Starting phenix.real_space_refine on Sun May 11 04:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx4_37900/05_2025/8wx4_37900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx4_37900/05_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_37900/05_2025/8wx4_37900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx4_37900/05_2025/8wx4_37900.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx4_37900/05_2025/8wx4_37900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx4_37900/05_2025/8wx4_37900.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7512 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" 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: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "A" 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: B Time building chain proxies: 6.32, per 1000 atoms: 0.84 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=2, 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 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: 1.69 Conformation dependent library (CDL) restraints added in 993.5 milliseconds 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: 0.69 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: 2.01 Time building geometry restraints manager: 2.00 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: 3955 16.38 - 32.76: 386 32.76 - 49.14: 98 49.14 - 65.52: 24 65.52 - 81.90: 5 Dihedral angle restraints: 4468 sinusoidal: 1672 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=" 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 dihedral pdb=" CA ASP B 373 " pdb=" CB ASP B 373 " pdb=" CG ASP B 373 " pdb=" OD1 ASP B 373 " ideal model delta sinusoidal sigma weight residual -30.00 -86.13 56.13 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4465 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: 2.03 - 2.60: 48 2.60 - 3.18: 6371 3.18 - 3.75: 12057 3.75 - 4.33: 16404 4.33 - 4.90: 27106 Nonbonded interactions: 61986 Sorted by model distance: nonbonded pdb=" SG CYS A 68 " pdb=" SG CYS A 141 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 133 " pdb=" SG CYS A 153 " model vdw 2.032 3.760 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 ... (remaining 61981 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: 0.04 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: 0.420 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.940 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- 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 7700 Z= 0.251 Angle : 0.707 16.688 10474 Z= 0.458 Chirality : 0.037 0.205 1228 Planarity : 0.004 0.034 1288 Dihedral : 14.158 81.900 2660 Min Nonbonded Distance : 2.031 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP A 453 HIS 0.003 0.001 HIS A 521 PHE 0.008 0.001 PHE A 492 TYR 0.021 0.001 TYR A 335 ARG 0.002 0.000 ARG A 137 Details of bonding type rmsd link_TRANS : bond 0.00647 ( 2) link_TRANS : angle 1.79698 ( 6) hydrogen bonds : bond 0.15313 ( 504) hydrogen bonds : angle 6.11565 ( 1506) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.37846 ( 4) covalent geometry : bond 0.00374 ( 7696) covalent geometry : angle 0.70606 (10464) *********************** 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 : 0.772 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: 0.1632 time to fit residues: 28.3428 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 : 0.756 ------------------------------------------------------------------------------- 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 81 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 87 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 B 395 HIS A 196 ASN ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.147451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111054 restraints weight = 8180.624| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.67 r_work: 0.3055 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7700 Z= 0.135 Angle : 0.526 6.783 10474 Z= 0.267 Chirality : 0.040 0.239 1228 Planarity : 0.004 0.024 1288 Dihedral : 5.704 50.447 1054 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.30 % Allowed : 10.46 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 960 helix: 0.71 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.11 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 94 HIS 0.002 0.000 HIS A 559 PHE 0.012 0.001 PHE A 120 TYR 0.014 0.001 TYR A 113 ARG 0.003 0.000 ARG B 426 Details of bonding type rmsd link_TRANS : bond 0.00098 ( 2) link_TRANS : angle 0.28452 ( 6) hydrogen bonds : bond 0.04491 ( 504) hydrogen bonds : angle 4.01782 ( 1506) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.33454 ( 4) covalent geometry : bond 0.00302 ( 7696) covalent geometry : angle 0.52612 (10464) *********************** 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 85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.745 Fit side-chains