Starting phenix.real_space_refine on Fri Aug 22 19:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx4_37900/08_2025/8wx4_37900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx4_37900/08_2025/8wx4_37900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wx4_37900/08_2025/8wx4_37900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx4_37900/08_2025/8wx4_37900.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx4_37900/08_2025/8wx4_37900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx4_37900/08_2025/8wx4_37900.cif" } resolution = 3.12 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= 0.089 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 40 5.16 5 C 4966 2.51 5 N 1224 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7512 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3738 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain breaks: 2 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: A Time building chain proxies: 2.10, per 1000 atoms: 0.28 Number of scatterers: 7512 At special positions: 0 Unit cell: (83.415, 120.765, 82.17, 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 40 16.00 O 1282 8.00 N 1224 7.00 C 4966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " LEU A 702 " - " LYS A 701 " " LEU B 702 " - " LYS B 701 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 259.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 75.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.539A pdb=" N CYS B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 99 removed outlier: 3.559A pdb=" N LEU B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.603A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 125 through 133 removed outlier: 4.188A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 181 removed outlier: 3.572A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 182 through 186 removed outlier: 5.436A pdb=" N ASP B 185 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 186' Processing helix chain 'B' and resid 187 through 220 removed outlier: 4.778A pdb=" N ILE B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 244 removed outlier: 3.514A pdb=" N GLY B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.652A pdb=" N LEU B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 347 Proline residue: B 330 - end of helix removed outlier: 3.728A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.205A pdb=" N LEU B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 400 through 430 removed outlier: 3.683A pdb=" N ARG B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.661A pdb=" N ILE B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 471 " --> pdb=" O PHE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 510 Processing helix chain 'B' and resid 531 through 559 removed outlier: 3.609A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 556 " --> pdb=" O ILE B 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 55 removed outlier: 3.539A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 99 removed outlier: 3.559A pdb=" N LEU A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 103 through 118 removed outlier: 3.603A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 125 through 133 removed outlier: 4.188A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 181 removed outlier: 3.572A pdb=" N ASN A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 182 through 186 removed outlier: 5.435A pdb=" N ASP A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 187 through 220 removed outlier: 4.778A pdb=" N ILE A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 244 removed outlier: 3.514A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.652A pdb=" N LEU A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 347 Proline residue: A 330 - end of helix removed outlier: 3.728A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.205A pdb=" N LEU A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 400 through 430 removed outlier: 3.683A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.661A pdb=" N ILE A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 510 Processing helix chain 'A' and resid 531 through 559 removed outlier: 3.609A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 434 through 438 Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 438 504 hydrogen bonds defined for protein. 