Starting phenix.real_space_refine on Sun Apr 5 06:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lxp_63488/04_2026/9lxp_63488_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lxp_63488/04_2026/9lxp_63488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lxp_63488/04_2026/9lxp_63488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lxp_63488/04_2026/9lxp_63488.map" model { file = "/net/cci-nas-00/data/ceres_data/9lxp_63488/04_2026/9lxp_63488_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lxp_63488/04_2026/9lxp_63488_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.034 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 4 5.49 5 S 42 5.16 5 C 5467 2.51 5 N 1426 2.21 5 O 1570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8509 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2715 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1537 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1527 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "R" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2452 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 302} Chain breaks: 5 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 2.13, per 1000 atoms: 0.25 Number of scatterers: 8509 At special positions: 0 Unit cell: (85.41, 102.2, 186.15, 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 42 16.00 P 4 15.00 O 1570 8.00 N 1426 7.00 C 5467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS R 397 " distance=2.25 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS C 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 393.2 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 17 sheets defined 30.1% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.912A pdb=" N ARG B 282 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.505A pdb=" N GLU B 364 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.941A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'L' and resid 2 through 33 Processing helix chain 'R' and resid 33 through 44 removed outlier: 4.183A pdb=" N GLN R 37 " --> pdb=" O THR R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 179 removed outlier: 3.668A pdb=" N THR R 178 " --> pdb=" O THR R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 212 removed outlier: 3.700A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 276 through 312 Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'R' and resid 329 through 347 removed outlier: 3.764A pdb=" N ALA R 333 " --> pdb=" O TRP R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.688A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 388 removed outlier: 3.891A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 401 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.570A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 473 Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.576A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 80 " --> pdb=" O CYS B 59 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 188 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.062A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.062A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 230 through 231 removed outlier: 3.595A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 10 removed outlier: 4.018A pdb=" N VAL C 8 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 14 through 15 removed outlier: 8.536A pdb=" N SER C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER C 55 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.081A pdb=" N TYR C 112 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 130 through 134 removed outlier: 6.272A pdb=" N TYR C 186 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 7 removed outlier: 5.967A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.559A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.551A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.617A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 151 445 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2376 1.33 - 1.46: 1643 1.46 - 1.58: 4619 1.58 - 1.70: 15 1.70 - 1.82: 57 Bond restraints: 8710 Sorted by residual: bond pdb=" OG1 TPO R 503 " pdb=" P TPO R 503 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO R 506 " pdb=" P TPO R 506 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3P TPO R 503 " pdb=" P TPO R 503 " ideal model delta sigma weight residual 1.528 1.611 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O2P TPO R 506 " pdb=" P TPO R 506 