Starting phenix.real_space_refine on Fri Oct 23 06:41:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjw_22900/10_2026/7kjw_22900.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.079 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: 8 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 15 5.16 5 Cl 1 4.86 5 C 5384 2.51 5 N 1428 2.21 5 O 1685 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8561 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4317 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 507} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3282 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 29, 'TRANS': 376} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNAv2': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Unusual residues: {'G47': 1} Classifications: {'DNA_mixed': 1, 'RNAv2': 21} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 13} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'EFZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8561 At special positions: 0 Unit cell: (78.72, 106.6, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 1 17.00 S 15 16.00 P 44 15.00 Mg 1 11.99 F 3 9.00 O 1685 8.00 N 1428 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 263.3 milliseconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.1% alpha, 13.4% beta 19 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.861A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 154 through 173 removed outlier: 4.683A pdb=" N ALA A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 4.002A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.127A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.780A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.165A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 removed outlier: 3.546A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.950A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.754A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 removed outlier: 4.085A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.549A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.536A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.147A pdb=" N TYR B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.521A pdb=" N PHE A 61 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 72 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.258A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 353 removed outlier: 8.120A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 327 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.513A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 465 through 468 removed outlier: 3.508A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 493 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA A 534 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 495 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.237A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 354 removed outlier: 5.654A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1290 1.30 - 1.43: 2498 1.43 - 1.55: 4975 1.55 - 1.68: 85 1.68 - 1.81: 28 Bond restraints: 8876 Sorted by residual: bond pdb=" O3' G D 70 " pdb=" P G47 D 71 " ideal model delta sigma weight residual 1.607 1.745 -0.138 1.20e-02 6.94e+03 1.32e+02 bond pdb=" CA ASP A 76 " pdb=" C ASP A 76 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.23e-02 6.61e+03 7.04e+01 bond pdb=" P G47 D 71 " pdb=" O5' G47 D 71 " ideal model delta sigma weight residual 1.684 1.589 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C13 EFZ A 602 " pdb=" F3 EFZ A 602 " ideal model delta sigma weight residual 1.329 1.400 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C13 EFZ A 602 " pdb=" F1 EFZ A 602 " ideal model delta sigma weight residual 1.329 1.398 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12065 1.96 - 3.92: 202 3.92 - 5.88: 17 5.88 - 7.84: 0 7.84 - 9.81: 1 Bond angle restraints: 12285 Sorted by residual: angle pdb=" C3' G D 70 " pdb=" O3' G D 70 " pdb=" P G47 D 71 " ideal model delta sigma weight residual 119.70 109.89 9.81 1.20e+00 6.94e-01 6.68e+01 angle pdb=" N ASP A 76 " pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.63e+00 3.76e-01 1.07e+01 angle pdb=" C VAL A 75 " pdb=" N ASP A 76 " pdb=" CA ASP A 76 " ideal model delta sigma weight residual 122.77 118.47 4.30 1.33e+00 5.65e-01 1.04e+01 angle pdb=" O ASP A 76 " pdb=" C ASP A 76 " pdb=" N PHE A 77 " ideal model delta sigma weight residual 123.22 126.69 -3.47 1.14e+00 7.69e-01 9.27e+00 angle pdb=" CA ASN A 474 " pdb=" C ASN A 474 " pdb=" N GLN A 475 " ideal model