1506 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: 0.98 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1140 1.30 - 1.43: 2074 1.43 - 1.55: 4422 1.55 - 1.68: 0 1.68 - 1.81: 60 Bond restraints: 7696 Sorted by residual: bond pdb=" C TYR B 52 " pdb=" O TYR B 52 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.31e-02 5.83e+03 1.94e+01 bond pdb=" C TYR A 52 " pdb=" O TYR A 52 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.31e-02 5.83e+03 1.94e+01 bond pdb=" C ASN A 203 " pdb=" O ASN A 203 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" C ASN B 203 " pdb=" O ASN B 203 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.59e-02 3.96e+03 1.76e+01 bond pdb=" C TYR A 335 " pdb=" O TYR A 335 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.26e-02 6.30e+03 1.60e+01 ... (remaining 7691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 10368 3.34 - 6.68: 92 6.68 - 10.01: 2 10.01 - 13.35: 0 13.35 - 16.69: 2 Bond angle restraints: 10464 Sorted by residual: angle pdb=" N LEU B 204 " pdb=" CA LEU B 204 " pdb=" C LEU B 204 " ideal model delta sigma weight residual 113.18 96.49 16.69 1.33e+00 5.65e-01 1.57e+02 angle pdb=" N LEU A 204 " pdb=" CA LEU A 204 " pdb=" C LEU A 204 " ideal model delta sigma weight residual 113.18 96.50 16.68 1.33e+00 5.65e-01 1.57e+02 angle pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" O ILE A 202 " ideal model delta sigma weight residual 121.27 115.46 5.81 1.04e+00 9.25e-01 3.13e+01 angle pdb=" CA ILE B 202 " pdb=" C ILE B 202 " pdb=" O ILE B 202 " ideal model delta sigma weight residual 121.27 115.49 5.78 1.04e+00 9.25e-01 3.09e+01 angle pdb=" O VAL B 334 " pdb=" C VAL B 334 " pdb=" N TYR B 335 " ideal model delta sigma weight residual 121.91 116.73 5.18 9.80e-01 1.04e+00 2.79e+01 ... (remaining 10459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 3958 16.38 - 32.76: 388 32.76 - 49.14: 98 49.14 - 65.52: 24 65.52 - 81.90: 6 Dihedral angle restraints: 4474 sinusoidal: 1678 harmonic: 2796 Sorted by residual: dihedral pdb=" SG CYS B 133 " pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" CA CYS B 153 " ideal model delta sinusoidal sigma weight residual -73.00 0.31 -73.31 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" SG CYS A 133 " pdb=" CB CYS A 153 " pdb=" SG CYS A 153 " pdb=" CA CYS A 153 " ideal model delta sinusoidal sigma weight residual -73.00 0.28 -73.28 1 2.00e+01 2.50e-03 1.71e+01 dihedral pdb=" CA ASP A 373 " pdb=" CB ASP A 373 " pdb=" CG ASP A 373 " pdb=" OD1 ASP A 373 " ideal model delta sinusoidal sigma weight residual -30.00 -86.15 56.15 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 974 0.041 - 0.082: 192 0.082 - 0.123: 50 0.123 - 0.164: 8 0.164 - 0.205: 4 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA ILE A 202 " pdb=" N ILE A 202 " pdb=" C ILE A 202 " pdb=" CB ILE A 202 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 202 " pdb=" N ILE B 202 " pdb=" C ILE B 202 " pdb=" CB ILE B 202 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE B 202 " pdb=" CA ILE B 202 " pdb=" CG1 ILE B 202 " pdb=" CG2 ILE B 202 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1225 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 464 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C SER A 464 " 0.059 2.00e-02 2.50e+03 pdb=" O SER A 464 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 465 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 464 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER B 464 " -0.059 2.00e-02 2.50e+03 pdb=" O SER B 464 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B 465 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 203 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ASN B 203 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B 203 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 204 " -0.017 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2271 2.82 - 3.34: 7226 3.34 - 3.86: 12600 3.86 - 4.38: 14791 4.38 - 4.90: 25092 Nonbonded interactions: 61980 Sorted by model distance: nonbonded pdb=" O SER B 519 " pdb=" OG SER B 519 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 519 " pdb=" OG SER A 519 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 181 " pdb=" OH TYR A 477 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASP B 181 " pdb=" OH TYR B 477 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR B 333 " pdb=" O GLY B 499 " model vdw 2.384 3.040 ... (remaining 61975 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 'B' selection = chain 'A' } 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: 0.530 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.460 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7702 Z= 0.251 Angle : 0.707 16.688 10478 Z= 0.458 Chirality : 0.037 0.205 1228 Planarity : 0.004 0.034 1288 Dihedral : 14.158 81.900 2660 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.53 % Allowed : 4.59 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: -1.64 (0.25), residues: 960 helix: -0.58 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.22 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 137 TYR 0.021 0.001 TYR A 335 PHE 0.008 0.001 PHE A 492 TRP 0.002 0.000 TRP A 453 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7696) covalent geometry : angle 0.70606 (10464) SS BOND : bond 0.00064 ( 4) SS BOND : angle 0.38081 ( 8) hydrogen bonds : bond 0.15313 ( 504) hydrogen bonds : angle 6.11565 ( 1506) link_TRANS : bond 0.00647 ( 2) link_TRANS : angle 1.79698 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.152 Fit side-chains REVERT: B 433 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7707 (tttt) REVERT: A 433 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7654 (tttt) REVERT: B 701 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7815 (mmtm) REVERT: A 701 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7828 (mmtm) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.0548 time to fit residues: 9.6637 Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain A residue 701 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 219 ASN A 196 ASN A 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.145042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108133 restraints weight = 8183.472| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.68 r_work: 0.3015 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7702 Z= 0.150 Angle : 0.549 7.000 10478 Z= 0.278 Chirality : 0.041 0.238 1228 Planarity : 0.004 0.027 1288 Dihedral : 5.630 46.691 1054 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.17 % Allowed : 10.46 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: -0.01 (0.28), residues: 960 helix: 0.71 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.08 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.015 0.001 TYR A 113 PHE 0.012 0.001 PHE B 194 TRP 0.011 0.001 TRP B 94 HIS 0.002 0.000 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7696) covalent geometry : angle 0.54930 (10464) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.37286 ( 8) hydrogen bonds : bond 0.04657 ( 504) hydrogen bonds : angle 4.04126 ( 1506) link_TRANS : bond 0.00055 ( 2) link_TRANS : angle 0.28356 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.176 Fit side-chains REVERT: B 226 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 433 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7373 (tttt) REVERT: B 489 MET cc_start: 0.8309 (mmt) cc_final: 0.7899 (tpp) REVERT: A 226 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: A 433 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7340 (tttt) REVERT: A 489 MET cc_start: 0.8280 (mmt) cc_final: 0.7888 (tpp) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.0809 time to fit residues: 9.5806 Evaluate side-chains 70 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.139406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102899 restraints weight = 8106.290| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.64 r_work: 0.2940 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7702 Z= 0.147 Angle : 0.527 6.471 10478 Z= 0.267 Chirality : 0.041 0.243 1228 Planarity : 0.004 0.025 1288 Dihedral : 4.902 41.787 1044 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.66 % Allowed : 12.12 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.39 (0.28), residues: 960 helix: 1.06 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.13 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 394 TYR 0.016 0.001 TYR B 113 PHE 0.012 0.001 PHE B 194 TRP 0.009 0.001 TRP B 94 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7696) covalent geometry : angle 0.52759 (10464) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.39303 ( 8) hydrogen bonds : bond 0.04812 ( 504) hydrogen bonds : angle 3.84907 ( 1506) link_TRANS : bond 0.00150 ( 2) link_TRANS : angle 0.37057 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.191 Fit side-chains REVERT: B 186 ARG cc_start: 0.7590 (mtt90) cc_final: 0.7262 (mtt90) REVERT: B 226 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: B 253 ASP cc_start: 0.6852 (p0) cc_final: 0.6441 (p0) REVERT: B 318 LEU cc_start: 0.8269 (tt) cc_final: 0.8041 (tt) REVERT: B 433 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7368 (tttt) REVERT: A 226 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 318 LEU cc_start: 0.8330 (tt) cc_final: 0.8091 (tt) REVERT: A 433 LYS cc_start: 0.7718 (ttpt) cc_final: 0.7337 (tttt) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.0720 time to fit residues: 8.8891 Evaluate side-chains 79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.138527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102264 restraints weight = 8177.925| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.61 r_work: 0.2930 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7702 Z= 0.130 Angle : 0.508 6.412 10478 Z= 0.255 Chirality : 0.040 0.198 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.614 39.255 1044 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.91 % Allowed : 12.88 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.75 (0.28), residues: 960 helix: 1.35 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -2.02 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.007 0.001 TYR A 335 PHE 0.011 0.001 PHE B 194 TRP 0.009 0.001 TRP A 94 HIS 0.002 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7696) covalent geometry : angle 0.50798 (10464) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.42835 ( 8) hydrogen bonds : bond 0.04416 ( 504) hydrogen bonds : angle 3.78211 ( 1506) link_TRANS : bond 0.00095 ( 2) link_TRANS : angle 0.45053 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.260 Fit side-chains REVERT: B 168 VAL cc_start: 0.8755 (t) cc_final: 0.8404 (t) REVERT: B 207 ILE cc_start: 0.8133 (mm) cc_final: 0.7911 (mt) REVERT: B 226 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: B 253 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6603 (p0) REVERT: B 318 