Starting phenix.real_space_refine on Thu Jul 2 13:58:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iss_35694/07_2026/8iss_35694.map" } resolution = 3.19 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= 0.002 sd= 0.149 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: 6 Type Number sf(0) Gaussians P 79 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 5310 2.51 5 N 1557 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8807 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 941 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "B" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1839 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 2 Chain: "C" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2018 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 18, 'TRANS': 238} Chain breaks: 1 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2298 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 21, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1710 Inner-chain residues flagged as termini: ['pdbres=" A E 47 "'] Classifications: {'RNA': 80} Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 29} Link IDs: {'rna2p': 18, 'rna3p': 61} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.02, per 1000 atoms: 0.23 Number of scatterers: 8807 At special positions: 0 Unit cell: (74.905, 86.51, 131.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 79 15.00 Mg 1 11.99 O 1833 8.00 N 1557 7.00 C 5310 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=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 230.2 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 37.3% alpha, 17.3% beta 28 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.609A pdb=" N ARG B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B 460 " --> pdb=" O ARG B 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 460' Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.667A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 112 Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.599A pdb=" N LYS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 230 removed outlier: 3.707A pdb=" N ARG C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 48 through 67 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 123 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.550A pdb=" N TYR D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.801A pdb=" N ALA D 414 " --> pdb=" O PRO D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.865A pdb=" N ALA D 459 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 84 removed outlier: 3.734A pdb=" N GLU A 78 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 91 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.671A pdb=" N THR A 108 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.918A pdb=" N LYS C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE C 259 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS C 291 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN C 261 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 258 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 244 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS C 262 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLY C 242 " --> pdb=" O CYS C 262 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 237 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE C 244 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER C 235 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL C 246 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE C 233 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA5, first strand: chain 'B' and resid 366 through 368 removed outlier: 4.114A pdb=" N TYR B 380 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 418 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 504 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE D 515 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU D 500 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA D 471 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP D 451 " --> pdb=" O ALA D 471 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET D 473 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 388 removed outlier: 4.066A pdb=" N LEU B 418 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 52 removed outlier: 4.195A pdb=" N SER C 11 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 5 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 4 " --> pdb=" O THR C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.395A pdb=" N ARG D 70 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 195 through 197 removed outlier: 3.566A pdb=" N VAL C 195 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 104 through 106 removed outlier: 5.010A pdb=" N GLN D 110 