delta sigma weight residual 117.22 113.77 3.45 1.17e+00 7.31e-01 8.72e+00 ... (remaining 12280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4608 17.23 - 34.45: 457 34.45 - 51.68: 96 51.68 - 68.91: 36 68.91 - 86.13: 10 Dihedral angle restraints: 5207 sinusoidal: 2439 harmonic: 2768 Sorted by residual: dihedral pdb=" CA GLN B 151 " pdb=" C GLN B 151 " pdb=" N GLY B 152 " pdb=" CA GLY B 152 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " pdb=" CG ASP A 76 " pdb=" OD1 ASP A 76 " ideal model delta sinusoidal sigma weight residual -30.00 -87.54 57.54 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" P G C 197 " pdb=" O5' G C 197 " pdb=" C5' G C 197 " pdb=" C4' G C 197 " ideal model delta sinusoidal sigma weight residual 175.00 129.80 45.20 3 1.30e+01 5.92e-03 1.08e+01 ... (remaining 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1217 0.071 - 0.142: 128 0.142 - 0.213: 3 0.213 - 0.284: 43 0.284 - 0.354: 1 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ASP A 76 " pdb=" N ASP A 76 " pdb=" C ASP A 76 " pdb=" CB ASP A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C3' G47 D 71 " pdb=" C4' G47 D 71 " pdb=" O3' G47 D 71 " pdb=" C2' G47 D 71 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" P C D 56 " pdb=" OP1 C D 56 " pdb=" OP2 C D 56 " pdb=" O5' C D 56 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1389 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G47 D 71 " -0.061 2.00e-02 2.50e+03 1.33e-01 5.71e+02 pdb=" N9 G47 D 71 " -0.010 2.00e-02 2.50e+03 pdb=" C8 G47 D 71 " 0.067 2.00e-02 2.50e+03 pdb=" N7 G47 D 71 " 0.091 2.00e-02 2.50e+03 pdb=" C5 G47 D 71 " 0.023 2.00e-02 2.50e+03 pdb=" C6 G47 D 71 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G47 D 71 " 0.062 2.00e-02 2.50e+03 pdb=" N1 G47 D 71 " -0.066 2.00e-02 2.50e+03 pdb=" C2 G47 D 71 " -0.128 2.00e-02 2.50e+03 pdb=" N2 G47 D 71 " -0.196 2.00e-02 2.50e+03 pdb=" N3 G47 D 71 " -0.116 2.00e-02 2.50e+03 pdb=" C4 G47 D 71 " -0.043 2.00e-02 2.50e+03 pdb=" C6A G47 D 71 " 0.365 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 75 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C VAL A 75 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 75 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 76 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 8 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 9 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " 0.028 5.00e-02 4.00e+02 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 722 2.74 - 3.28: 8418 3.28 - 3.82: 14894 3.82 - 4.36: 18787 4.36 - 4.90: 31118 Nonbonded interactions: 73939 Sorted by model distance: nonbonded pdb=" OD2 ASP B 76 " pdb=" NH1 ARG B 78 " model vdw 2.198 3.120 nonbonded pdb=" NH1 ARG B 72 " pdb=" O LYS B 73 " model vdw 2.223 3.120 nonbonded pdb=" O ASN A 348 " pdb=" ND2 ASN A 348 " model vdw 2.236 3.120 nonbonded pdb=" OH TYR B 354 " pdb=" OE1 GLU B 370 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG A 277 " pdb=" O ALA A 355 " model vdw 2.243 3.120 ... (remaining 73934 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: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.004 0.138 8877 Z= 0.224 Angle : 0.543 9.805 12285 Z= 0.273 Chirality : 0.059 0.354 1392 Planarity : 0.005 0.133 1378 Dihedral : 14.589 86.132 3421 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.33 % Rotamer: Outliers : 0.87 % Allowed : 0.37 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.64 (0.29), residues: 937 helix: 1.63 (0.31), residues: 319 sheet: -0.77 (0.42), residues: 164 loop : 0.14 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 72 TYR 0.015 0.001 TYR A 483 PHE 0.004 0.001 PHE B 346 TRP 0.018 0.001 TRP B 414 HIS 0.003 0.000 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.22 ( 8876) covalent geometry : angle 0.54278 / 0.27 (12285) hydrogen bonds : bond 0.22133 / 14.54 ( 357) hydrogen bonds : angle 8.10229 / 5.85 ( 922) Misc. bond : bond 0.04910 / 3.