LEU cc_start: 0.8350 (tt) cc_final: 0.8101 (tt) REVERT: B 341 THR cc_start: 0.8200 (p) cc_final: 0.7843 (p) REVERT: B 433 LYS cc_start: 0.7760 (ttpt) cc_final: 0.7419 (tttt) REVERT: A 133 CYS cc_start: 0.5375 (OUTLIER) cc_final: 0.5168 (p) REVERT: A 168 VAL cc_start: 0.8762 (t) cc_final: 0.8436 (t) REVERT: A 207 ILE cc_start: 0.8135 (mm) cc_final: 0.7920 (mt) REVERT: A 226 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: A 253 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6638 (p0) REVERT: A 318 LEU cc_start: 0.8367 (tt) cc_final: 0.8119 (tt) REVERT: A 341 THR cc_start: 0.8204 (p) cc_final: 0.7843 (p) REVERT: A 433 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7488 (tttt) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 0.0687 time to fit residues: 7.7536 Evaluate side-chains 77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.136760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099498 restraints weight = 8077.899| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.68 r_work: 0.2893 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7702 Z= 0.136 Angle : 0.512 6.187 10478 Z= 0.259 Chirality : 0.041 0.267 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.300 38.141 1040 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.17 % Allowed : 13.90 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 0.93 (0.28), residues: 960 helix: 1.49 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.95 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.009 0.001 TYR A 113 PHE 0.011 0.001 PHE B 194 TRP 0.008 0.001 TRP B 94 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7696) covalent geometry : angle 0.51218 (10464) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.61062 ( 8) hydrogen bonds : bond 0.04518 ( 504) hydrogen bonds : angle 3.72922 ( 1506) link_TRANS : bond 0.00023 ( 2) link_TRANS : angle 0.29273 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.228 Fit side-chains REVERT: B 226 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: B 253 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6796 (p0) REVERT: B 318 LEU cc_start: 0.8378 (tt) cc_final: 0.8136 (tt) REVERT: B 341 THR cc_start: 0.8257 (p) cc_final: 0.7899 (p) REVERT: B 433 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7556 (tttt) REVERT: A 129 ARG cc_start: 0.6219 (ttm-80) cc_final: 0.5999 (ttm170) REVERT: A 133 CYS cc_start: 0.5409 (OUTLIER) cc_final: 0.5005 (p) REVERT: A 226 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: A 253 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6827 (p0) REVERT: A 318 LEU cc_start: 0.8606 (tt) cc_final: 0.8372 (tt) REVERT: A 341 THR cc_start: 0.8239 (p) cc_final: 0.7878 (p) REVERT: A 433 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7539 (tttt) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.0728 time to fit residues: 7.4790 Evaluate side-chains 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.137572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100437 restraints weight = 8019.962| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.67 r_work: 0.2908 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7702 Z= 0.123 Angle : 0.489 6.218 10478 Z= 0.247 Chirality : 0.040 0.236 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.224 37.991 1040 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.42 % Allowed : 14.03 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.16 (0.28), residues: 960 helix: 1.66 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.85 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.007 0.001 TYR B 113 PHE 0.010 0.001 PHE B 194 TRP 0.007 0.001 TRP A 94 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7696) covalent geometry : angle 0.48959 (10464) SS BOND : bond 0.00041 ( 4) SS BOND : angle 0.46812 ( 8) hydrogen bonds : bond 0.04244 ( 504) hydrogen bonds : angle 3.69169 ( 1506) link_TRANS : bond 0.00003 ( 2) link_TRANS : angle 0.25079 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.230 Fit side-chains REVERT: B 117 MET cc_start: 0.8200 (mmm) cc_final: 0.7911 (mmt) REVERT: B 186 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7472 (mtt-85) REVERT: B 207 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7847 (mm) REVERT: B 226 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: B 253 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6757 (p0) REVERT: B 318 LEU cc_start: 0.8342 (tt) cc_final: 0.8095 (tt) REVERT: B 341 THR cc_start: 0.8119 (p) cc_final: 0.7755 (p) REVERT: B 433 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7497 (tttt) REVERT: B 484 MET cc_start: 0.7255 (mtp) cc_final: 0.7045 (mtt) REVERT: A 117 MET cc_start: 0.8217 (mmm) cc_final: 0.7943 (mmt) REVERT: A 133 CYS cc_start: 0.5502 (OUTLIER) cc_final: 0.5147 (p) REVERT: A 207 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 226 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 253 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6805 (p0) REVERT: A 318 LEU cc_start: 0.8563 (tt) cc_final: 0.8322 (tt) REVERT: A 341 THR cc_start: 0.8115 (p) cc_final: 0.7749 (p) REVERT: A 433 