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 78 " --> pdb=" O HIS D 127 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2461 1.34 - 1.45: 1946 1.45 - 1.57: 4569 1.57 - 1.69: 157 1.69 - 1.81: 43 Bond restraints: 9176 Sorted by residual: bond pdb=" C ASP A 132 " pdb=" N PRO A 133 " ideal model delta sigma weight residual 1.326 1.339 -0.013 1.44e-02 4.82e+03 7.58e-01 bond pdb=" C ALA B 8 " pdb=" N PRO B 9 " ideal model delta sigma weight residual 1.335 1.342 -0.007 8.70e-03 1.32e+04 7.27e-01 bond pdb=" CG LYS B 330 " pdb=" CD LYS B 330 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.02e-01 bond pdb=" CB LYS B 330 " pdb=" CG LYS B 330 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.83e-01 bond pdb=" CD LYS B 330 " pdb=" CE LYS B 330 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.54e-01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 12709 2.28 - 4.56: 100 4.56 - 6.84: 4 6.84 - 9.12: 1 9.12 - 11.40: 1 Bond angle restraints: 12815 Sorted by residual: angle pdb=" CG LYS D 32 " pdb=" CD LYS D 32 " pdb=" CE LYS D 32 " ideal model delta sigma weight residual 111.30 122.70 -11.40 2.30e+00 1.89e-01 2.46e+01 angle pdb=" CB LYS B 330 " pdb=" CG LYS B 330 " pdb=" CD LYS B 330 " ideal model delta sigma weight residual 111.30 118.42 -7.12 2.30e+00 1.89e-01 9.60e+00 angle pdb=" C LEU C 113 " pdb=" N GLU C 114 " pdb=" CA GLU C 114 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.69e+00 angle pdb=" CA TYR B 343 " pdb=" CB TYR B 343 " pdb=" CG TYR B 343 " ideal model delta sigma weight residual 113.90 109.49 4.41 1.80e+00 3.09e-01 6.02e+00 angle pdb=" C TYR B 318 " pdb=" N GLU B 319 " pdb=" CA GLU B 319 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 ... (remaining 12810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.10: 4607 19.10 - 38.19: 563 38.19 - 57.29: 153 57.29 - 76.38: 15 76.38 - 95.48: 14 Dihedral angle restraints: 5352 sinusoidal: 2771 harmonic: 2581 Sorted by residual: dihedral pdb=" CA LYS B 320 " pdb=" C LYS B 320 " pdb=" N GLU B 321 " pdb=" CA GLU B 321 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE D 510 " pdb=" C ILE D 510 " pdb=" N SER D 511 " pdb=" CA SER D 511 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PHE D 502 " pdb=" C PHE D 502 " pdb=" N ALA D 503 " pdb=" CA ALA D 503 " ideal model delta harmonic sigma weight residual 180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1016 0.028 - 0.057: 320 0.057 - 0.085: 66 0.085 - 0.113: 58 0.113 - 0.142: 18 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA VAL B 355 " pdb=" N VAL B 355 " pdb=" C VAL B 355 " pdb=" CB VAL B 355 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL D 482 " pdb=" N VAL D 482 " pdb=" C VAL D 482 " pdb=" CB VAL D 482 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE C 259 " pdb=" N ILE C 259 " pdb=" C ILE C 259 " pdb=" CB ILE C 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1475 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 114 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU C 114 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU C 114 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 115 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 39 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 40 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 372 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO B 373 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.020 5.00e-02 4.00e+02 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 138 2.60 - 3.18: 7492 3.18 - 3.75: 14396 3.75 - 4.33: 19760 4.33 - 4.90: 32234 Nonbonded interactions: 74020 Sorted by model distance: nonbonded pdb=" O2' G E 50 " pdb=" OP2 U E 54 " model vdw 2.026 3.040 nonbonded pdb=" O GLY A 158 " pdb=" OG SER C 303 " model vdw 2.042 3.040 nonbonded pdb=" OP2 G E 12 " pdb="MG MG E 101 " model vdw 2.051 2.170 nonbonded pdb=" O2' C E 35 " pdb=" O3' G E 38 " model vdw 2.071 3.040 nonbonded pdb=" O2' C E 35 " pdb=" O2' G E 38 " model vdw 2.091 3.040 ... (remaining 74015 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: 0.600 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.003 0.027 9176 Z= 0.116 Angle : 0.514 11.398 12815 Z= 0.264 Chirality : 0.036 0.142 1478 Planarity : 0.004 0.044 1344 Dihedral : 16.910 95.477 3684 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.39 % Allowed : 22.51 % Favored : 77.09 % 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: -1.16 (0.29), residues: 873 helix: 0.81 (0.30), residues: 316 sheet: -2.26 (0.40), residues: 165 loop : -1.34 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 10 TYR 0.017 0.001 TYR D 155 PHE 0.010 0.001 PHE D 512 TRP 0.014 0.001 TRP D 99 HIS 0.003 0.001 HIS C 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9176) covalent geometry : angle 0.51437 / 0.26 (12815) hydrogen bonds : bond 0.15745 / 10.52 ( 