Starting phenix.real_space_refine on Sun Apr 5 02:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mcs_63804/04_2026/9mcs_63804_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mcs_63804/04_2026/9mcs_63804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mcs_63804/04_2026/9mcs_63804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mcs_63804/04_2026/9mcs_63804.map" model { file = "/net/cci-nas-00/data/ceres_data/9mcs_63804/04_2026/9mcs_63804_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mcs_63804/04_2026/9mcs_63804_trim.cif" } resolution = 2.51 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4792 2.51 5 N 1102 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7128 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3554 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 447} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 2.25, per 1000 atoms: 0.32 Number of scatterers: 7128 At special positions: 0 Unit cell: (71.764, 107.18, 77.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1206 8.00 N 1102 7.00 C 4792 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: 0.67 Conformation dependent library (CDL) restraints added in 266.6 milliseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.622A pdb=" N PHE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 135 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 166 removed outlier: 4.049A pdb=" N GLY A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.583A pdb=" N TRP A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.623A pdb=" N GLN A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.768A pdb=" N LEU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.793A pdb=" N ILE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.773A pdb=" N LEU A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.601A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 298 through 325 removed outlier: 4.966A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Proline residue: A 318 - end of helix Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.774A pdb=" N GLN A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 367 Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.780A pdb=" N TRP A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.583A pdb=" N GLY A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 467 through 484 removed outlier: 6.527A pdb=" N THR A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.739A pdb=" N ASN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.454A pdb=" N ILE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 544 Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'B' and resid 91 through 107 removed outlier: 3.621A pdb=" N PHE B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 135 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 163 through 166 removed outlier: 4.047A pdb=" N GLY B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.583A pdb=" N TRP B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 183 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.622A pdb=" N GLN B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.767A pdb=" N LEU B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.793A pdb=" N ILE B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.774A pdb=" N LEU B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.600A pdb=" N LEU B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 298 through 325 removed outlier: 4.965A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Proline residue: B 309 - end of helix Proline residue: B 318 - end of helix Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.774A pdb=" N GLN B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 367 Processing helix chain 'B' and resid 376 through 391 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.779A pdb=" N TRP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.583A pdb=" N GLY B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 