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.236 Fit side-chains REVERT: A 76 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6611 (t70) REVERT: A 223 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5706 (ptmt) REVERT: A 388 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7508 (tptp) REVERT: B 43 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7676 (mtpt) REVERT: B 173 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7736 (ttmm) REVERT: B 212 TRP cc_start: 0.6863 (m100) cc_final: 0.6106 (t60) REVERT: B 323 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8229 (mtmt) outliers start: 7 outliers final: 1 residues processed: 125 average time/residue: 0.5763 time to fit residues: 76.4974 Evaluate side-chains 74 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 348 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN A 487 GLN B 91 GLN B 151 GLN B 278 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119185 restraints weight = 9919.691| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.54 r_work: 0.3290 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8877 Z= 0.128 Angle : 0.577 8.658 12285 Z= 0.275 Chirality : 0.047 0.296 1392 Planarity : 0.004 0.037 1378 Dihedral : 11.064 73.302 1550 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.24 % Allowed : 8.96 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.59 (0.28), residues: 937 helix: 1.55 (0.29), residues: 336 sheet: -0.87 (0.41), residues: 157 loop : 0.10 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 199 TYR 0.008 0.001 TYR A 144 PHE 0.012 0.001 PHE B 416 TRP 0.011 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8876) covalent geometry : angle 0.57728 / 0.28 (12285) hydrogen bonds : bond 0.04422 / 2.95 ( 357) hydrogen bonds : angle 5.17548 / 3.73 ( 922) Misc. bond : bond 0.00103 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.316 Fit side-chains REVERT: A 223 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.5621 (ptmt) REVERT: A 291 GLU cc_start: 0.7228 (tt0) cc_final: 0.6898 (tt0) REVERT: A 388 LYS cc_start: 0.8480 (mtmt) cc_final: 0.7825 (tptp) REVERT: A 511 ASP cc_start: 0.7534 (m-30) cc_final: 0.7142 (t0) REVERT: B 43 LYS cc_start: 0.8321 (ttpp) cc_final: 0.7909 (mtpt) REVERT: B 173 LYS cc_start: 0.8389 (ttpt) cc_final: 0.7968 (ttmm) REVERT: B 212 TRP cc_start: 0.7126 (m100) cc_final: 0.6047 (t60) REVERT: B 399 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7929 (mm-30) outliers start: 10 outliers final: 3 residues processed: 91 average time/residue: 0.4660 time to fit residues: 45.6411 Evaluate side-chains 73 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [13, 47, 45, 36, 21, 58, 84, 54, 96, 24, 83] chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 54 optimal weight: 0.0270 chunk 96 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116887 restraints weight = 9931.625| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.53 r_work: 0.3247 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8877 Z= 0.161 Angle : 0.571 7.581 12285 Z= 0.269 Chirality : 0.046 0.237 1392 Planarity : 0.004 0.043 1378 Dihedral : 10.840 69.995 1548 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.74 % Allowed : 10.07 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.40 (0.28), residues: 937 helix: 1.32 (0.28), residues: 340 sheet: -0.99 (0.40), residues: 157 loop : 0.05 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 211 TYR 0.011 0.001 TYR B 144 PHE 0.014 0.002 PHE B 416 TRP 0.013 0.001 TRP A 402 HIS 0.002 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 8876) covalent geometry : angle 0.57050 / 0.27 (12285) hydrogen bonds : bond 0.03853 / 2.55 ( 357) hydrogen bonds : angle 4.88824 / 3.52 ( 922) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.284 Fit side-chains REVERT: A 16 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6689 (mtt) REVERT: A 76 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6234 (t70) REVERT: A 223 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5437 (ptmt) REVERT: A 298 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 388 LYS cc_start: 0.8508 (mtmt) cc_final: 0.7844 (tptp) REVERT: A 509 GLN cc_start: 0.8598 (mt0) cc_final: 0.8396 (mt0) REVERT: A 511 ASP cc_start: 0.7568 (m-30) cc_final: 0.7175 (t0) REVERT: B 43 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7879 (mtpt) REVERT: B 173 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8037 (ttmm) REVERT: B 211 ARG cc_start: 0.7367 (mtm110) cc_final: 0.7117 (mtp85) REVERT: B 212 TRP cc_start: 0.7250 (m100) cc_final: 0.6008 (t60) REVERT: B 399 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7909 (mm-30) REVERT: B 423 VAL cc_start: 0.8615 (p) cc_final: 0.8294 (t) outliers start: 22 outliers final: 5 residues processed: 92 average time/residue: 0.4550 time to fit residues: 45.1453 Evaluate side-chains 79 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [25, 77, 57, 72, 63, 9, 35, 31, 96, 91, 61] chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116333 restraints weight = 10050.514| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.55 r_work: 0.3242 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8877 Z= 0.163 Angle : 0.558 7.540 12285 Z= 0.265 Chirality : 0.045 0.220 1392 Planarity : 0.004 0.044 1378 Dihedral : 10.829 