 0.016 0.001 TYR A 445 ARG 0.005 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 323) hydrogen bonds : angle 5.67102 ( 894) SS BOND : bond 0.00325 ( 3) SS BOND : angle 0.81231 ( 6) covalent geometry : bond 0.00256 ( 9126) covalent geometry : angle 0.64361 (12369) Misc. bond : bond 0.00084 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.166 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: 0.9298 (mtp85) cc_final: 0.9056 (ptp-170) REVERT: A 229 ASN cc_start: 0.9371 (OUTLIER) cc_final: 0.9019 (t0) REVERT: A 259 MET cc_start: 0.9162 (mtm) cc_final: 0.8875 (mtp) REVERT: A 380 MET cc_start: 0.9018 (ttm) cc_final: 0.8791 (ttm) REVERT: A 439 ASP cc_start: 0.9317 (t0) cc_final: 0.8981 (t0) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 0.3661 time to fit residues: 45.1314 Evaluate side-chains 84 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain D residue 29 VAL 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: 4.9990 chunk 90 optimal weight: 0.9990 chunk 102 optimal weight: 0.0040 chunk 85 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 D 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050536 restraints weight = 54343.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051946 restraints weight = 33139.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052921 restraints weight = 23599.576| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9132 Z= 0.115 Angle : 0.624 6.997 12375 Z= 0.329 Chirality : 0.041 0.209 1406 Planarity : 0.005 0.069 1623 Dihedral : 5.716 54.709 1302 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.61 % Favored : 87.31 % Rotamer: Outliers : 2.29 % Allowed : 21.22 % Favored : 76.49 % 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: -3.40 (0.23), residues: 1174 helix: -0.30 (0.26), residues: 391 sheet: -3.39 (0.36), residues: 127 loop : -3.44 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 323) hydrogen bonds : angle 5.28025 ( 894) SS BOND : bond 0.00256 ( 3) SS BOND : angle 0.72294 ( 6) covalent geometry : bond 0.00257 ( 9126) covalent geometry : angle 0.62403 (12369) Misc. bond : bond 0.00032 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.9169 (mtm) cc_final: 0.8893 (mtp) REVERT: A 325 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7992 (mtp180) REVERT: A 342 ARG cc_start: 0.8408 (ptm160) cc_final: 0.8042 (ptp-170) REVERT: A 439 ASP cc_start: 0.9296 (t0) cc_final: 0.8982 (t0) REVERT: B 190 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8990 (t) REVERT: B 204 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: B 208 ARG cc_start: 0.8855 (tpp80) cc_final: 0.7837 (ttm-80) REVERT: B 354 PHE cc_start: 0.7828 (m-10) cc_final: 0.6677 (m-10) REVERT: D 3 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: E 64 LYS cc_start: 0.9277 (mtpp) cc_final: 0.9061 (ttmm) outliers start: 20 outliers final: 8 residues processed: 104 average time/residue: 0.3440 time to fit residues: 44.8520 Evaluate side-chains 92 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 259 PHE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 29 VAL 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: 3.9990 chunk 96 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN B 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052030 restraints weight = 53595.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053397 restraints weight = 33357.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054384 restraints weight = 23992.954| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9132 Z= 0.110 Angle : 0.609 8.131 12375 Z= 0.319 Chirality : 0.040 0.150 1406 Planarity : 0.004 0.068 1623 Dihedral : 5.336 49.631 1302 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 2.52 % Allowed : 22.71 % Favored : 74.77 % 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: -3.07 (0.23), residues: 1174 helix: 0.04 (0.26), residues: 394 sheet: -2.96 (0.39), residues: 127 loop : -3.35 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.008 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 323) hydrogen bonds : angle 5.02448 ( 894) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.65497 ( 6) covalent geometry : bond 0.00248 ( 9126) covalent geometry : angle 0.60913 (12369) Misc. bond : bond 0.00028 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.105 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 75 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7707 (mmm-85) REVERT: A 344 HIS cc_start: 0.9106 (OUTLIER) cc_final: 0.8819 (m170) REVERT: A 412 TYR cc_start: 0.8051 (p90) cc_final: 0.7365 (p90) REVERT: A 439 ASP cc_start: 0.9307 (t0) cc_final: 0.8958 (t0) REVERT: B 204 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: B 208 ARG cc_start: 0.8856 (tpp80) cc_final: 0.7821 (tpt170) REVERT: B 354 PHE cc_start: 0.7646 (m-10) cc_final: 0.7382 (m-10) REVERT: C 81 GLN cc_start: 0.9192 (mt0) cc_final: 0.8860 (mt0) REVERT: E 82 MET cc_start: 0.5384 (mmm) cc_final: 0.4764 (mmm) outliers start: 22 outliers final: 10 residues processed: 105 average time/residue: 0.3520 time to fit residues: 46.4096 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 : 1.023 ------------------------------------------------------------------------------- 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 256 HIS Chi-restraints excluded: chain A residue 344 HIS 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 D residue 29 VAL 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: 0.0970 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 44 optimal weight: 0.0770 chunk 65 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 overall best weight: 0.8738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052050 restraints weight = 54498.