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3P TPO R 506 " pdb=" P TPO R 506 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 8705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 11622 3.20 - 6.41: 221 6.41 - 9.61: 10 9.61 - 12.81: 2 12.81 - 16.01: 1 Bond angle restraints: 11856 Sorted by residual: angle pdb=" CA VAL B 70 " pdb=" CB VAL B 70 " pdb=" CG1 VAL B 70 " ideal model delta sigma weight residual 110.40 126.41 -16.01 1.70e+00 3.46e-01 8.87e+01 angle pdb=" N VAL R 432 " pdb=" CA VAL R 432 " pdb=" C VAL R 432 " ideal model delta sigma weight residual 111.67 104.91 6.76 9.50e-01 1.11e+00 5.06e+01 angle pdb=" C LEU L 7 " pdb=" N MET L 8 " pdb=" CA MET L 8 " ideal model delta sigma weight residual 120.28 128.43 -8.15 1.34e+00 5.57e-01 3.70e+01 angle pdb=" C MET R 425 " pdb=" CA MET R 425 " pdb=" CB MET R 425 " ideal model delta sigma weight residual 116.63 109.68 6.95 1.16e+00 7.43e-01 3.59e+01 angle pdb=" C ASP B 69 " pdb=" N VAL B 70 " pdb=" CA VAL B 70 " ideal model delta sigma weight residual 120.77 128.22 -7.45 1.46e+00 4.69e-01 2.60e+01 ... (remaining 11851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4927 17.97 - 35.94: 167 35.94 - 53.90: 38 53.90 - 71.87: 6 71.87 - 89.84: 6 Dihedral angle restraints: 5144 sinusoidal: 1926 harmonic: 3218 Sorted by residual: dihedral pdb=" CB CYS B 81 " pdb=" SG CYS B 81 " pdb=" SG CYS R 397 " pdb=" CB CYS R 397 " ideal model delta sinusoidal sigma weight residual 93.00 175.21 -82.21 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CA ASP B 67 " pdb=" C ASP B 67 " pdb=" N LEU B 68 " pdb=" CA LEU B 68 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR B 249 " pdb=" C TYR B 249 " pdb=" N LYS B 250 " pdb=" CA LYS B 250 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 5141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1328 0.145 - 0.290: 35 0.290 - 0.435: 1 0.435 - 0.581: 0 0.581 - 0.726: 1 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CB VAL B 70 " pdb=" CA VAL B 70 " pdb=" CG1 VAL B 70 " pdb=" CG2 VAL B 70 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA ASP B 67 " pdb=" N ASP B 67 " pdb=" C ASP B 67 " pdb=" CB ASP B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB THR R 325 " pdb=" CA THR R 325 " pdb=" OG1 THR R 325 " pdb=" CG2 THR R 325 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1362 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS R 223 " 0.051 2.00e-02 2.50e+03 3.87e-02 2.24e+01 pdb=" CG HIS R 223 " -0.066 2.00e-02 2.50e+03 pdb=" ND1 HIS R 223 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS R 223 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS R 223 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS R 223 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 417 " -0.046 2.00e-02 2.50e+03 3.12e-02 1.71e+01 pdb=" CG PHE R 417 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE R 417 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE R 417 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE R 417 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE R 417 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE R 417 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 61 " -0.050 2.00e-02 2.50e+03 3.10e-02 1.68e+01 pdb=" CG PHE B 61 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 61 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 61 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE B 61 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 61 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 61 " -0.030 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 133 2.65 - 3.22: 8068 3.22 - 3.78: 12690 3.78 - 4.34: 17966 4.34 - 4.90: 29702 Nonbonded interactions: 68559 Sorted by model distance: nonbonded pdb=" O TYR R 429 " pdb=" OG1 THR R 430 " model vdw 2.093 3.040 nonbonded pdb=" OG SER C 20 " pdb=" OD1 ASN C 87 " model vdw 2.143 3.040 nonbonded pdb=" OD2 ASP B 297 " pdb=" OH TYR C 60 " model vdw 2.174 3.040 nonbonded pdb=" NZ LYS B 107 " pdb=" O ASN R 507 " model vdw 2.174 3.120 nonbonded pdb=" CE3 TRP R 361 " pdb=" OE1 GLN R 364 " model vdw 2.193 3.340 ... (remaining 68554 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 0.215 8714 Z= 0.416 Angle : 0.976 16.013 11864 Z= 0.652 Chirality : 0.061 0.726 1365 Planarity : 0.006 0.080 1481 Dihedral : 10.225 89.840 3056 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 0.66 % Allowed : 4.39 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1064 helix: 1.66 (0.30), residues: 285 sheet: 1.02 (0.30), residues: 335 loop : -0.56 