REVERT: B 226 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: B 433 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7359 (tttt) REVERT: B 489 MET cc_start: 0.8245 (mmt) cc_final: 0.7838 (tpp) REVERT: A 226 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: A 433 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7328 (tttt) REVERT: A 489 MET cc_start: 0.8239 (mmt) cc_final: 0.7852 (tpp) outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 0.1683 time to fit residues: 20.3474 Evaluate side-chains 68 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 133 CYS 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 47 optimal weight: 0.4980 chunk 25 optimal weight: 0.0980 chunk 88 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 40 optimal weight: 0.0270 chunk 31 optimal weight: 0.0270 chunk 84 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.149204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113063 restraints weight = 8143.809| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.68 r_work: 0.3080 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7700 Z= 0.103 Angle : 0.469 6.257 10474 Z= 0.237 Chirality : 0.038 0.247 1228 Planarity : 0.003 0.028 1288 Dihedral : 4.957 46.050 1044 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.17 % Allowed : 12.37 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 960 helix: 1.32 (0.21), residues: 710 sheet: None (None), residues: 0 loop : -1.97 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.001 0.000 HIS B 559 PHE 0.009 0.001 PHE B 492 TYR 0.010 0.001 TYR B 113 ARG 0.001 0.000 ARG B 426 Details of bonding type rmsd link_TRANS : bond 0.00056 ( 2) link_TRANS : angle 0.08155 ( 6) hydrogen bonds : bond 0.03845 ( 504) hydrogen bonds : angle 3.66907 ( 1506) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.29003 ( 4) covalent geometry : bond 0.00209 ( 7696) covalent geometry : angle 0.46874 (10464) *********************** 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 85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.735 Fit side-chains REVERT: B 226 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: B 253 ASP cc_start: 0.6543 (p0) cc_final: 0.6086 (p0) REVERT: B 433 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7360 (tttt) REVERT: A 226 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: A 433 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7314 (tttt) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.1376 time to fit residues: 17.7507 Evaluate side-chains 71 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 87 LEU 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 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 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 67 optimal weight: 0.0030 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.4708 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.143569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107992 restraints weight = 8074.072| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.61 r_work: 0.3009 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7700 Z= 0.115 Angle : 0.494 6.421 10474 Z= 0.246 Chirality : 0.040 0.266 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.541 46.104 1044 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.91 % Allowed : 13.78 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 960 helix: 1.45 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.95 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS A 559 PHE 0.011 0.001 PHE B 194 TYR 0.012 0.001 TYR A 113 ARG 0.002 0.000 ARG A 186 Details of bonding type rmsd link_TRANS : bond 0.00075 ( 2) link_TRANS : angle 0.26015 ( 6) hydrogen bonds : bond 0.03982 ( 504) hydrogen bonds : angle 3.61486 ( 1506) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.32001 ( 4) covalent geometry : bond 0.00255 ( 7696) covalent geometry : angle 0.49371 (10464) *********************** 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 : 0.804 Fit side-chains REVERT: B 226 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: B 253 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6382 (p0) REVERT: B 318 LEU cc_start: 0.8246 (tt) cc_final: 0.8041 (tt) REVERT: B 433 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7362 (tttt) REVERT: B 489 MET cc_start: 0.8311 (mmt) cc_final: 0.7732 (mmt) REVERT: A 226 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: A 253 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6457 (p0) REVERT: A 318 LEU cc_start: 0.8536 (tt) cc_final: 0.8310 (tt) REVERT: A 433 LYS cc_start: 0.7734 (ttpt) cc_final: 0.7344 (tttt) outliers start: 15 outliers final: 8 residues processed: 80 average time/residue: 0.1423 time to fit residues: 17.2747 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 : 0.756 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098101 restraints weight = 8099.187| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.69 r_work: 0.2872 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7700 Z= 0.156 Angle : 0.547 6.476 10474 Z= 0.274 Chirality : 0.042 0.205 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.409 42.324 1040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.04 % Allowed : 14.