467 through 484 removed outlier: 6.528A pdb=" N THR B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.739A pdb=" N ASN B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 512 through 519 removed outlier: 4.454A pdb=" N ILE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 544 Processing helix chain 'B' and resid 545 through 554 484 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1056 1.29 - 1.42: 2034 1.42 - 1.55: 4196 1.55 - 1.68: 6 1.68 - 1.81: 48 Bond restraints: 7340 Sorted by residual: bond pdb=" C LEU B 362 " pdb=" O LEU B 362 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.16e-02 7.43e+03 4.20e+01 bond pdb=" C LEU A 362 " pdb=" O LEU A 362 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.16e-02 7.43e+03 4.07e+01 bond pdb=" C3 OAA A 600 " pdb=" C4 OAA A 600 " ideal model delta sigma weight residual 1.551 1.431 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C3 OAA B 600 " pdb=" C4 OAA B 600 " ideal model delta sigma weight residual 1.551 1.431 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C THR B 363 " pdb=" O THR B 363 " ideal model delta sigma weight residual 1.236 1.168 0.069 1.15e-02 7.56e+03 3.55e+01 ... (remaining 7335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 9676 2.60 - 5.21: 288 5.21 - 7.81: 62 7.81 - 10.41: 10 10.41 - 13.02: 6 Bond angle restraints: 10042 Sorted by residual: angle pdb=" C PHE B 213 " pdb=" CA PHE B 213 " pdb=" CB PHE B 213 " ideal model delta sigma weight residual 109.56 121.31 -11.75 1.65e+00 3.67e-01 5.07e+01 angle pdb=" C PHE A 213 " pdb=" CA PHE A 213 " pdb=" CB PHE A 213 " ideal model delta sigma weight residual 109.56 121.26 -11.70 1.65e+00 3.67e-01 5.03e+01 angle pdb=" N LEU A 366 " pdb=" CA LEU A 366 " pdb=" C LEU A 366 " ideal model delta sigma weight residual 113.23 105.72 7.51 1.24e+00 6.50e-01 3.67e+01 angle pdb=" N LEU B 366 " pdb=" CA LEU B 366 " pdb=" C LEU B 366 " ideal model delta sigma weight residual 113.23 105.73 7.50 1.24e+00 6.50e-01 3.66e+01 angle pdb=" N LEU B 211 " pdb=" CA LEU B 211 " pdb=" C LEU B 211 " ideal model delta sigma weight residual 113.50 106.39 7.11 1.23e+00 6.61e-01 3.34e+01 ... (remaining 10037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 3742 16.13 - 32.26: 292 32.26 - 48.39: 60 48.39 - 64.52: 12 64.52 - 80.64: 6 Dihedral angle restraints: 4112 sinusoidal: 1458 harmonic: 2654 Sorted by residual: dihedral pdb=" CA LEU B 256 " pdb=" C LEU B 256 " pdb=" N GLY B 257 " pdb=" CA GLY B 257 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N GLY A 257 " pdb=" CA GLY A 257 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE B 232 " pdb=" C ILE B 232 " pdb=" N PHE B 233 " pdb=" CA PHE B 233 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 817 0.051 - 0.103: 269 0.103 - 0.154: 71 0.154 - 0.205: 5 0.205 - 0.257: 16 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA SER A 226 " pdb=" N SER A 226 " pdb=" C SER A 226 " pdb=" CB SER A 226 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA SER B 466 " pdb=" N SER B 466 " pdb=" C SER B 466 " pdb=" CB SER B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL B 212 " pdb=" CA VAL B 212 " pdb=" CG1 VAL B 212 " pdb=" CG2 VAL B 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1175 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 223 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.21e+01 pdb=" C PRO B 223 " -0.081 2.00e-02 2.50e+03 pdb=" O PRO B 223 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 224 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 223 " -0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C PRO A 223 " 0.081 2.00e-02 2.50e+03 pdb=" O PRO A 223 " -0.029 2.00e-02 2.50e+03 pdb=" N SER A 224 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 359 " 0.019 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C THR B 359 " -0.063 2.00e-02 2.50e+03 pdb=" O THR B 359 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 360 " 0.021 2.00e-02 2.50e+03 