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.032 0.002 TYR R 296 PHE 0.050 0.004 PHE B 61 TRP 0.043 0.004 TRP R 437 HIS 0.023 0.002 HIS L 9 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 8710) covalent geometry : angle 0.96512 (11856) SS BOND : bond 0.10812 ( 4) SS BOND : angle 5.78897 ( 8) hydrogen bonds : bond 0.19225 ( 423) hydrogen bonds : angle 7.37215 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 251 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 LEU cc_start: 0.7202 (mt) cc_final: 0.6849 (mt) REVERT: B 272 TYR cc_start: 0.7679 (m-80) cc_final: 0.7477 (m-80) REVERT: C 68 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7434 (mmmt) REVERT: C 174 HIS cc_start: 0.6322 (m-70) cc_final: 0.5965 (m-70) REVERT: E 107 ILE cc_start: 0.7969 (mt) cc_final: 0.7587 (mt) REVERT: E 117 PHE cc_start: 0.7519 (m-80) cc_final: 0.7310 (m-80) REVERT: E 137 LEU cc_start: 0.5787 (mp) cc_final: 0.5198 (mm) REVERT: E 138 ASN cc_start: 0.6239 (m110) cc_final: 0.5706 (t0) REVERT: E 174 TYR cc_start: 0.7101 (m-80) cc_final: 0.6207 (m-80) REVERT: R 166 ASN cc_start: 0.4219 (m110) cc_final: 0.3953 (p0) REVERT: R 220 ASN cc_start: 0.7234 (m-40) cc_final: 0.6222 (t0) REVERT: R 223 HIS cc_start: 0.8017 (m-70) cc_final: 0.7776 (m-70) REVERT: R 311 PHE cc_start: 0.6901 (m-80) cc_final: 0.6661 (m-10) REVERT: R 315 PHE cc_start: 0.4935 (t80) cc_final: 0.4527 (t80) REVERT: R 358 ASN cc_start: 0.5665 (m-40) cc_final: 0.5348 (p0) REVERT: R 374 ASN cc_start: 0.6396 (t0) cc_final: 0.5396 (p0) REVERT: R 408 LYS cc_start: 0.8033 (tptm) cc_final: 0.7316 (tppt) REVERT: R 441 MET cc_start: 0.7427 (mmt) cc_final: 0.7100 (mmt) REVERT: R 457 ILE cc_start: 0.7941 (mm) cc_final: 0.7658 (pt) outliers start: 6 outliers final: 2 residues processed: 253 average time/residue: 0.1267 time to fit residues: 41.0708 Evaluate side-chains 162 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 445 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 161 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 GLN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.155371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.114312 restraints weight = 18081.136| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.73 r_work: 0.3630 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8714 Z= 0.182 Angle : 0.675 11.320 11864 Z= 0.350 Chirality : 0.045 0.201 1365 Planarity : 0.005 0.039 1481 Dihedral : 5.368 81.960 1201 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 2.96 % Allowed : 9.98 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1064 helix: 2.17 (0.30), residues: 279 sheet: 0.85 (0.29), residues: 337 loop : -0.53 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 285 TYR 0.025 0.002 TYR R 191 PHE 0.018 0.002 PHE R 335 TRP 0.019 0.002 TRP L 14 HIS 0.006 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8710) covalent geometry : angle 0.67296 (11856) SS BOND : bond 0.00935 ( 4) SS BOND : angle 2.25482 ( 8) hydrogen bonds : bond 0.04454 ( 423) hydrogen bonds : angle 5.01752 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 ASP cc_start: 0.6283 (m-30) cc_final: 0.6078 (m-30) REVERT: B 358 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5280 (mm-30) REVERT: C 68 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7543 (mmmt) REVERT: C 106 TRP cc_start: 0.6275 (m100) cc_final: 0.2629 (t-100) REVERT: C 174 HIS cc_start: 0.6254 (m-70) cc_final: 0.5839 (m-70) REVERT: E 136 LEU cc_start: 0.5234 (tp) cc_final: 0.4976 (tp) REVERT: E 137 LEU cc_start: 0.6380 (mp) cc_final: 0.5923 (mm) REVERT: E 138 ASN cc_start: 0.6615 (m110) cc_final: 0.5824 (t0) REVERT: E 140 PHE cc_start: 0.7561 (p90) cc_final: 0.6914 (p90) REVERT: R 166 ASN cc_start: 0.4390 (m110) cc_final: 0.3868 (p0) REVERT: R 180 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7101 (mm-30) REVERT: R 189 MET cc_start: 0.6712 (mtt) cc_final: 0.6194 (mtp) REVERT: R 219 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8073 (ttp80) REVERT: R 223 HIS cc_start: 0.8007 (m-70) cc_final: 0.7555 (m-70) REVERT: R 231 MET cc_start: 0.8472 (mtm) cc_final: 0.8090 (mtm) REVERT: R 290 TYR cc_start: 0.7627 (t80) cc_final: 0.7406 (t80) REVERT: R 295 ASN cc_start: 0.6716 (t0) cc_final: 0.6323 (t0) REVERT: R 358 ASN cc_start: 0.6117 (m-40) cc_final: 0.5842 (p0) REVERT: R 408 LYS cc_start: 0.7751 (tptm) cc_final: 0.6972 (tppt) REVERT: R 425 MET cc_start: 0.7669 (tmm) cc_final: 0.7225 (tmm) REVERT: R 457 ILE cc_start: 0.7906 (mm) cc_final: 0.7628 (pt) outliers start: 27 outliers final: 14 residues processed: 