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 960 helix: 1.42 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.89 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.002 PHE A 194 TYR 0.019 0.002 TYR A 113 ARG 0.004 0.001 ARG B 186 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 2) link_TRANS : angle 0.65600 ( 6) hydrogen bonds : bond 0.05023 ( 504) hydrogen bonds : angle 3.83699 ( 1506) SS BOND : bond 0.01197 ( 2) SS BOND : angle 1.13032 ( 4) covalent geometry : bond 0.00374 ( 7696) covalent geometry : angle 0.54666 (10464) *********************** 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 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.715 Fit side-chains REVERT: B 168 VAL cc_start: 0.8677 (t) cc_final: 0.8336 (t) REVERT: B 226 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: B 253 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6767 (p0) REVERT: B 318 LEU cc_start: 0.8320 (tt) cc_final: 0.8082 (tt) REVERT: B 433 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7396 (tttt) REVERT: A 168 VAL cc_start: 0.8699 (t) cc_final: 0.8445 (t) REVERT: A 226 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: A 318 LEU cc_start: 0.8340 (tt) cc_final: 0.8096 (tt) REVERT: A 433 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7415 (tttt) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.2333 time to fit residues: 23.8736 Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 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 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.136782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.100647 restraints weight = 8083.748| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.61 r_work: 0.2908 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7700 Z= 0.128 Angle : 0.504 6.198 10474 Z= 0.253 Chirality : 0.040 0.192 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.309 41.458 1040 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 14.67 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.28), residues: 960 helix: 1.59 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.84 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE B 194 TYR 0.008 0.001 TYR B 113 ARG 0.001 0.000 ARG B 102 Details of bonding type rmsd link_TRANS : bond 0.00011 ( 2) link_TRANS : angle 0.42520 ( 6) hydrogen bonds : bond 0.04465 ( 504) hydrogen bonds : angle 3.74200 ( 1506) SS BOND : bond 0.00070 ( 2) SS BOND : angle 0.59064 ( 4) covalent geometry : bond 0.00296 ( 7696) covalent geometry : angle 0.50359 (10464) *********************** 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 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.804 Fit side-chains REVERT: B 33 ARG cc_start: 0.7511 (ptp-170) cc_final: 0.7184 (ptm160) REVERT: B 186 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7332 (mtt-85) REVERT: B 226 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 253 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6738 (p0) REVERT: B 318 LEU cc_start: 0.8327 (tt) cc_final: 0.8087 (tt) REVERT: B 433 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7489 (tttt) REVERT: B 484 MET cc_start: 0.7406 (mtp) cc_final: 0.7135 (mtt) REVERT: A 33 ARG cc_start: 0.7506 (ptp-170) cc_final: 0.7192 (ptm160) REVERT: A 186 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7356 (mtt-85) REVERT: A 226 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: A 253 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6733 (p0) REVERT: A 318 LEU cc_start: 0.8355 (tt) cc_final: 0.8110 (tt) REVERT: A 433 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7496 (tttt) outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.2155 time to fit residues: 22.4830 Evaluate side-chains 79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 248 ILE 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 54 ILE Chi-restraints excluded: chain A residue 56 SER 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 248 ILE 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 62 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 85 optimal weight: 0.0370 chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.139553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103579 restraints weight = 7996.871| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.60 r_work: 0.2949 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7700 Z= 0.108 Angle : 0.480 6.077 10474 Z= 0.242 Chirality : 0.040 0.268 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.214 39.716 1040 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.79 % Allowed : 15.