378) hydrogen bonds : angle 6.94196 / 4.64 ( 979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.264 Fit side-chains REVERT: B 11 ARG cc_start: 0.6382 (ttm110) cc_final: 0.5869 (mtp85) outliers start: 3 outliers final: 3 residues processed: 102 average time/residue: 0.1110 time to fit residues: 14.8052 Evaluate side-chains 93 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 74 optimal weight: 0.7980 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 GLN C 211 HIS D 507 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.180928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145192 restraints weight = 9801.368| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.96 r_work: 0.3360 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9176 Z= 0.118 Angle : 0.540 6.242 12815 Z= 0.275 Chirality : 0.038 0.193 1478 Planarity : 0.004 0.044 1344 Dihedral : 11.324 91.557 1939 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.88 % Allowed : 21.60 % Favored : 75.52 % 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: -0.50 (0.30), residues: 873 helix: 1.39 (0.31), residues: 300 sheet: -1.87 (0.42), residues: 157 loop : -0.94 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 10 TYR 0.016 0.002 TYR B 343 PHE 0.013 0.001 PHE A 139 TRP 0.015 0.001 TRP D 99 HIS 0.004 0.001 HIS C 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9176) covalent geometry : angle 0.54023 / 0.28 (12815) hydrogen bonds : bond 0.04378 / 2.82 ( 378) hydrogen bonds : angle 4.93356 / 3.35 ( 979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6175 (mm) cc_final: 0.5974 (mm) REVERT: A 49 MET cc_start: 0.5763 (mpp) cc_final: 0.5267 (mpp) REVERT: A 71 MET cc_start: 0.6138 (mmm) cc_final: 0.5624 (mmm) REVERT: A 145 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: B 11 ARG cc_start: 0.6097 (ttm110) cc_final: 0.5535 (mtp85) REVERT: B 380 TYR cc_start: 0.6781 (m-80) cc_final: 0.6523 (m-80) REVERT: C 103 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5080 (mp0) REVERT: C 272 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: D 22 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 85 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: D 497 ASP cc_start: 0.7645 (m-30) cc_final: 0.7425 (t0) outliers start: 22 outliers final: 5 residues processed: 127 average time/residue: 0.0996 time to fit residues: 16.9847 Evaluate side-chains 98 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 478 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 10.0000 chunk 81 optimal weight: 0.0070 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 48 ASN D 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140540 restraints weight = 9772.487| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.93 r_work: 0.3485 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9176 Z= 0.127 Angle : 0.522 6.263 12815 Z= 0.266 Chirality : 0.037 0.149 1478 Planarity : 0.004 0.045 1344 Dihedral : 11.047 91.128 1938 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.40 % Allowed : 21.60 % Favored : 75.00 % 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: -0.38 (0.30), residues: 873 helix: 1.38 (0.31), residues: 307 sheet: -1.66 (0.42), residues: 158 loop : -0.88 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 10 TYR 0.016 0.002 TYR B 343 PHE 0.014 0.001 PHE A 139 TRP 0.011 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9176) covalent geometry : angle 0.52200 / 0.27 (12815) hydrogen bonds : bond 0.04140 / 2.66 ( 378) hydrogen bonds : angle 4.54834 / 3.10 ( 979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6109 (mm) cc_final: 0.5770 (mm) REVERT: A 71 MET cc_start: 0.6151 (mmm) cc_final: 0.5479 (mmm) REVERT: A 128 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6325 (pttp) REVERT: A 145 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 11 ARG cc_start: 0.6003 (ttm110) cc_final: 0.5490 (mtp85) REVERT: B 41 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7381 (mtp85) REVERT: B 380 TYR cc_start: 0.6791 (m-80) cc_final: 0.6487 (m-80) REVERT: C 45 ARG cc_start: 0.7839 (ttt180) cc_final: 0.7441 (mtp-110) REVERT: C 272 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7015 (mm-40) REVERT: D 22 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 81 GLU cc_start: 0.7426 (tt0) cc_final: 0.7023 (tt0) REVERT: D 85 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6595 (pm20) outliers start: 26 outliers final: 12 residues processed: 117 average time/residue: 0.1066 time to fit residues: 16.6520 Evaluate side-chains 106 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 55 optimal weight: 0.0870 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 43 ASN ** D 403 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.174764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138572 restraints weight = 