185 average time/residue: 0.1030 time to fit residues: 25.5580 Evaluate side-chains 155 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 78 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN E 7 GLN E 101 GLN E 138 ASN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN R 220 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.156357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.116756 restraints weight = 18129.676| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.78 r_work: 0.3659 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8714 Z= 0.131 Angle : 0.638 10.847 11864 Z= 0.323 Chirality : 0.044 0.185 1365 Planarity : 0.004 0.036 1481 Dihedral : 5.059 81.035 1196 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 2.63 % Allowed : 10.75 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 1064 helix: 2.01 (0.30), residues: 279 sheet: 0.87 (0.29), residues: 338 loop : -0.51 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 285 TYR 0.021 0.001 TYR R 191 PHE 0.035 0.002 PHE R 335 TRP 0.016 0.001 TRP L 14 HIS 0.006 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8710) covalent geometry : angle 0.62862 (11856) SS BOND : bond 0.00232 ( 4) SS BOND : angle 4.29898 ( 8) hydrogen bonds : bond 0.03891 ( 423) hydrogen bonds : angle 4.74065 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8868 (mp) REVERT: B 189 GLN cc_start: 0.6777 (tt0) cc_final: 0.6470 (tt0) REVERT: B 192 MET cc_start: 0.4938 (OUTLIER) cc_final: 0.4383 (mtm) REVERT: B 358 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5651 (mm-30) REVERT: C 148 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6585 (mt) REVERT: C 174 HIS cc_start: 0.6315 (m-70) cc_final: 0.5938 (m-70) REVERT: E 12 LEU cc_start: 0.6797 (mt) cc_final: 0.6211 (mt) REVERT: E 136 LEU cc_start: 0.5452 (tp) cc_final: 0.5033 (tp) REVERT: E 137 LEU cc_start: 0.6441 (mp) cc_final: 0.5684 (mm) REVERT: E 138 ASN cc_start: 0.6661 (m-40) cc_final: 0.5807 (t0) REVERT: E 210 PHE cc_start: 0.6098 (p90) cc_final: 0.5227 (m-80) REVERT: L 28 ILE cc_start: 0.7842 (pt) cc_final: 0.7577 (mm) REVERT: R 166 ASN cc_start: 0.4330 (m110) cc_final: 0.3793 (p0) REVERT: R 202 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7806 (mm) REVERT: R 223 HIS cc_start: 0.8008 (m-70) cc_final: 0.7538 (m-70) REVERT: R 241 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: R 358 ASN cc_start: 0.5981 (m-40) cc_final: 0.5725 (p0) REVERT: R 408 LYS cc_start: 0.7674 (tptm) cc_final: 0.6916 (tppt) REVERT: R 425 MET cc_start: 0.7694 (tmm) cc_final: 0.7274 (tmm) REVERT: R 457 ILE cc_start: 0.7804 (mm) cc_final: 0.7522 (pt) REVERT: R 463 ASN cc_start: 0.6428 (t0) cc_final: 0.6167 (t0) outliers start: 24 outliers final: 11 residues processed: 165 average time/residue: 0.0921 time to fit residues: 20.7773 Evaluate side-chains 155 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.156013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.118406 restraints weight = 18285.589| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 4.15 r_work: 0.3629 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8714 Z= 0.131 Angle : 0.614 11.862 11864 Z= 0.312 Chirality : 0.043 0.188 1365 Planarity : 0.004 0.037 1481 Dihedral : 4.957 81.496 1196 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.55 % Favored : 94.27 % Rotamer: Outliers : 3.07 % Allowed : 11.95 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 1064 helix: 1.98 (0.31), residues: 280 sheet: 0.84 (0.29), residues: 339 loop : -0.55 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 285 TYR 0.022 0.001 TYR E 141 PHE 0.027 0.002 PHE R 335 TRP 0.017 0.001 TRP R 352 HIS 0.008 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8710) covalent geometry : angle 0.60384 (11856) SS BOND : bond 0.00268 ( 4) SS BOND : angle 4.34973 ( 8) hydrogen bonds : bond 0.03732 ( 423) hydrogen bonds : angle 4.66163 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8856 (mp) REVERT: B 192 MET cc_start: 0.4957 (OUTLIER) cc_final: 0.4622 (mtm) REVERT: B 358 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5355 (mm-30) REVERT: C 106 TRP cc_start: 0.6202 (m100) cc_final: 0.2653 (t-100) REVERT: C 148 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6619 (mt) REVERT: C 174 HIS cc_start: 0.6349 (m-70) cc_final: 0.5917 (m-70) REVERT: E 12 LEU cc_start: 0.6758 (mt) cc_final: 0.6204 (mt) REVERT: E 136 LEU cc_start: 0.5574 (tp) cc_final: 0.5193 (tp) REVERT: E 137 LEU cc_start: 0.6535 (mp) cc_final: 0.5852 (mm) REVERT: E 138 ASN cc_start: 0.6898 (m-40) cc_final: 