71.366 1546 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.86 % Allowed : 11.44 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.36 (0.28), residues: 937 helix: 1.30 (0.29), residues: 339 sheet: -1.01 (0.40), residues: 157 loop : 0.01 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.010 0.001 TYR A 483 PHE 0.014 0.002 PHE B 416 TRP 0.014 0.001 TRP A 402 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 8876) covalent geometry : angle 0.55830 / 0.26 (12285) hydrogen bonds : bond 0.03588 / 2.38 ( 357) hydrogen bonds : angle 4.76320 / 3.42 ( 922) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.284 Fit side-chains REVERT: A 223 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.5440 (ptmt) REVERT: A 298 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: A 388 LYS cc_start: 0.8498 (mtmt) cc_final: 0.7892 (tptp) REVERT: A 511 ASP cc_start: 0.7711 (m-30) cc_final: 0.7450 (t0) REVERT: B 43 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7957 (mtpt) REVERT: B 173 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8085 (ttmm) REVERT: B 211 ARG cc_start: 0.7535 (mtm110) cc_final: 0.7261 (mtp85) REVERT: B 212 TRP cc_start: 0.7337 (m100) cc_final: 0.6130 (t60) REVERT: B 302 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: B 423 VAL cc_start: 0.8614 (p) cc_final: 0.8306 (t) outliers start: 23 outliers final: 8 residues processed: 90 average time/residue: 0.4440 time to fit residues: 43.2008 Evaluate side-chains 77 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [50, 58, 36, 13, 5, 88, 3, 80, 78, 42, 7] chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117638 restraints weight = 9944.846| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.54 r_work: 0.3261 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8877 Z= 0.132 Angle : 0.534 7.519 12285 Z= 0.252 Chirality : 0.044 0.196 1392 Planarity : 0.004 0.045 1378 Dihedral : 10.837 72.034 1546 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.61 % Allowed : 11.94 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.43 (0.28), residues: 937 helix: 1.35 (0.29), residues: 339 sheet: -0.96 (0.41), residues: 157 loop : 0.06 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.021 0.001 TYR A 127 PHE 0.011 0.001 PHE B 416 TRP 0.014 0.001 TRP A 402 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8876) covalent geometry : angle 0.53398 / 0.25 (12285) hydrogen bonds : bond 0.03305 / 2.18 ( 357) hydrogen bonds : angle 4.62573 / 3.33 ( 922) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.257 Fit side-chains REVERT: A 76 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6158 (t0) REVERT: A 223 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.5429 (ptmt) REVERT: A 298 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 388 LYS cc_start: 0.8462 (mtmt) cc_final: 0.7902 (tptp) REVERT: A 511 ASP cc_start: 0.7620 (m-30) cc_final: 0.7374 (t0) REVERT: B 43 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7971 (mtpt) REVERT: B 173 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8114 (ttmm) REVERT: B 186 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 212 TRP cc_start: 0.7280 (m100) cc_final: 0.6157 (t60) REVERT: B 423 VAL cc_start: 0.8630 (p) cc_final: 0.8352 (t) outliers start: 21 outliers final: 6 residues processed: 92 average time/residue: 0.4415 time to fit residues: 43.9718 Evaluate side-chains 74 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [77, 79, 52, 33, 46, 22, 13, 21, 93, 62, 54] chunk 77 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 464 GLN ** 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 = 0.3974 r_free = 0.3974 target = 0.164055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126617 restraints weight = 9869.417| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.51 r_work: 0.3394 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8877 Z= 0.115 Angle : 0.523 7.517 12285 Z= 0.248 Chirality : 0.044 0.174 1392 Planarity : 0.004 0.045 1378 Dihedral : 10.841 72.441 1546 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.99 % Allowed : 13.43 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.28), residues: 937 helix: 1.41 (0.29), residues: 339 sheet: -0.90 (0.41), residues: 157 loop : 0.12 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 211 TYR 0.020 0.001 TYR A 127 PHE 0.007 0.001 PHE A 160 TRP 0.014 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8876) covalent geometry : angle 0.52339 / 0.25 (12285) hydrogen bonds : bond 0.03165 / 2.08 ( 357) hydrogen bonds : angle 4.51085 / 3.25 ( 922) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.243 Fit