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 960 helix: 1.79 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.79 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS B 348 PHE 0.009 0.001 PHE B 194 TYR 0.005 0.001 TYR A 335 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd link_TRANS : bond 0.00009 ( 2) link_TRANS : angle 0.23548 ( 6) hydrogen bonds : bond 0.03935 ( 504) hydrogen bonds : angle 3.61175 ( 1506) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.54770 ( 4) covalent geometry : bond 0.00234 ( 7696) covalent geometry : angle 0.48009 (10464) *********************** 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 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.717 Fit side-chains REVERT: B 117 MET cc_start: 0.8210 (mmm) cc_final: 0.7832 (mmt) REVERT: B 186 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7403 (mtt-85) REVERT: B 207 ILE cc_start: 0.8137 (mm) cc_final: 0.7804 (mt) REVERT: B 226 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: B 253 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6723 (p0) REVERT: B 318 LEU cc_start: 0.8316 (tt) cc_final: 0.8071 (tt) REVERT: B 433 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7531 (tttt) REVERT: B 484 MET cc_start: 0.7162 (mtp) cc_final: 0.6926 (mtt) REVERT: A 186 ARG cc_start: 0.7683 (mtt90) cc_final: 0.7399 (mtt-85) REVERT: A 207 ILE cc_start: 0.8111 (mm) cc_final: 0.7832 (mt) REVERT: A 226 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: A 253 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6744 (p0) REVERT: A 318 LEU cc_start: 0.8342 (tt) cc_final: 0.8101 (tt) REVERT: A 433 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7555 (tttt) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1692 time to fit residues: 17.0518 Evaluate side-chains 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.137565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101439 restraints weight = 8079.566| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.61 r_work: 0.2922 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7700 Z= 0.122 Angle : 0.493 6.198 10474 Z= 0.247 Chirality : 0.040 0.253 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.194 38.242 1040 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.30 % Allowed : 14.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 960 helix: 1.76 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 395 PHE 0.011 0.001 PHE B 194 TYR 0.007 0.001 TYR A 52 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd link_TRANS : bond 0.00004 ( 2) link_TRANS : angle 0.25378 ( 6) hydrogen bonds : bond 0.04223 ( 504) hydrogen bonds : angle 3.65464 ( 1506) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.48299 ( 4) covalent geometry : bond 0.00283 ( 7696) covalent geometry : angle 0.49290 (10464) *********************** 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 80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.741 Fit side-chains REVERT: B 33 ARG cc_start: 0.7535 (ptp-170) cc_final: 0.7174 (ptm160) REVERT: B 117 MET cc_start: 0.8253 (mmm) cc_final: 0.7573 (mmt) REVERT: B 186 ARG cc_start: 0.7731 (mtt90) cc_final: 0.6692 (mtm110) REVERT: B 226 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: B 253 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6836 (p0) REVERT: B 318 LEU cc_start: 0.8341 (tt) cc_final: 0.8087 (tt) REVERT: B 433 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7567 (tttt) REVERT: A 33 ARG cc_start: 0.7527 (ptp-170) cc_final: 0.7193 (ptm160) REVERT: A 186 ARG cc_start: 0.7709 (mtt90) cc_final: 0.6656 (mtm110) REVERT: A 226 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: A 253 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6791 (p0) REVERT: A 318 LEU cc_start: 0.8560 (tt) cc_final: 0.8317 (tt) REVERT: A 433 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7582 (tttt) outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.2047 time to fit residues: 21.0502 Evaluate side-chains 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 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 80 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.138434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.102649 restraints weight = 8093.395| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.61 r_work: 0.2935 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7700 Z= 0.112 Angle : 0.478 5.939 10474 Z= 0.240 Chirality : 0.039 0.249 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.138 37.141 1040 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.66 % Allowed : 15.31 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 960 helix: 1.85 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 94 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 198 TYR 0.007 0.001 TYR A 52 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd link_TRANS : bond 