0.6110 (t0) REVERT: E 210 PHE cc_start: 0.5988 (p90) cc_final: 0.5170 (m-80) REVERT: L 28 ILE cc_start: 0.7922 (pt) cc_final: 0.7653 (mm) REVERT: R 202 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7795 (mm) REVERT: R 241 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: R 358 ASN cc_start: 0.5984 (m-40) cc_final: 0.5716 (p0) REVERT: R 408 LYS cc_start: 0.7663 (tptm) cc_final: 0.6907 (tppt) REVERT: R 425 MET cc_start: 0.7755 (tmm) cc_final: 0.7368 (tmm) REVERT: R 457 ILE cc_start: 0.7769 (mm) cc_final: 0.7485 (pt) REVERT: R 463 ASN cc_start: 0.6455 (t0) cc_final: 0.6195 (t0) outliers start: 28 outliers final: 12 residues processed: 165 average time/residue: 0.0966 time to fit residues: 21.9012 Evaluate side-chains 153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 237 GLN E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.152817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.112929 restraints weight = 18066.602| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.56 r_work: 0.3579 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8714 Z= 0.242 Angle : 0.721 15.666 11864 Z= 0.371 Chirality : 0.046 0.197 1365 Planarity : 0.005 0.041 1481 Dihedral : 5.445 87.081 1196 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.55 % Rotamer: Outliers : 2.96 % Allowed : 13.60 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.27), residues: 1064 helix: 1.72 (0.31), residues: 279 sheet: 0.45 (0.28), residues: 340 loop : -0.69 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 285 TYR 0.028 0.002 TYR E 92 PHE 0.035 0.002 PHE R 335 TRP 0.016 0.002 TRP C 50 HIS 0.006 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 8710) covalent geometry : angle 0.71093 (11856) SS BOND : bond 0.00682 ( 4) SS BOND : angle 4.63487 ( 8) hydrogen bonds : bond 0.04118 ( 423) hydrogen bonds : angle 4.99478 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8070 (mp0) cc_final: 0.7797 (mp0) REVERT: B 77 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7955 (pttm) REVERT: B 192 MET cc_start: 0.4941 (OUTLIER) cc_final: 0.4641 (mtm) REVERT: B 358 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5201 (mm-30) REVERT: C 106 TRP cc_start: 0.6397 (m100) cc_final: 0.2659 (t-100) REVERT: C 148 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6618 (mt) REVERT: C 174 HIS cc_start: 0.6326 (m-70) cc_final: 0.5823 (m-70) REVERT: E 136 LEU cc_start: 0.5739 (tp) cc_final: 0.5312 (tp) REVERT: E 137 LEU cc_start: 0.6617 (mp) cc_final: 0.5999 (mm) REVERT: E 138 ASN cc_start: 0.6973 (m-40) cc_final: 0.6262 (t0) REVERT: E 166 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7999 (mt-10) REVERT: E 210 PHE cc_start: 0.6320 (p90) cc_final: 0.5406 (m-80) REVERT: R 32 MET cc_start: 0.4267 (pmm) cc_final: 0.3513 (pmm) REVERT: R 166 ASN cc_start: 0.4354 (m110) cc_final: 0.3242 (p0) REVERT: R 202 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7862 (mm) REVERT: R 241 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: R 317 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6910 (tm-30) REVERT: R 358 ASN cc_start: 0.6012 (m-40) cc_final: 0.5713 (p0) REVERT: R 408 LYS cc_start: 0.7782 (tptm) cc_final: 0.6948 (tppt) REVERT: R 425 MET cc_start: 0.7875 (tmm) cc_final: 0.7457 (tmm) REVERT: R 457 ILE cc_start: 0.7724 (mm) cc_final: 0.7437 (pt) outliers start: 27 outliers final: 13 residues processed: 155 average time/residue: 0.0904 time to fit residues: 19.4459 Evaluate side-chains 144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 48 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 237 GLN E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN R 364 GLN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.152211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.113263 restraints weight = 17467.463| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.43 r_work: 0.3651 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8714 Z= 0.143 Angle : 0.636 13.442 11864 Z= 0.324 Chirality : 0.043 0.172 1365 Planarity : 0.004 0.039 1481 Dihedral : 5.154 85.749 1196 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.55 % Rotamer: Outliers : 3.07 % Allowed : 13.38 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.27), residues: 1064 helix: 1.78 (0.31), residues: 280 sheet: 0.51 (0.29), residues: 340 loop : -0.69 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 285 TYR 0.030 0.001 TYR R 305 PHE 0.037 0.002 PHE R 335 TRP 0.017 0.002 TRP L 14 HIS 0.007 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8710) covalent