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7508 (tttt) REVERT: A 484 MET cc_start: 0.7246 (mtp) cc_final: 0.7038 (mtt) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.0674 time to fit residues: 7.0805 Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 74 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.138144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.101800 restraints weight = 7989.071| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.61 r_work: 0.2932 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7702 Z= 0.115 Angle : 0.482 6.185 10478 Z= 0.242 Chirality : 0.039 0.228 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.155 37.793 1040 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.55 % Allowed : 13.65 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.32 (0.28), residues: 960 helix: 1.77 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.006 0.001 TYR A 52 PHE 0.010 0.001 PHE A 194 TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7696) covalent geometry : angle 0.48202 (10464) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.46182 ( 8) hydrogen bonds : bond 0.04092 ( 504) hydrogen bonds : angle 3.63893 ( 1506) link_TRANS : bond 0.00008 ( 2) link_TRANS : angle 0.18654 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.266 Fit side-chains REVERT: B 117 MET cc_start: 0.8246 (mmm) cc_final: 0.7233 (mmt) REVERT: B 186 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7410 (mtt-85) REVERT: B 226 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: B 253 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6796 (p0) REVERT: B 318 LEU cc_start: 0.8581 (tt) cc_final: 0.8344 (tt) REVERT: B 341 THR cc_start: 0.8103 (p) cc_final: 0.7757 (p) REVERT: B 433 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7579 (tttt) REVERT: A 117 MET cc_start: 0.8292 (mmm) cc_final: 0.7311 (mmt) REVERT: A 133 CYS cc_start: 0.5500 (OUTLIER) cc_final: 0.5145 (p) REVERT: A 186 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7445 (mtt-85) REVERT: A 207 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 226 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: A 253 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 318 LEU cc_start: 0.8594 (tt) cc_final: 0.8357 (tt) REVERT: A 341 THR cc_start: 0.8096 (p) cc_final: 0.7750 (p) REVERT: A 433 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7612 (tttt) outliers start: 20 outliers final: 12 residues processed: 71 average time/residue: 0.0720 time to fit residues: 7.1891 Evaluate side-chains 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0170 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.137504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.100173 restraints weight = 8036.686| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.70 r_work: 0.2907 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7702 Z= 0.121 Angle : 0.488 6.230 10478 Z= 0.245 Chirality : 0.040 0.210 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.126 37.654 1040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.17 % Allowed : 14.41 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.31 (0.28), residues: 960 helix: 1.77 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.007 0.001 TYR A 52 PHE 0.010 0.001 PHE B 194 TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7696) covalent geometry : angle 0.48840 (10464) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.42781 ( 8) hydrogen bonds : bond 0.04192 ( 504) hydrogen bonds : angle 3.65962 ( 1506) link_TRANS : bond 0.00013 ( 2) link_TRANS : angle 0.16671 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.174 Fit side-chains REVERT: B 33 ARG cc_start: 0.7514 (ptp-170) cc_final: 0.7297 (ptm160) REVERT: B 117 MET cc_start: 0.8241 (mmm) cc_final: 0.7589 (mmt) REVERT: B 186 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7371 (mtt-85) REVERT: B 226 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 253 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6812 (p0) REVERT: B 318 LEU cc_start: 0.8561 (tt) cc_final: 0.8316 (tt) REVERT: B 341 THR cc_start: 0.8087 (p) cc_final: 0.7732 (p) REVERT: A 117 MET cc_start: 0.8276 (mmm) cc_final: 0.7628 (mmt) REVERT: A 133 CYS cc_start: 0.5507 (OUTLIER) cc_final: 0.5158 (p) REVERT: A 186 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6658 (mtm110) REVERT: A 226 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: A 253 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6862 (p0) REVERT: A 318 LEU cc_start: 0.8581 (tt) cc_final: 0.8332 (tt) REVERT: A 341 THR cc_start: 0.8075 (p) cc_final: 0.7718 (p) REVERT: A 433 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7510 (tttt) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 0.0665 time to fit residues: 6.4926 Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.137754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.100696 restraints weight = 7986.281| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.69 r_work: 0.2914 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7702 Z= 0.117 Angle : 0.484 6.203 10478 Z= 0.243 Chirality : 0.039 0.203 