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053422 restraints weight = 34009.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054360 restraints weight = 24548.517| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.047 9132 Z= 0.113 Angle : 0.606 10.376 12375 Z= 0.317 Chirality : 0.042 0.382 1406 Planarity : 0.005 0.089 1623 Dihedral : 5.185 44.790 1302 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 2.29 % Allowed : 23.51 % Favored : 74.20 % 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: -2.83 (0.23), residues: 1174 helix: 0.27 (0.27), residues: 398 sheet: -2.72 (0.40), residues: 127 loop : -3.27 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 114 HIS 0.002 0.000 HIS A 382 PHE 0.013 0.001 PHE B 336 TYR 0.012 0.001 TYR A 445 ARG 0.006 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 323) hydrogen bonds : angle 4.80479 ( 894) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.66297 ( 6) covalent geometry : bond 0.00257 ( 9126) covalent geometry : angle 0.60636 (12369) Misc. bond : bond 0.00016 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7521 (mmt90) cc_final: 0.6348 (mmp80) REVERT: A 344 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8799 (m170) REVERT: A 439 ASP cc_start: 0.9296 (t0) cc_final: 0.8944 (t0) REVERT: B 204 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: B 208 ARG cc_start: 0.8799 (tpp80) cc_final: 0.7858 (tpt170) REVERT: C 81 GLN cc_start: 0.9219 (mt0) cc_final: 0.9000 (mt0) REVERT: E 82 MET cc_start: 0.5294 (mmm) cc_final: 0.4776 (mmt) outliers start: 20 outliers final: 9 residues processed: 103 average time/residue: 0.4013 time to fit residues: 53.2776 Evaluate side-chains 89 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 256 HIS Chi-restraints excluded: chain A residue 344 HIS 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 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: 7.9990 chunk 80 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.063037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053290 restraints weight = 52956.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054698 restraints weight = 32849.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055674 restraints weight = 23464.095| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9132 Z= 0.106 Angle : 0.597 9.768 12375 Z= 0.309 Chirality : 0.040 0.306 1406 Planarity : 0.005 0.079 1623 Dihedral : 4.924 40.052 1302 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % 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: -2.68 (0.24), residues: 1174 helix: 0.23 (0.26), residues: 407 sheet: -2.64 (0.42), residues: 120 loop : -3.12 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.007 0.001 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 323) hydrogen bonds : angle 4.67060 ( 894) SS BOND : bond 0.00386 ( 3) SS BOND : angle 0.38686 ( 6) covalent geometry : bond 0.00239 ( 9126) covalent geometry : angle 0.59753 (12369) Misc. bond : bond 0.00021 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.126 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: 0.7277 (mmt90) cc_final: 0.6255 (mmp80) REVERT: A 306 MET cc_start: 0.8068 (mmm) cc_final: 0.7457 (mmm) REVERT: A 342 ARG cc_start: 0.8484 (ptm160) cc_final: 0.8184 (ptp-170) REVERT: A 344 HIS cc_start: 0.9126 (OUTLIER) cc_final: 0.8826 (m170) REVERT: A 419 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9174 (tt) REVERT: A 439 ASP cc_start: 0.9209 (t0) cc_final: 0.8852 (t0) REVERT: B 171 GLN cc_start: 0.9048 (tp40) cc_final: 0.7226 (pm20) REVERT: B 204 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: E 82 MET cc_start: 0.5406 (mmm) cc_final: 0.4437 (mmm) outliers start: 18 outliers final: 8 residues processed: 101 average time/residue: 0.3229 time to fit residues: 41.8373 Evaluate side-chains 92 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 344 HIS Chi-restraints excluded: chain A residue 419 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 C residue 68 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** 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 = 0.3294 r_free = 0.3294 target = 0.061009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051252 restraints weight = 54683.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052612 restraints weight = 34076.