geometry : angle 0.62922 (11856) SS BOND : bond 0.00517 ( 4) SS BOND : angle 3.50788 ( 8) hydrogen bonds : bond 0.03695 ( 423) hydrogen bonds : angle 4.73334 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8030 (mp0) cc_final: 0.7732 (mp0) REVERT: B 77 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7821 (pttm) REVERT: B 358 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5265 (mm-30) REVERT: C 16 GLN cc_start: 0.8305 (mt0) cc_final: 0.7840 (mm-40) REVERT: C 106 TRP cc_start: 0.6240 (m100) cc_final: 0.2636 (t-100) REVERT: C 148 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6572 (mt) REVERT: C 174 HIS cc_start: 0.6238 (m-70) cc_final: 0.5719 (m-70) REVERT: E 136 LEU cc_start: 0.5606 (tp) cc_final: 0.5367 (tp) REVERT: E 137 LEU cc_start: 0.6573 (mp) cc_final: 0.6005 (mm) REVERT: E 138 ASN cc_start: 0.6917 (m-40) cc_final: 0.6516 (m-40) REVERT: E 141 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.6470 (t80) REVERT: E 149 TRP cc_start: 0.4631 (m100) cc_final: 0.4281 (m100) REVERT: E 166 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7951 (mt-10) REVERT: E 210 PHE cc_start: 0.6421 (p90) cc_final: 0.5405 (m-80) REVERT: L 28 ILE cc_start: 0.7859 (pt) cc_final: 0.7649 (mm) REVERT: R 32 MET cc_start: 0.4155 (pmm) cc_final: 0.3528 (pmm) REVERT: R 37 GLN cc_start: 0.7592 (mm-40) cc_final: 0.6973 (tm-30) REVERT: R 166 ASN cc_start: 0.4370 (m110) cc_final: 0.3123 (p0) REVERT: R 202 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7755 (mm) REVERT: R 241 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: R 317 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6891 (tm-30) REVERT: R 358 ASN cc_start: 0.5952 (m-40) cc_final: 0.5656 (p0) REVERT: R 425 MET cc_start: 0.7812 (tmm) cc_final: 0.7443 (tmm) REVERT: R 457 ILE cc_start: 0.7694 (mm) cc_final: 0.7412 (pt) outliers start: 28 outliers final: 14 residues processed: 155 average time/residue: 0.0951 time to fit residues: 20.2112 Evaluate side-chains 144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain E residue 141 TYR Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 67 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 HIS R 364 GLN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.151902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.113295 restraints weight = 18108.162| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.43 r_work: 0.3630 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8714 Z= 0.220 Angle : 0.687 13.595 11864 Z= 0.354 Chirality : 0.045 0.247 1365 Planarity : 0.004 0.041 1481 Dihedral : 5.423 88.801 1196 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.55 % Rotamer: Outliers : 3.18 % Allowed : 14.14 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.27), residues: 1064 helix: 1.67 (0.31), residues: 280 sheet: 0.24 (0.28), residues: 342 loop : -0.76 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 285 TYR 0.025 0.002 TYR E 92 PHE 0.033 0.002 PHE R 335 TRP 0.021 0.002 TRP L 14 HIS 0.006 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 8710) covalent geometry : angle 0.68297 (11856) SS BOND : bond 0.00754 ( 4) SS BOND : angle 2.89459 ( 8) hydrogen bonds : bond 0.03957 ( 423) hydrogen bonds : angle 4.87027 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8185 (mp0) cc_final: 0.7848 (mp0) REVERT: B 77 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8146 (pttm) REVERT: B 358 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5644 (mm-30) REVERT: C 16 GLN cc_start: 0.8464 (mt0) cc_final: 0.8024 (mm-40) REVERT: C 148 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6662 (mt) REVERT: C 174 HIS cc_start: 0.6391 (m-70) cc_final: 0.5872 (m-70) REVERT: E 81 PRO cc_start: 0.8252 (Cg_exo) cc_final: 0.8041 (Cg_endo) REVERT: E 137 LEU cc_start: 0.6716 (mp) cc_final: 0.6425 (mm) REVERT: E 166 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8121 (mt-10) REVERT: E 210 PHE cc_start: 0.6574 (p90) cc_final: 0.5658 (m-80) REVERT: L 28 ILE cc_start: 0.7973 (pt) cc_final: 0.7760 (mm) REVERT: R 32 MET cc_start: 0.4453 (pmm) cc_final: 0.3871 (pmm) REVERT: R 202 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7904 (mm) REVERT: R 241 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: R 408 LYS cc_start: 0.7778 (tptt) cc_final: 0.6964 (tppt) REVERT: R 425 MET cc_start: 0.7886 (tmm) cc_final: 0.7537 (tmm) REVERT: R 457 ILE cc_start: 0.7737 (mm) cc_final: 0.7453 (pt) outliers start: 29 outliers final: 15 residues processed: 147 average time/residue: 0.0994 time to fit residues: 19.9816 