side-chains REVERT: A 11 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7686 (ptmm) REVERT: A 223 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5353 (ptmt) REVERT: A 298 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 388 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7885 (tptp) REVERT: A 511 ASP cc_start: 0.7668 (m-30) cc_final: 0.7428 (t0) REVERT: B 43 LYS cc_start: 0.8363 (ttpp) cc_final: 0.7996 (mtpt) REVERT: B 186 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 211 ARG cc_start: 0.7407 (mtm110) cc_final: 0.7048 (mtp85) REVERT: B 212 TRP cc_start: 0.7274 (m100) cc_final: 0.6209 (t60) REVERT: B 423 VAL cc_start: 0.8598 (p) cc_final: 0.8360 (t) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 0.4425 time to fit residues: 39.2970 Evaluate side-chains 75 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [6, 12, 89, 19, 69, 58, 36, 26, 71, 95, 97] chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 GLN B 161 GLN B 332 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113920 restraints weight = 10046.876| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.43 r_work: 0.3203 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 8877 Z= 0.277 Angle : 0.631 9.037 12285 Z= 0.302 Chirality : 0.048 0.178 1392 Planarity : 0.004 0.046 1378 Dihedral : 10.885 70.642 1546 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.86 % Allowed : 13.06 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.20 (0.27), residues: 937 helix: 1.11 (0.29), residues: 332 sheet: -1.05 (0.41), residues: 157 loop : -0.03 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 211 TYR 0.029 0.002 TYR A 127 PHE 0.014 0.002 PHE B 416 TRP 0.014 0.002 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.28 ( 8876) covalent geometry : angle 0.63111 / 0.30 (12285) hydrogen bonds : bond 0.03895 / 2.55 ( 357) hydrogen bonds : angle 4.88676 / 3.51 ( 922) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.318 Fit side-chains REVERT: A 223 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5429 (ptmt) REVERT: A 388 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7822 (tptp) REVERT: A 511 ASP cc_start: 0.7663 (m-30) cc_final: 0.7374 (t0) REVERT: B 43 LYS cc_start: 0.8454 (ttpp) cc_final: 0.7986 (mtpt) REVERT: B 70 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7631 (pttt) REVERT: B 186 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: B 211 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7023 (mtp85) REVERT: B 212 TRP cc_start: 0.7279 (m100) cc_final: 0.6212 (t60) REVERT: B 284 ARG cc_start: 0.7442 (mmp-170) cc_final: 0.7213 (mmp-170) outliers start: 23 outliers final: 11 residues processed: 83 average time/residue: 0.5032 time to fit residues: 44.9024 Evaluate side-chains 74 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [33, 4, 24, 87, 89, 71, 19, 73, 72, 57, 65] chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117571 restraints weight = 9984.820| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.42 r_work: 0.3252 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8877 Z= 0.127 Angle : 0.536 7.510 12285 Z= 0.254 Chirality : 0.044 0.164 1392 Planarity : 0.004 0.045 1378 Dihedral : 10.905 72.816 1546 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.99 % Allowed : 13.81 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.43 (0.28), residues: 937 helix: 1.36 (0.29), residues: 333 sheet: -0.97 (0.41), residues: 158 loop : 0.08 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 211 TYR 0.023 0.001 TYR A 127 PHE 0.010 0.001 PHE B 416 TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8876) covalent geometry : angle 0.53567 / 0.25 (12285) hydrogen bonds : bond 0.03250 / 2.13 ( 357) hydrogen bonds : angle 4.59234 / 3.30 ( 922) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.346 Fit side-chains REVERT: A 11 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7611 (ptmm) REVERT: A 223 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5373 (ptmt) REVERT: A 388 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7828 (tptp) REVERT: A 511 ASP cc_start: 0.7586 (m-30) cc_final: 0.7324 (t0) REVERT: B 43 LYS cc_start: 0.8363 (ttpp) cc_final: 0.7959 (mtpt) REVERT: B 211 ARG cc_start: 0.7453 (mtm110) cc_final: 0.7041 (mtp85) REVERT: B 212 TRP cc_start: 0.7300 (m100) cc_final: 0.6236 (t60) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.4564 time to fit residues: 39.1815 Evaluate side-chains 76 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [88, 46, 24, 1, 59, 12, 49, 28, 79, 77, 27] chunk 88 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 0.0020 