9834.984| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.96 r_work: 0.3395 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9176 Z= 0.193 Angle : 0.575 6.452 12815 Z= 0.291 Chirality : 0.039 0.139 1478 Planarity : 0.005 0.049 1344 Dihedral : 11.235 90.368 1938 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.80 % Allowed : 21.60 % Favored : 74.61 % 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: -0.50 (0.30), residues: 873 helix: 1.16 (0.30), residues: 307 sheet: -1.65 (0.41), residues: 168 loop : -0.84 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 10 TYR 0.019 0.002 TYR B 343 PHE 0.016 0.002 PHE A 139 TRP 0.012 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 9176) covalent geometry : angle 0.57528 / 0.29 (12815) hydrogen bonds : bond 0.04672 / 3.01 ( 378) hydrogen bonds : angle 4.56267 / 3.10 ( 979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5610 (mm) REVERT: A 71 MET cc_start: 0.6211 (mmm) cc_final: 0.5440 (mmm) REVERT: A 128 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6314 (pttp) REVERT: A 145 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 154 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8461 (ptmt) REVERT: B 41 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7416 (mtp85) REVERT: B 435 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: C 45 ARG cc_start: 0.8022 (ttt180) cc_final: 0.7595 (mtp-110) REVERT: C 272 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7012 (mt0) REVERT: D 81 GLU cc_start: 0.7404 (tt0) cc_final: 0.7000 (tt0) REVERT: D 85 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6590 (pm20) REVERT: D 172 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6878 (tt0) outliers start: 29 outliers final: 17 residues processed: 119 average time/residue: 0.1113 time to fit residues: 17.6419 Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.181665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145870 restraints weight = 9755.429| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.97 r_work: 0.3479 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9176 Z= 0.102 Angle : 0.494 6.340 12815 Z= 0.252 Chirality : 0.037 0.141 1478 Planarity : 0.004 0.047 1344 Dihedral : 11.163 93.307 1938 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.93 % Allowed : 22.51 % Favored : 73.56 % 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: -0.14 (0.30), residues: 873 helix: 1.48 (0.31), residues: 307 sheet: -1.55 (0.42), residues: 160 loop : -0.63 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 10 TYR 0.027 0.002 TYR D 119 PHE 0.013 0.001 PHE A 139 TRP 0.009 0.001 TRP D 82 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9176) covalent geometry : angle 0.49448 / 0.25 (12815) hydrogen bonds : bond 0.03927 / 2.54 ( 378) hydrogen bonds : angle 4.29904 / 2.96 ( 979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5452 (mm) REVERT: A 71 MET cc_start: 0.5874 (mmm) cc_final: 0.5251 (mmm) REVERT: A 145 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: A 154 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8446 (ptmt) REVERT: B 41 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7278 (mtp85) REVERT: B 380 TYR cc_start: 0.6755 (m-80) cc_final: 0.6457 (m-80) REVERT: B 435 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: C 45 ARG cc_start: 0.7918 (ttt180) cc_final: 0.7471 (mtp-110) REVERT: C 272 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6926 (mm-40) REVERT: D 81 GLU cc_start: 0.7376 (tt0) cc_final: 0.6957 (tt0) REVERT: D 85 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: D 172 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6930 (tt0) REVERT: D 408 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6992 (mp) outliers start: 30 outliers final: 16 residues processed: 127 average time/residue: 0.0800 time to fit residues: 13.9062 Evaluate side-chains 118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144063 restraints weight = 9791.221| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.97 r_work: 0.3416 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.121 Angle : 0.512 8.387 12815 Z= 0.257 Chirality : 0.037 0.150 1478 Planarity : 0.004 0.046 1344 Dihedral : 11.129 91.923 1938 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.53 % Allowed : 22.91 % Favored : 73.56 % 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: -0.07 (0.30), residues: 873 helix: 1.47 (0.30), residues: 309 sheet: -1.51 (0.43), residues: 160 loop : -0.53 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 10 TYR 0.021 0.002 TYR B 343 PHE 0.012 0.001 PHE A 139 TRP 0.010 0.001 TRP D 82 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9176) covalent geometry : angle 0.51183 / 0.26 (12815) hydrogen bonds : bond 0.04030 / 2.59 ( 378) hydrogen bonds : angle 4.23868 / 2.91 ( 979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5412 (mm) REVERT: A 49 MET cc_start: 0.5245 (mmm) cc_final: 0.4974 (mmt) REVERT: A 71 MET cc_start: 0.5827 (mmm) cc_final: 0.5207 (mmm) REVERT: A 145 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: B 380 TYR cc_start: 0.6826 (m-80) cc_final: 0.6547 (m-80) REVERT: B 435 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: D 81 GLU cc_start: 0.7274 (tt0) cc_final: 0.6841 (tt0) REVERT: D 85 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: D 172 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7046 (tt0) REVERT: D 408 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6729 (mp) outliers start: 27 outliers final: 16 residues processed: 118 average time/residue: 0.1171 time to fit residues: 18.5279 Evaluate side-chains 112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 73 optimal weight: 0.3980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135582 restraints weight = 9946.484| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.97 r_work: 0.3450 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9176 Z= 0.183 Angle : 0.564 8.439 12815 Z= 0.284 Chirality : 0.039 0.138 1478 Planarity : 0.005 0.060 1344 Dihedral : 11.264 90.771 1938 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.53 % Allowed : 23.30 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.14 (0.30), residues: 873 helix: 1.33 (0.30), residues: 309 sheet: -1.49 (0.42), residues: 167 loop : -0.49 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 10 TYR 0.024 0.002 TYR B 343 PHE 0.014 0.002 PHE A 139 TRP 0.011 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 9176) covalent geometry : angle 0.56401 / 0.28 (12815) hydrogen bonds : bond 0.04499 / 2.89 ( 378) hydrogen bonds : angle 4.34914 / 2.98 ( 979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5510 (mm) REVERT: A 71 MET cc_start: 0.5921 (mmm) cc_final: 0.5303 (mmm) REVERT: A 145 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: A 160 MET cc_start: 0.7216 (mmp) cc_final: 0.6966 (mmm) REVERT: B 380 TYR cc_start: 0.6870 (m-80) cc_final: 0.6624 (m-80) REVERT: B 390 HIS cc_start: 0.7415 (m90) cc_final: 0.6983 (m170) REVERT: B 435 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: C 45 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7459 (mtp85) REVERT: D 81 GLU cc_start: 0.7404 (tt0) cc_final: 0.6998 (tt0) REVERT: D 85 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: D 408 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6817 (mp) outliers start: 27 outliers final: 16 residues processed: 118 average time/residue: 0.1056 time to fit residues: 16.8517 Evaluate side-chains 110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137446 restraints weight = 9929.562| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3338 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9176 Z= 0.217 Angle : 0.608 8.924 12815 Z= 0.303 Chirality : 0.040 0.146 1478 Planarity : 0.005 0.054 1344 Dihedral : 11.453 91.207 1938 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.93 % Allowed : 23.30 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.30), residues: 873 helix: 1.11 (0.30), residues: 308 sheet: -1.58 (0.42), residues: 167 loop : -0.55 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 10 TYR 0.033 0.003 TYR D 119 PHE 0.015 0.002 PHE B 6 TRP 0.013 0.001 TRP D 82 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 ( 9176) covalent geometry : angle 0.60762 / 0.30 (12815) hydrogen bonds : bond 0.04782 / 3.09 ( 378) hydrogen bonds : angle 4.47900 / 3.07 ( 979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5478 (mm) REVERT: A 52 LEU cc_start: 0.7305 (mp) cc_final: 0.7076 (mp) REVERT: A 71 MET cc_start: 0.6059 (mmm) cc_final: 0.5400 (mmt) REVERT: A 145 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: A 160 MET cc_start: 0.7257 (mmp) cc_final: 0.7021 (mmm) REVERT: B 380 TYR cc_start: 0.6879 (m-80) cc_final: 0.6588 (m-80) REVERT: B 390 HIS cc_start: 0.7374 (m90) cc_final: 0.6979 (m170) REVERT: B 396 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7882 (ttp80) REVERT: B 435 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: C 45 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7452 (mtp85) REVERT: C 95 GLN cc_start: 0.6314 (mp10) cc_final: 0.5872 (mm-40) REVERT: D 408 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6881 (mp) REVERT: D 462 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6277 (mtm-85) outliers start: 30 outliers final: 23 residues processed: 117 average time/residue: 0.1073 time to fit residues: 16.9240 Evaluate side-chains 118 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 65 optimal weight: 0.0030 chunk 49 optimal weight: 0.9980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142642 restraints weight = 9753.039| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.95 r_work: 