Evaluate side-chains 144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 288 PHE Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.0570 chunk 66 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 9 optimal weight: 3.9990 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.153734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.115152 restraints weight = 17821.498| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.57 r_work: 0.3732 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8714 Z= 0.124 Angle : 0.622 12.022 11864 Z= 0.316 Chirality : 0.043 0.237 1365 Planarity : 0.005 0.074 1481 Dihedral : 5.143 86.319 1196 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.61 % Favored : 95.21 % Rotamer: Outliers : 2.41 % Allowed : 15.02 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.27), residues: 1064 helix: 1.96 (0.32), residues: 271 sheet: 0.48 (0.29), residues: 340 loop : -0.63 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 233 TYR 0.023 0.001 TYR R 191 PHE 0.032 0.001 PHE R 335 TRP 0.018 0.002 TRP L 14 HIS 0.006 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8710) covalent geometry : angle 0.61851 (11856) SS BOND : bond 0.00346 ( 4) SS BOND : angle 2.46473 ( 8) hydrogen bonds : bond 0.03557 ( 423) hydrogen bonds : angle 4.59397 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8112 (mp0) cc_final: 0.7784 (mp0) REVERT: B 63 TYR cc_start: 0.8801 (p90) cc_final: 0.8547 (p90) REVERT: B 77 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8112 (pttm) REVERT: B 222 ASN cc_start: 0.6380 (t0) cc_final: 0.6142 (t0) REVERT: C 16 GLN cc_start: 0.8404 (mt0) cc_final: 0.7965 (mm-40) REVERT: C 148 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6672 (mt) REVERT: C 174 HIS cc_start: 0.6421 (m-70) cc_final: 0.5917 (m-70) REVERT: E 137 LEU cc_start: 0.6617 (mp) cc_final: 0.6345 (mm) REVERT: E 166 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8077 (mt-10) REVERT: E 210 PHE cc_start: 0.6396 (p90) cc_final: 0.5486 (m-80) REVERT: L 28 ILE cc_start: 0.7944 (pt) cc_final: 0.7733 (mm) REVERT: R 32 MET cc_start: 0.4347 (pmm) cc_final: 0.3925 (pmm) REVERT: R 37 GLN cc_start: 0.7495 (mm-40) cc_final: 0.6923 (tm-30) REVERT: R 202 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7799 (mm) REVERT: R 241 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: R 408 LYS cc_start: 0.7775 (tptt) cc_final: 0.6955 (tppt) REVERT: R 425 MET cc_start: 0.7811 (tmm) cc_final: 0.7511 (tmm) REVERT: R 457 ILE cc_start: 0.7671 (mm) cc_final: 0.7455 (pt) outliers start: 22 outliers final: 15 residues processed: 147 average time/residue: 0.0972 time to fit residues: 19.4917 Evaluate side-chains 140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 380 ASN Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 440 GLN Chi-restraints excluded: chain R residue 444 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 80 optimal weight: 0.0570 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 59 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 HIS L 10 GLN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.154659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.116299 restraints weight = 18117.561| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 3.53 r_work: 0.3756 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8714 Z= 0.117 Angle : 0.624 11.979 11864 Z= 0.314 Chirality : 0.043 0.226 1365 Planarity : 0.004 0.060 1481 Dihedral : 4.961 84.727 1196 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 2.08 % Allowed : 15.24 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1064 helix: 1.97 (0.32), residues: 271 sheet: 0.64 (0.29), residues: 334 loop : -0.64 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 21 TYR 0.018 0.001 TYR R 305 PHE 0.032 0.001 PHE R 335 TRP 0.020 0.002 TRP L 14 HIS 0.007 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8710) covalent geometry : angle 0.62131 (11856) SS BOND : bond 0.00397 ( 4) SS BOND : angle 2.13458 ( 8) hydrogen bonds : bond 0.03421 ( 423) hydrogen bonds : angle 4.47117 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8099 (mp0) cc_final: 0.7755 (mp0) REVERT: B 63 TYR cc_start: 0.8793 (p90) cc_final: 0.8540 (p90) REVERT: B 77 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8129 (pttm) REVERT: B 222 ASN cc_start: 0.6391 (t0) cc_final: 0.6132 (t0) REVERT: C 16 GLN cc_start: 0.8387 (mt0) cc_final: 0.7998 (mm-40) REVERT: C 148 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6672 (mt) REVERT: C 174 HIS cc_start: 0.6359 (m-70) cc_final: 