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.0020 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117653 restraints weight = 10007.182| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.43 r_work: 0.3259 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8877 Z= 0.135 Angle : 0.539 7.559 12285 Z= 0.255 Chirality : 0.044 0.164 1392 Planarity : 0.004 0.045 1378 Dihedral : 10.859 72.434 1546 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.11 % Allowed : 13.81 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.28), residues: 937 helix: 1.26 (0.29), residues: 340 sheet: -0.93 (0.41), residues: 158 loop : 0.17 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 211 TYR 0.028 0.001 TYR A 483 PHE 0.010 0.001 PHE B 416 TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8876) covalent geometry : angle 0.53879 / 0.26 (12285) hydrogen bonds : bond 0.03227 / 2.11 ( 357) hydrogen bonds : angle 4.55439 / 3.28 ( 922) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.336 Fit side-chains REVERT: A 223 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.5371 (ptmt) REVERT: A 388 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7836 (tptp) REVERT: A 511 ASP cc_start: 0.7583 (m-30) cc_final: 0.7321 (t0) REVERT: B 43 LYS cc_start: 0.8369 (ttpp) cc_final: 0.7964 (mtpt) REVERT: B 70 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7608 (pttt) REVERT: B 211 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7059 (mtp85) REVERT: B 212 TRP cc_start: 0.7328 (m100) cc_final: 0.6268 (t60) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.4693 time to fit residues: 40.1743 Evaluate side-chains 77 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [11, 39, 43, 71, 1, 72, 49, 73, 32, 50, 19] chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117821 restraints weight = 9960.731| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.42 r_work: 0.3263 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8877 Z= 0.134 Angle : 0.538 7.547 12285 Z= 0.255 Chirality : 0.044 0.164 1392 Planarity : 0.004 0.045 1378 Dihedral : 10.844 72.630 1546 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.24 % Allowed : 13.93 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.28), residues: 937 helix: 1.24 (0.29), residues: 342 sheet: -0.90 (0.41), residues: 158 loop : 0.16 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 211 TYR 0.023 0.001 TYR A 127 PHE 0.010 0.001 PHE B 416 TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 8876) covalent geometry : angle 0.53800 / 0.26 (12285) hydrogen bonds : bond 0.03195 / 2.09 ( 357) hydrogen bonds : angle 4.52636 / 3.26 ( 922) Misc. bond : bond 0.00021 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.309 Fit side-chains REVERT: A 11 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7631 (ptmm) REVERT: A 223 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5323 (ptmt) REVERT: A 388 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7836 (tptp) REVERT: A 511 ASP cc_start: 0.7579 (m-30) cc_final: 0.7317 (t0) REVERT: B 43 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7954 (mtpt) REVERT: B 70 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7605 (pttt) REVERT: B 211 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7073 (mtp85) REVERT: B 212 TRP cc_start: 0.7323 (m100) cc_final: 0.6274 (t60) outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 0.4736 time to fit residues: 40.3894 Evaluate side-chains 75 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: [37, 97, 22, 82, 41, 6, 86, 42, 30, 66, 89] chunk 37 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117590 restraints weight = 9734.299| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.63 r_work: 0.3265 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8877 Z= 0.126 Angle : 0.533 7.525 12285 Z= 0.253 Chirality : 0.043 0.163 1392 Planarity : 0.004 0.045 1378 Dihedral : 10.826 72.932 1546 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.87 % Allowed : 14.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.50 (0.28), residues: 937 helix: 1.29 (0.29), residues: 342 sheet: -0.86 (0.41), residues: 158 loop : 0.17 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 211 TYR 0.027 0.001 TYR A 483 PHE 0.010 0.001 PHE B 416 TRP 0.015 0.001 TRP A 402 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8876) covalent geometry : angle 0.53339 / 0.25 (12285) hydrogen bonds : bond 0.03144 / 2.06 ( 357) hydrogen bonds : angle 4.47326 / 3.22 ( 922) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2705.76 seconds wall clock time: 47 minutes 1.36 seconds (2821.36 seconds total)