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2456 2.85 - 3.37: 6817 3.37 - 3.88: 12713 3.88 - 4.39: 14976 4.39 - 4.90: 25097 Nonbonded interactions: 62059 Sorted by model distance: nonbonded pdb=" O TRP B 259 " pdb=" OG1 THR B 263 " model vdw 2.343 3.040 nonbonded pdb=" O TRP A 259 " pdb=" OG1 THR A 263 " model vdw 2.343 3.040 nonbonded pdb=" NH2 ARG B 228 " pdb=" O ALA B 278 " model vdw 2.349 3.120 nonbonded pdb=" NH2 ARG A 228 " pdb=" O ALA A 278 " model vdw 2.349 3.120 nonbonded pdb=" O VAL A 387 " pdb=" OG1 THR A 391 " model vdw 2.381 3.040 ... (remaining 62054 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.470 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.040 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:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.009 0.120 7340 Z= 0.575 Angle : 1.104 13.017 10042 Z= 0.658 Chirality : 0.059 0.257 1178 Planarity : 0.007 0.058 1210 Dihedral : 12.866 80.645 2424 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.28 % Allowed : 4.13 % Favored : 95.59 % Cbeta Deviations : 0.24 % 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: -3.86 (0.21), residues: 936 helix: -2.51 (0.13), residues: 740 sheet: None (None), residues: 0 loop : -1.65 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 116 TYR 0.033 0.003 TYR B 325 PHE 0.028 0.002 PHE B 265 TRP 0.020 0.002 TRP B 411 HIS 0.005 0.002 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00921 ( 7340) covalent geometry : angle 1.10410 (10042) hydrogen bonds : bond 0.16313 ( 484) hydrogen bonds : angle 7.78266 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.220 Fit side-chains REVERT: A 167 ASP cc_start: 0.8739 (t70) cc_final: 0.8519 (t0) REVERT: A 218 LEU cc_start: 0.8176 (tp) cc_final: 0.7846 (mp) REVERT: B 167 ASP cc_start: 0.8943 (t70) cc_final: 0.8555 (t0) REVERT: B 218 LEU cc_start: 0.7993 (tp) cc_final: 0.7781 (mp) REVERT: B 301 ASP cc_start: 0.7815 (m-30) cc_final: 0.7513 (m-30) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.5502 time to fit residues: 77.8658 Evaluate side-chains 93 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 295 GLN A 340 GLN B 120 GLN B 195 GLN B 340 GLN B 423 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102912 restraints weight = 7768.180| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.23 r_work: 0.3017 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7340 Z= 0.153 Angle : 0.618 9.585 10042 Z= 0.312 Chirality : 0.041 0.209 1178 Planarity : 0.005 0.050 1210 Dihedral : 5.873 58.032 988 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 10.61 % Favored : 87.60 % 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: -0.77 (0.26), residues: 936 helix: -0.30 (0.18), residues: 748 sheet: None (None), residues: 0 loop : -0.72 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 228 TYR 0.016 0.002 TYR A 322 PHE 0.022 0.002 PHE B 265 TRP 0.016 0.002 TRP B 446 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7340) covalent geometry : angle 0.61782 (10042) hydrogen bonds : bond 0.04042 ( 484) hydrogen bonds : angle 4.71793 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.335 Fit side-chains REVERT: A 167 ASP cc_start: 0.9196 (t70) cc_final: 0.8923 (t0) REVERT: A 218 LEU cc_start: 0.8132 (tp) cc_final: 0.7809 (mp) REVERT: A 437 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7491 (mtpt) REVERT: B 167 ASP cc_start: 0.9216 (t70) cc_final: 0.9016 (t0) REVERT: B 195 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: B 218 LEU cc_start: 0.8063 (tp) cc_final: 0.7781 (mp) REVERT: B 437 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7584 (mtpt) REVERT: B 544 LEU cc_start: 0.8492 (mp) cc_final: 0.8260 (mm) outliers start: 13 outliers final: 3 residues processed: 114 average time/residue: 0.5938 time to fit residues: 71.3045 Evaluate side-chains 99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 501 ASN B 88 GLN B 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.098211 restraints weight = 