0.5887 (m-70) REVERT: E 140 PHE cc_start: 0.7775 (p90) cc_final: 0.7425 (p90) REVERT: E 149 TRP cc_start: 0.5533 (m100) cc_final: 0.4582 (m-10) REVERT: E 166 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8048 (mt-10) REVERT: E 210 PHE cc_start: 0.6309 (p90) cc_final: 0.5469 (m-80) REVERT: R 32 MET cc_start: 0.4303 (pmm) cc_final: 0.3911 (pmm) REVERT: R 37 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6914 (tm-30) REVERT: R 189 MET cc_start: 0.6380 (mtt) cc_final: 0.6078 (ptm) REVERT: R 335 PHE cc_start: 0.6149 (m-80) cc_final: 0.5740 (m-80) REVERT: R 408 LYS cc_start: 0.7749 (tptt) cc_final: 0.6952 (tppt) REVERT: R 425 MET cc_start: 0.7863 (tmm) cc_final: 0.7585 (tmm) outliers start: 19 outliers final: 10 residues processed: 143 average time/residue: 0.0899 time to fit residues: 17.7111 Evaluate side-chains 130 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** 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 = 0.4413 r_free = 0.4413 target = 0.152610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.115746 restraints weight = 17617.718| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.30 r_work: 0.3639 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8714 Z= 0.145 Angle : 0.650 12.308 11864 Z= 0.331 Chirality : 0.043 0.227 1365 Planarity : 0.004 0.056 1481 Dihedral : 5.038 85.142 1196 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 1.86 % Allowed : 16.89 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 1064 helix: 1.81 (0.31), residues: 273 sheet: 0.48 (0.28), residues: 342 loop : -0.58 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 21 TYR 0.019 0.001 TYR R 191 PHE 0.039 0.002 PHE L 23 TRP 0.022 0.002 TRP L 14 HIS 0.006 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8710) covalent geometry : angle 0.64766 (11856) SS BOND : bond 0.00390 ( 4) SS BOND : angle 2.13108 ( 8) hydrogen bonds : bond 0.03535 ( 423) hydrogen bonds : angle 4.54443 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8022 (mp0) cc_final: 0.7696 (mp0) REVERT: B 63 TYR cc_start: 0.8762 (p90) cc_final: 0.8482 (p90) REVERT: B 77 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8001 (pttm) REVERT: B 222 ASN cc_start: 0.6240 (t0) cc_final: 0.6020 (t0) REVERT: C 16 GLN cc_start: 0.8306 (mt0) cc_final: 0.7945 (mm-40) REVERT: C 106 TRP cc_start: 0.6205 (m100) cc_final: 0.2633 (t-100) REVERT: C 148 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6626 (mt) REVERT: C 174 HIS cc_start: 0.6302 (m-70) cc_final: 0.5856 (m-70) REVERT: E 140 PHE cc_start: 0.7677 (p90) cc_final: 0.7307 (p90) REVERT: E 149 TRP cc_start: 0.5497 (m100) cc_final: 0.4616 (m-10) REVERT: E 166 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7970 (mt-10) REVERT: E 210 PHE cc_start: 0.6332 (p90) cc_final: 0.5591 (m-80) REVERT: L 23 PHE cc_start: 0.6849 (t80) cc_final: 0.6444 (t80) REVERT: R 32 MET cc_start: 0.4213 (pmm) cc_final: 0.3759 (pmm) REVERT: R 37 GLN cc_start: 0.7499 (mm-40) cc_final: 0.6919 (tm-30) REVERT: R 335 PHE cc_start: 0.6123 (m-80) cc_final: 0.5720 (m-80) REVERT: R 408 LYS cc_start: 0.7768 (tptt) cc_final: 0.6969 (tppt) REVERT: R 425 MET cc_start: 0.7903 (tmm) cc_final: 0.7637 (tmm) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.0974 time to fit residues: 17.6795 Evaluate side-chains 135 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 138 ASN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.151771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.113044 restraints weight = 17570.597| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.32 r_work: 0.3614 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8714 Z= 0.159 Angle : 0.668 13.359 11864 Z= 0.339 Chirality : 0.044 0.225 1365 Planarity : 0.005 0.051 1481 Dihedral : 5.107 85.668 1196 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.61 % Favored : 95.21 % Rotamer: Outliers : 1.86 % Allowed : 17.54 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 1064 helix: 1.68 (0.32), residues: 274 sheet: 0.46 (0.28), residues: 340 loop : -0.66 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 21 TYR 0.016 0.001 TYR E 92 PHE 0.046 0.002 PHE L 23 TRP 0.023 0.002 TRP L 14 HIS 0.007 0.001 HIS R 42 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8710) covalent geometry : angle 0.66570 (11856) SS BOND : bond 0.00418 ( 4) SS BOND : angle 2.05330 ( 8) hydrogen bonds : bond 0.03612 ( 423) hydrogen bonds : angle 4.61971 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.24 seconds wall clock time: 52 minutes 5.72 seconds (3125.72 seconds total)