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053567 restraints weight = 24504.076| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9132 Z= 0.126 Angle : 0.630 9.609 12375 Z= 0.325 Chirality : 0.041 0.264 1406 Planarity : 0.005 0.080 1623 Dihedral : 4.966 34.614 1302 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 1.95 % Allowed : 24.66 % Favored : 73.39 % 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: -2.53 (0.24), residues: 1174 helix: 0.49 (0.27), residues: 399 sheet: -2.62 (0.41), residues: 129 loop : -3.06 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.009 0.001 PHE A 162 TYR 0.012 0.001 TYR A 445 ARG 0.011 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 323) hydrogen bonds : angle 4.68753 ( 894) SS BOND : bond 0.00243 ( 3) SS BOND : angle 0.51106 ( 6) covalent geometry : bond 0.00289 ( 9126) covalent geometry : angle 0.63042 (12369) Misc. bond : bond 0.00010 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8840 (t0) REVERT: A 439 ASP cc_start: 0.9218 (t0) cc_final: 0.8867 (t0) REVERT: A 458 ARG cc_start: 0.7315 (mmm160) cc_final: 0.7110 (mmm160) REVERT: B 171 GLN cc_start: 0.9080 (tp40) cc_final: 0.7148 (pm20) REVERT: B 204 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: B 208 ARG cc_start: 0.8768 (tpp80) cc_final: 0.7860 (tpt170) REVERT: E 82 MET cc_start: 0.5432 (mmm) cc_final: 0.4708 (mmm) outliers start: 17 outliers final: 9 residues processed: 100 average time/residue: 0.3445 time to fit residues: 43.5097 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 : 1.092 ------------------------------------------------------------------------------- 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 256 HIS Chi-restraints excluded: chain B residue 204 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.0040 chunk 94 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 0.0980 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.1168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.064548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054743 restraints weight = 54371.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.056186 restraints weight = 33164.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057201 restraints weight = 23520.469| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9132 Z= 0.111 Angle : 0.636 11.109 12375 Z= 0.324 Chirality : 0.040 0.246 1406 Planarity : 0.005 0.087 1623 Dihedral : 4.717 34.145 1302 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.72 % Allowed : 25.34 % Favored : 72.94 % 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: -2.46 (0.24), residues: 1174 helix: 0.45 (0.27), residues: 407 sheet: -2.37 (0.42), residues: 125 loop : -3.04 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.002 0.000 HIS A 62 PHE 0.011 0.001 PHE A 162 TYR 0.012 0.001 TYR A 445 ARG 0.008 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 323) hydrogen bonds : angle 4.51784 ( 894) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.46438 ( 6) covalent geometry : bond 0.00252 ( 9126) covalent geometry : angle 0.63562 (12369) Misc. bond : bond 0.00020 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.033 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: 0.7122 (mmt90) cc_final: 0.6238 (mmp80) REVERT: A 61 LYS cc_start: 0.9326 (ptpp) cc_final: 0.9017 (pttt) REVERT: A 229 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8623 (t0) REVERT: A 342 ARG cc_start: 0.8480 (ptm160) cc_final: 0.8138 (ptp-170) REVERT: A 419 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9050 (tt) REVERT: A 439 ASP cc_start: 0.9147 (t0) cc_final: 0.8778 (t0) REVERT: A 458 ARG cc_start: 0.7234 (mmm160) cc_final: 0.7012 (mmm160) REVERT: C 81 GLN cc_start: 0.9161 (mt0) cc_final: 0.8882 (mm110) REVERT: E 12 VAL cc_start: 0.6880 (OUTLIER) cc_final: 0.6643 (m) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.3338 time to fit residues: 42.3405 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 256 HIS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 195 HIS 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 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 overall best weight: 1.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** 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 = 0.3326 r_free = 0.3326 target = 0.062256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052530 restraints weight = 53755.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053948 restraints weight = 32852.