7671.615| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.22 r_work: 0.2950 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7340 Z= 0.145 Angle : 0.584 9.741 10042 Z= 0.294 Chirality : 0.041 0.206 1178 Planarity : 0.004 0.038 1210 Dihedral : 5.564 59.270 986 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.10 % Allowed : 12.12 % Favored : 86.78 % 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: 0.48 (0.28), residues: 936 helix: 0.54 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.11 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 228 TYR 0.017 0.002 TYR A 322 PHE 0.025 0.002 PHE B 265 TRP 0.016 0.002 TRP B 411 HIS 0.004 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7340) covalent geometry : angle 0.58401 (10042) hydrogen bonds : bond 0.03969 ( 484) hydrogen bonds : angle 4.49705 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.275 Fit side-chains REVERT: A 167 ASP cc_start: 0.9218 (t70) cc_final: 0.8971 (t0) REVERT: A 218 LEU cc_start: 0.8295 (tp) cc_final: 0.7980 (mp) REVERT: A 345 LYS cc_start: 0.7224 (mttt) cc_final: 0.6782 (mmtm) REVERT: A 435 VAL cc_start: 0.8399 (m) cc_final: 0.8152 (t) REVERT: A 437 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7529 (mtpt) REVERT: B 218 LEU cc_start: 0.8199 (tp) cc_final: 0.7939 (mp) REVERT: B 435 VAL cc_start: 0.8406 (m) cc_final: 0.8124 (t) REVERT: B 437 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7604 (mtpt) REVERT: B 544 LEU cc_start: 0.8520 (mp) cc_final: 0.8289 (mm) outliers start: 8 outliers final: 2 residues processed: 99 average time/residue: 0.6290 time to fit residues: 65.5002 Evaluate side-chains 91 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.097256 restraints weight = 7772.826| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.26 r_work: 0.2933 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7340 Z= 0.142 Angle : 0.574 9.532 10042 Z= 0.288 Chirality : 0.041 0.203 1178 Planarity : 0.004 0.034 1210 Dihedral : 5.473 58.582 986 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.83 % Allowed : 12.26 % Favored : 86.91 % 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: 1.12 (0.29), residues: 936 helix: 0.96 (0.20), residues: 750 sheet: None (None), residues: 0 loop : 0.25 (0.52), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 228 TYR 0.016 0.002 TYR A 322 PHE 0.023 0.002 PHE A 265 TRP 0.016 0.002 TRP A 411 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7340) covalent geometry : angle 0.57438 (10042) hydrogen bonds : bond 0.03901 ( 484) hydrogen bonds : angle 4.37544 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.260 Fit side-chains REVERT: A 116 ARG cc_start: 0.8460 (tpt170) cc_final: 0.7830 (tpt170) REVERT: A 167 ASP cc_start: 0.9167 (t70) cc_final: 0.8964 (t0) REVERT: A 218 LEU cc_start: 0.8283 (tp) cc_final: 0.7984 (mp) REVERT: A 345 LYS cc_start: 0.7167 (mttt) cc_final: 0.6815 (mppt) REVERT: A 437 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7637 (mtpt) REVERT: B 218 LEU cc_start: 0.8281 (tp) cc_final: 0.7985 (mp) REVERT: B 337 LYS cc_start: 0.7492 (ttmt) cc_final: 0.6842 (tppt) REVERT: B 345 LYS cc_start: 0.7173 (mttt) cc_final: 0.6762 (mmtm) REVERT: B 437 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7569 (mtpt) REVERT: B 544 LEU cc_start: 0.8598 (mp) cc_final: 0.8354 (mm) outliers start: 6 outliers final: 2 residues processed: 95 average time/residue: 0.6312 time to fit residues: 63.0346 Evaluate side-chains 91 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.0030 chunk 2 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101361 restraints weight = 7842.606| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.27 r_work: 0.2991 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7340 Z= 0.103 Angle : 0.517 8.191 10042 Z= 0.259 Chirality : 0.039 0.169 1178 Planarity : 0.003 0.029 1210 Dihedral : 5.215 58.340 986 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.24 % Allowed : 12.12 % Favored : 86.64 % 