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.088 36.880 1040 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.17 % Allowed : 14.67 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.39 (0.28), residues: 960 helix: 1.83 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.007 0.001 TYR B 52 PHE 0.010 0.001 PHE A 194 TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7696) covalent geometry : angle 0.48414 (10464) SS BOND : bond 0.00028 ( 4) SS BOND : angle 0.41671 ( 8) hydrogen bonds : bond 0.04116 ( 504) hydrogen bonds : angle 3.63500 ( 1506) link_TRANS : bond 0.00005 ( 2) link_TRANS : angle 0.13953 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 33 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7174 (ptm160) REVERT: B 117 MET cc_start: 0.8200 (mmm) cc_final: 0.7596 (mmt) REVERT: B 186 ARG cc_start: 0.7730 (mtt90) cc_final: 0.6553 (mtm110) REVERT: B 226 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 253 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6824 (p0) REVERT: B 318 LEU cc_start: 0.8541 (tt) cc_final: 0.8301 (tt) REVERT: B 341 THR cc_start: 0.8022 (p) cc_final: 0.7665 (p) REVERT: B 518 MET cc_start: 0.6163 (mmm) cc_final: 0.5876 (mmm) REVERT: A 117 MET cc_start: 0.8210 (mmm) cc_final: 0.7629 (mmt) REVERT: A 186 ARG cc_start: 0.7708 (mtt90) cc_final: 0.6631 (mtm110) REVERT: A 226 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: A 253 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 318 LEU cc_start: 0.8557 (tt) cc_final: 0.8315 (tt) REVERT: A 341 THR cc_start: 0.8016 (p) cc_final: 0.7658 (p) REVERT: A 433 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7495 (tttt) REVERT: A 518 MET cc_start: 0.6146 (mmm) cc_final: 0.5860 (mmm) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 0.0552 time to fit residues: 5.4081 Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 0.0040 chunk 32 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.140089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103240 restraints weight = 7963.081| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.70 r_work: 0.2959 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7702 Z= 0.103 Angle : 0.468 6.133 10478 Z= 0.234 Chirality : 0.039 0.205 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.003 36.122 1040 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 14.80 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.56 (0.28), residues: 960 helix: 1.95 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.74 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.005 0.001 TYR A 52 PHE 0.008 0.001 PHE A 194 TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7696) covalent geometry : angle 0.46775 (10464) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.37568 ( 8) hydrogen bonds : bond 0.03789 ( 504) hydrogen bonds : angle 3.56156 ( 1506) link_TRANS : bond 0.00009 ( 2) link_TRANS : angle 0.11058 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.169 Fit side-chains REVERT: B 117 MET cc_start: 0.8264 (mmm) cc_final: 0.7553 (mmt) REVERT: B 186 ARG cc_start: 0.7874 (mtt90) cc_final: 0.6718 (mtm110) REVERT: B 226 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: B 253 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6901 (p0) REVERT: B 318 LEU cc_start: 0.8600 (tt) cc_final: 0.8367 (tt) REVERT: B 341 THR cc_start: 0.8002 (p) cc_final: 0.7707 (p) REVERT: A 117 MET cc_start: 0.8313 (mmm) cc_final: 0.7637 (mmt) REVERT: A 133 CYS cc_start: 0.5559 (OUTLIER) cc_final: 0.5199 (p) REVERT: A 186 ARG cc_start: 0.7759 (mtt90) cc_final: 0.6726 (mtm110) REVERT: A 226 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: A 253 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6896 (p0) REVERT: A 318 LEU cc_start: 0.8612 (tt) cc_final: 0.8378 (tt) REVERT: A 341 THR cc_start: 0.8014 (p) cc_final: 0.7714 (p) REVERT: A 433 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7606 (tttt) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.0643 time to fit residues: 6.8797 Evaluate side-chains 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100560 restraints weight = 7972.257| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.68 r_work: 0.2924 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7702 Z= 0.122 Angle : 0.490 6.238 10478 Z= 0.246 Chirality : 0.040 0.272 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.017 36.088 1040 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.91 % Allowed : 14.92 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.48 (0.28), residues: 960 helix: 1.89 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.73 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.008 0.001 TYR B 52 PHE 0.010 0.001 PHE A 194 TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7696) covalent geometry : angle 0.49007 (10464) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.38447 ( 8) hydrogen bonds : bond 0.04174 ( 504) hydrogen bonds : angle 3.62125 ( 1506) link_TRANS : bond 0.00020 ( 2) link_TRANS : angle 0.11653 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.62 seconds wall clock time: 24 minutes 45.56 seconds (1485.56 seconds total)