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054931 restraints weight = 23366.194| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9132 Z= 0.124 Angle : 0.659 15.004 12375 Z= 0.332 Chirality : 0.041 0.231 1406 Planarity : 0.005 0.087 1623 Dihedral : 4.754 29.737 1302 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % 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: -2.32 (0.24), residues: 1174 helix: 0.62 (0.27), residues: 399 sheet: -2.45 (0.42), residues: 130 loop : -2.91 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 114 HIS 0.002 0.001 HIS A 158 PHE 0.008 0.001 PHE A 162 TYR 0.012 0.001 TYR A 445 ARG 0.011 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 323) hydrogen bonds : angle 4.59657 ( 894) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.47337 ( 6) covalent geometry : bond 0.00295 ( 9126) covalent geometry : angle 0.65913 (12369) Misc. bond : bond 0.00012 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.071 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 229 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8548 (t0) REVERT: A 439 ASP cc_start: 0.9111 (t0) cc_final: 0.8761 (t0) REVERT: A 458 ARG cc_start: 0.7345 (mmm160) cc_final: 0.7079 (mmm160) REVERT: A 467 MET cc_start: 0.7912 (mpp) cc_final: 0.7441 (ppp) REVERT: B 171 GLN cc_start: 0.9206 (tp40) cc_final: 0.7191 (pm20) REVERT: B 214 CYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8837 (t) REVERT: B 349 LYS cc_start: 0.9033 (ptpp) cc_final: 0.8775 (ptpp) REVERT: E 12 VAL cc_start: 0.6803 (OUTLIER) cc_final: 0.6556 (m) REVERT: E 82 MET cc_start: 0.5419 (mmm) cc_final: 0.4649 (mmm) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.3258 time to fit residues: 39.9391 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 : 1.260 ------------------------------------------------------------------------------- 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 256 HIS Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 214 CYS 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 E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL 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: 4.9990 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** 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 = 0.3304 r_free = 0.3304 target = 0.061356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051687 restraints weight = 53426.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053074 restraints weight = 33042.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054019 restraints weight = 23637.198| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9132 Z= 0.130 Angle : 0.678 13.877 12375 Z= 0.343 Chirality : 0.041 0.234 1406 Planarity : 0.005 0.091 1623 Dihedral : 4.894 27.495 1302 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 1.49 % Allowed : 25.92 % 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: -2.24 (0.24), residues: 1174 helix: 0.70 (0.27), residues: 399 sheet: -2.48 (0.41), residues: 130 loop : -2.86 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 114 HIS 0.003 0.001 HIS A 158 PHE 0.008 0.001 PHE E 98 TYR 0.013 0.001 TYR A 412 ARG 0.013 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 323) hydrogen bonds : angle 4.65594 ( 894) SS BOND : bond 0.00197 ( 3) SS BOND : angle 0.40619 ( 6) covalent geometry : bond 0.00305 ( 9126) covalent geometry : angle 0.67829 (12369) Misc. bond : bond 0.00014 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.019 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 229 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8823 (t0) REVERT: A 236 LYS cc_start: 0.9369 (tppt) cc_final: 0.8969 (tppt) REVERT: A 439 ASP cc_start: 0.9114 (t0) cc_final: 0.8761 (t0) REVERT: A 458 ARG cc_start: 0.7310 (mmm160) cc_final: 0.7029 (mmm160) REVERT: A 467 MET cc_start: 0.7842 (mpp) cc_final: 0.7383 (ppp) REVERT: B 171 GLN cc_start: 0.9224 (tp40) cc_final: 0.7124 (pm20) REVERT: B 208 ARG cc_start: 0.8756 (tpp80) cc_final: 0.7860 (tpt170) REVERT: B 214 CYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8765 (t) REVERT: B 349 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8757 (ptpp) REVERT: C 81 GLN cc_start: 0.9160 (mt0) cc_final: 0.8919 (mt0) REVERT: E 12 VAL cc_start: 0.6838 (OUTLIER) cc_final: 0.6593 (m) REVERT: E 82 MET cc_start: 0.5223 (mmm) cc_final: 0.4501 (mmm) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.3488 time to fit residues: 41.4256 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 256 HIS Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3269 r_free = 0.3269 target = 0.060128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050299 restraints weight = 55079.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051688 restraints weight = 33875.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052662 restraints weight = 24136.271| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9132 Z= 0.142 Angle : 0.699 13.322 12375 Z= 0.355 Chirality : 0.042 0.231 1406 Planarity : 0.005 0.090 1623 Dihedral : 5.038 25.239 1302 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % 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: -2.24 (0.25), residues: 1174 helix: 0.70 (0.27), residues: 399 sheet: -2.52 (0.42), residues: 130 loop : -2.85 (0.23), residues: 645 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 0.008 0.001 PHE E 98 TYR 0.015 0.001 TYR A 412 ARG 0.013 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 323) hydrogen bonds : angle 4.73363 ( 894) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.41264 ( 6) covalent geometry : bond 0.00332 ( 9126) covalent geometry : angle 0.69893 (12369) Misc. bond : bond 0.00015 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.50 seconds wall clock time: 51 minutes 38.39 seconds (3098.39 seconds total)