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: 1.63 (0.29), residues: 936 helix: 1.32 (0.20), residues: 748 sheet: None (None), residues: 0 loop : 0.42 (0.51), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.013 0.001 TYR A 322 PHE 0.023 0.001 PHE A 361 TRP 0.017 0.001 TRP A 411 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7340) covalent geometry : angle 0.51746 (10042) hydrogen bonds : bond 0.03360 ( 484) hydrogen bonds : angle 4.16903 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.237 Fit side-chains REVERT: A 116 ARG cc_start: 0.8531 (tpt170) cc_final: 0.7892 (tpt170) REVERT: A 167 ASP cc_start: 0.9140 (t70) cc_final: 0.8882 (t0) REVERT: A 218 LEU cc_start: 0.8238 (tp) cc_final: 0.7914 (mp) REVERT: A 274 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7366 (mtp) REVERT: A 345 LYS cc_start: 0.7090 (mttt) cc_final: 0.6754 (mppt) REVERT: A 437 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7691 (mtpt) REVERT: B 218 LEU cc_start: 0.8243 (tp) cc_final: 0.7935 (mp) REVERT: B 337 LYS cc_start: 0.7459 (ttmt) cc_final: 0.6834 (tppt) REVERT: B 345 LYS cc_start: 0.7088 (mttt) cc_final: 0.6678 (mmtm) REVERT: B 437 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7708 (mtpt) REVERT: B 544 LEU cc_start: 0.8484 (mp) cc_final: 0.8271 (mm) outliers start: 9 outliers final: 0 residues processed: 92 average time/residue: 0.6189 time to fit residues: 59.9858 Evaluate side-chains 86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099936 restraints weight = 7779.810| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.26 r_work: 0.2971 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7340 Z= 0.114 Angle : 0.528 8.685 10042 Z= 0.264 Chirality : 0.039 0.175 1178 Planarity : 0.003 0.030 1210 Dihedral : 5.193 58.586 986 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.55 % Allowed : 13.64 % Favored : 85.81 % 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: 1.84 (0.29), residues: 936 helix: 1.47 (0.20), residues: 750 sheet: None (None), residues: 0 loop : 0.48 (0.52), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 228 TYR 0.014 0.001 TYR A 322 PHE 0.022 0.001 PHE B 361 TRP 0.016 0.001 TRP B 411 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7340) covalent geometry : angle 0.52785 (10042) hydrogen bonds : bond 0.03462 ( 484) hydrogen bonds : angle 4.12667 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.264 Fit side-chains REVERT: A 167 ASP cc_start: 0.9153 (t70) cc_final: 0.8904 (t0) REVERT: A 218 LEU cc_start: 0.8293 (tp) cc_final: 0.7972 (mp) REVERT: A 337 LYS cc_start: 0.7466 (tttm) cc_final: 0.6822 (tppt) REVERT: A 345 LYS cc_start: 0.7131 (mttt) cc_final: 0.6742 (mppt) REVERT: A 437 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7676 (mtpt) REVERT: B 218 LEU cc_start: 0.8266 (tp) cc_final: 0.7945 (mp) REVERT: B 274 MET cc_start: 0.7780 (mtp) cc_final: 0.7378 (mtp) REVERT: B 337 LYS cc_start: 0.7451 (ttmt) cc_final: 0.6855 (tppt) REVERT: B 345 LYS cc_start: 0.7110 (mttt) cc_final: 0.6783 (mppt) REVERT: B 437 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7652 (mtpt) REVERT: B 544 LEU cc_start: 0.8533 (mp) cc_final: 0.8311 (mm) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.6463 time to fit residues: 61.1694 Evaluate side-chains 87 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain B residue 135 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.096375 restraints weight = 7761.854| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.27 r_work: 0.2918 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7340 Z= 0.146 Angle : 0.565 9.059 10042 Z= 0.284 Chirality : 0.041 0.200 1178 Planarity : 0.004 0.031 1210 Dihedral : 5.318 57.273 986 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.55 % Allowed : 13.77 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.77 (0.29), residues: 936 helix: 1.44 (0.20), residues: 750 sheet: None (None), residues: 0 loop : 0.38 (0.52), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.015 0.002 