0.3382 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9176 Z= 0.122 Angle : 0.538 7.693 12815 Z= 0.270 Chirality : 0.038 0.137 1478 Planarity : 0.005 0.052 1344 Dihedral : 11.376 93.798 1938 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.01 % Allowed : 24.74 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.30), residues: 873 helix: 1.43 (0.30), residues: 309 sheet: -1.44 (0.42), residues: 165 loop : -0.44 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 10 TYR 0.027 0.002 TYR B 348 PHE 0.013 0.001 PHE A 139 TRP 0.009 0.001 TRP D 99 HIS 0.003 0.001 HIS C 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9176) covalent geometry : angle 0.53786 / 0.27 (12815) hydrogen bonds : bond 0.04128 / 2.67 ( 378) hydrogen bonds : angle 4.31662 / 2.98 ( 979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5317 (mm) REVERT: A 71 MET cc_start: 0.5839 (mmm) cc_final: 0.5245 (mmm) REVERT: A 145 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: B 11 ARG cc_start: 0.5976 (ttm110) cc_final: 0.5587 (tpp-160) REVERT: B 380 TYR cc_start: 0.6830 (m-80) cc_final: 0.6537 (m-80) REVERT: B 390 HIS cc_start: 0.7381 (m90) cc_final: 0.6990 (m170) REVERT: B 435 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: C 45 ARG cc_start: 0.7888 (ttt180) cc_final: 0.7437 (mtp85) REVERT: D 85 GLU cc_start: 0.7574 (pm20) cc_final: 0.7306 (pm20) REVERT: D 172 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7193 (tt0) outliers start: 23 outliers final: 15 residues processed: 110 average time/residue: 0.1045 time to fit residues: 15.8663 Evaluate side-chains 104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 3.9990 chunk 36 optimal weight: 0.0020 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.177690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141594 restraints weight = 9846.038| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.97 r_work: 0.3433 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9176 Z= 0.109 Angle : 0.526 10.226 12815 Z= 0.263 Chirality : 0.037 0.136 1478 Planarity : 0.005 0.057 1344 Dihedral : 11.324 93.787 1938 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.62 % Allowed : 24.48 % Favored : 72.91 % 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: 0.09 (0.30), residues: 873 helix: 1.57 (0.30), residues: 308 sheet: -1.43 (0.44), residues: 159 loop : -0.40 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 10 TYR 0.029 0.002 TYR B 348 PHE 0.012 0.001 PHE A 139 TRP 0.009 0.001 TRP D 82 HIS 0.003 0.001 HIS C 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9176) covalent geometry : angle 0.52569 / 0.26 (12815) hydrogen bonds : bond 0.03946 / 2.55 ( 378) hydrogen bonds : angle 4.23980 / 2.93 ( 979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5139 (mm) REVERT: A 71 MET cc_start: 0.5876 (mmm) cc_final: 0.5398 (mmm) REVERT: A 145 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: B 11 ARG cc_start: 0.6022 (ttm110) cc_final: 0.5658 (tpp-160) REVERT: B 380 TYR cc_start: 0.6748 (m-80) cc_final: 0.6472 (m-80) REVERT: B 390 HIS cc_start: 0.7315 (m90) cc_final: 0.6986 (m170) REVERT: B 435 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: C 53 MET cc_start: 0.7895 (mtp) cc_final: 0.7661 (mtm) REVERT: D 85 GLU cc_start: 0.7521 (pm20) cc_final: 0.7283 (pm20) REVERT: D 172 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7210 (tt0) REVERT: D 462 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6224 (mtm-85) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.0994 time to fit residues: 13.9300 Evaluate side-chains 102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 486 CYS Chi-restraints excluded: chain D residue 523 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 48 ASN B 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144295 restraints weight = 9687.432| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.97 r_work: 0.3410 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9176 Z= 0.121 Angle : 0.530 9.826 12815 Z= 0.264 Chirality : 0.037 0.135 1478 Planarity : 0.005 0.058 1344 Dihedral : 11.299 92.736 1938 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.75 % Allowed : 24.35 % Favored : 72.91 % 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: 0.12 (0.30), residues: 873 helix: 1.57 (0.30), residues: 309 sheet: -1.36 (0.44), residues: 159 loop : -0.39 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 10 TYR 0.021 0.002 TYR D 119 PHE 0.012 0.001 PHE A 139 TRP 0.010 0.001 TRP D 82 HIS 0.003 0.001 HIS C 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9176) covalent geometry : angle 0.53005 / 0.26 (12815) hydrogen bonds : bond 0.04003 / 2.58 ( 378) hydrogen bonds : angle 4.23591 / 2.92 ( 979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.03 seconds wall clock time: 40 minutes 18.30 seconds (2418.30 seconds total)