TYR A 322 PHE 0.025 0.002 PHE A 361 TRP 0.015 0.001 TRP A 411 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7340) covalent geometry : angle 0.56512 (10042) hydrogen bonds : bond 0.03831 ( 484) hydrogen bonds : angle 4.25074 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.261 Fit side-chains REVERT: A 167 ASP cc_start: 0.9144 (t70) cc_final: 0.8871 (t0) REVERT: A 218 LEU cc_start: 0.8369 (tp) cc_final: 0.8029 (mp) REVERT: A 337 LYS cc_start: 0.7462 (tttm) cc_final: 0.6809 (tppt) REVERT: A 345 LYS cc_start: 0.7169 (mttt) cc_final: 0.6774 (mppt) REVERT: A 437 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7664 (mtpt) REVERT: B 115 THR cc_start: 0.8456 (m) cc_final: 0.8196 (p) REVERT: B 218 LEU cc_start: 0.8300 (tp) cc_final: 0.7974 (mp) REVERT: B 337 LYS cc_start: 0.7452 (ttmt) cc_final: 0.6845 (tppt) REVERT: B 345 LYS cc_start: 0.7134 (mttt) cc_final: 0.6789 (mppt) REVERT: B 437 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7581 (mtpt) REVERT: B 544 LEU cc_start: 0.8599 (mp) cc_final: 0.8361 (mm) outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.6519 time to fit residues: 59.5833 Evaluate side-chains 86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.094983 restraints weight = 7787.582| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.27 r_work: 0.2893 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7340 Z= 0.162 Angle : 0.586 9.388 10042 Z= 0.295 Chirality : 0.043 0.220 1178 Planarity : 0.004 0.032 1210 Dihedral : 5.411 56.016 986 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.69 % Allowed : 13.50 % Favored : 85.81 % 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: 1.71 (0.29), residues: 936 helix: 1.40 (0.20), residues: 750 sheet: None (None), residues: 0 loop : 0.35 (0.51), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.016 0.002 TYR A 322 PHE 0.029 0.002 PHE B 361 TRP 0.014 0.002 TRP B 411 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7340) covalent geometry : angle 0.58567 (10042) hydrogen bonds : bond 0.04052 ( 484) hydrogen bonds : angle 4.34460 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.267 Fit side-chains REVERT: A 167 ASP cc_start: 0.9174 (t70) cc_final: 0.8962 (t0) REVERT: A 218 LEU cc_start: 0.8358 (tp) cc_final: 0.8019 (mp) REVERT: A 337 LYS cc_start: 0.7489 (tttm) cc_final: 0.6833 (tppt) REVERT: A 345 LYS cc_start: 0.7197 (mttt) cc_final: 0.6809 (mppt) REVERT: A 437 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7649 (mtpt) REVERT: B 115 THR cc_start: 0.8474 (m) cc_final: 0.8224 (p) REVERT: B 218 LEU cc_start: 0.8353 (tp) cc_final: 0.8029 (mp) REVERT: B 337 LYS cc_start: 0.7476 (ttmt) cc_final: 0.6861 (tppt) REVERT: B 345 LYS cc_start: 0.7165 (mttt) cc_final: 0.6812 (mppt) REVERT: B 437 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7661 (mtpt) REVERT: B 544 LEU cc_start: 0.8642 (mp) cc_final: 0.8395 (mm) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.6535 time to fit residues: 61.1185 Evaluate side-chains 88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 135 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098660 restraints weight = 7708.001| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.25 r_work: 0.2947 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7340 Z= 0.119 Angle : 0.535 8.625 10042 Z= 0.269 Chirality : 0.040 0.190 1178 Planarity : 0.003 0.030 1210 Dihedral : 5.222 56.179 986 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.69 % Allowed : 14.60 % Favored : 84.71 % 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: 1.97 (0.29), residues: 936 helix: 1.60 (0.20), residues: 746 sheet: None (None), residues: 0 loop : 0.36 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.014 0.001 TYR A 322 PHE 0.029 0.001 PHE A 361 TRP 0.017 0.001 TRP A 411 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7340) covalent geometry : angle 0.53457 (10042) hydrogen bonds : bond 0.03580 ( 484) hydrogen bonds : angle 4.17672 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.278 Fit side-chains REVERT: A 167 ASP cc_start: 0.9138 (t70) cc_final: 0.8836 (t0) REVERT: A 218 LEU cc_start: 0.8351 (tp) cc_final: 0.8024 (mp) REVERT: A 337 LYS cc_start: 0.7459 (tttm) cc_final: 0.6831 (tppt) REVERT: A 345 LYS cc_start: 0.7161 (mttt) cc_final: 0.6755 (mppt) REVERT: A 437 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7623 (mtpt) REVERT: B 115 THR cc_start: 0.8451 (m) cc_final: 0.8186 (p) REVERT: B 218 LEU cc_start: 0.8291 (tp) cc_final: 0.7965 (mp) REVERT: B 337 LYS cc_start: 0.7405 (ttmt) cc_final: 0.6816 (tppt) REVERT: B 345 LYS cc_start: 0.7158 (mttt) cc_final: 0.6820 (mppt) REVERT: B 437 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7632 (mtpt) REVERT: B 544 LEU cc_start: 0.8575 (mp) cc_final: 0.8353 (mm) outliers start: 5 outliers final: 2 residues processed: 91 average time/residue: 0.6630 time to fit residues: 63.3858 Evaluate side-chains 86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099678 restraints weight = 7765.180| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.28 r_work: 0.2959 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7340 Z= 0.111 Angle : 0.523 8.124 10042 Z= 0.263 Chirality : 0.039 0.173 1178 Planarity : 0.003 0.030 1210 Dihedral : 5.155 56.621 986 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.28 % Allowed : 14.88 % Favored : 84.85 % 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: 2.10 (0.29), residues: 936 helix: 1.67 (0.20), residues: 748 sheet: None (None), residues: 0 loop : 0.48 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.014 0.001 TYR A 322 PHE 0.029 0.001 PHE B 361 TRP 0.018 0.001 TRP A 411 HIS 0.003 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7340) covalent geometry : angle 0.52274 (10042) hydrogen bonds : bond 0.03446 ( 484) hydrogen bonds : angle 4.09272 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.268 Fit side-chains REVERT: A 116 ARG cc_start: 0.8443 (tpt170) cc_final: 0.7936 (tpt170) REVERT: A 167 ASP cc_start: 0.9151 (t70) cc_final: 0.8905 (t0) REVERT: A 218 LEU cc_start: 0.8361 (tp) cc_final: 0.8005 (mp) REVERT: A 337 LYS cc_start: 0.7410 (tttm) cc_final: 0.6808 (tppt) REVERT: A 345 LYS cc_start: 0.7144 (mttt) cc_final: 0.6610 (ttpp) REVERT: A 437 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7605 (mtpt) REVERT: B 88 GLN cc_start: 0.5236 (tp40) cc_final: 0.5022 (tp-100) REVERT: B 115 THR cc_start: 0.8445 (m) cc_final: 0.8170 (p) REVERT: B 218 LEU cc_start: 0.8288 (tp) cc_final: 0.7942 (mp) REVERT: B 337 LYS cc_start: 0.7362 (ttmt) cc_final: 0.6787 (tppt) REVERT: B 345 LYS cc_start: 0.7137 (mttt) cc_final: 0.6784 (mppt) REVERT: B 437 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7601 (mtpt) REVERT: B 544 LEU cc_start: 0.8538 (mp) cc_final: 0.8312 (mm) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.6648 time to fit residues: 61.5060 Evaluate side-chains 87 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.109522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093337 restraints weight = 7721.123| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.26 r_work: 0.2879 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7340 Z= 0.197 Angle : 0.615 9.578 10042 Z= 0.311 Chirality : 0.045 0.230 1178 Planarity : 0.004 0.034 1210 Dihedral : 5.495 55.314 986 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.28 % Allowed : 14.60 % Favored : 85.12 % 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: 1.68 (0.29), residues: 936 helix: 1.38 (0.20), residues: 750 sheet: None (None), residues: 0 loop : 0.29 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.017 0.002 TYR B 322 PHE 0.028 0.002 PHE A 361 TRP 0.013 0.002 TRP A 411 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 7340) covalent geometry : angle 0.61542 (10042) hydrogen bonds : bond 0.04321 ( 484) hydrogen bonds : angle 4.39463 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.36 seconds wall clock time: 40 minutes 24.70 seconds (2424.70 seconds total)