0.00004 ( 2) link_TRANS : angle 0.21727 ( 6) hydrogen bonds : bond 0.04018 ( 504) hydrogen bonds : angle 3.59711 ( 1506) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.46572 ( 4) covalent geometry : bond 0.00251 ( 7696) covalent geometry : angle 0.47786 (10464) *********************** 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 77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.786 Fit side-chains REVERT: B 117 MET cc_start: 0.8239 (mmm) cc_final: 0.7510 (mmt) REVERT: B 186 ARG cc_start: 0.7723 (mtt90) cc_final: 0.6701 (mtm110) REVERT: B 226 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: B 253 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6853 (p0) REVERT: B 318 LEU cc_start: 0.8323 (tt) cc_final: 0.8078 (tt) REVERT: B 433 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7585 (tttt) REVERT: B 484 MET cc_start: 0.7142 (mtp) cc_final: 0.6942 (mtt) REVERT: B 489 MET cc_start: 0.8449 (mmt) cc_final: 0.8011 (mmt) REVERT: A 168 VAL cc_start: 0.8712 (t) cc_final: 0.8393 (t) REVERT: A 186 ARG cc_start: 0.7770 (mtt90) cc_final: 0.6778 (mtm110) REVERT: A 226 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: A 253 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6841 (p0) REVERT: A 318 LEU cc_start: 0.8545 (tt) cc_final: 0.8305 (tt) REVERT: A 372 PHE cc_start: 0.6978 (t80) cc_final: 0.6699 (t80) REVERT: A 433 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7565 (tttt) REVERT: A 489 MET cc_start: 0.8452 (mmt) cc_final: 0.8012 (mmt) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.1690 time to fit residues: 18.3663 Evaluate side-chains 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.101972 restraints weight = 8066.466| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.61 r_work: 0.2929 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7700 Z= 0.119 Angle : 0.485 5.810 10474 Z= 0.244 Chirality : 0.040 0.254 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.151 36.641 1040 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.79 % Allowed : 15.31 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.28), residues: 960 helix: 1.80 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 559 PHE 0.010 0.001 PHE A 198 TYR 0.007 0.001 TYR A 52 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd link_TRANS : bond 0.00022 ( 2) link_TRANS : angle 0.21310 ( 6) hydrogen bonds : bond 0.04138 ( 504) hydrogen bonds : angle 3.65714 ( 1506) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.43663 ( 4) covalent geometry : bond 0.00271 ( 7696) covalent geometry : angle 0.48530 (10464) ********************** 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 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.814 Fit side-chains REVERT: B 117 MET cc_start: 0.8283 (mmm) cc_final: 0.7577 (mmt) REVERT: B 186 ARG cc_start: 0.7716 (mtt90) cc_final: 0.6751 (mtm110) REVERT: B 226 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 253 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6866 (p0) REVERT: B 318 LEU cc_start: 0.8344 (tt) cc_final: 0.8101 (tt) REVERT: B 372 PHE cc_start: 0.7008 (t80) cc_final: 0.6713 (t80) REVERT: B 433 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7618 (tttt) REVERT: B 484 MET cc_start: 0.7293 (mtp) cc_final: 0.7063 (mtt) REVERT: A 168 VAL cc_start: 0.8752 (t) cc_final: 0.8432 (t) REVERT: A 186 ARG cc_start: 0.7809 (mtt90) cc_final: 0.6831 (mtm110) REVERT: A 226 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: A 253 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6843 (p0) REVERT: A 318 LEU cc_start: 0.8563 (tt) cc_final: 0.8326 (tt) REVERT: A 372 PHE cc_start: 0.6969 (t80) cc_final: 0.6666 (t80) REVERT: A 433 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7601 (tttt) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.1760 time to fit residues: 18.6255 Evaluate side-chains 75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 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 2 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 = 0.139706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103306 restraints weight = 7972.882| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.68 r_work: 0.2949 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7700 Z= 0.106 Angle : 0.470 5.733 10474 Z= 0.236 Chirality : 0.039 0.251 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.090 36.100 1040 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.04 % Allowed : 14.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.28), residues: 960 helix: 1.93 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.74 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE A 198 TYR 0.005 0.001 TYR A 52 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd link_TRANS : bond 0.00002 ( 2) link_TRANS : angle 0.13656 ( 6) hydrogen bonds : bond 0.03873 ( 504) hydrogen bonds : angle 3.61064 ( 1506) SS BOND : bond 0.00041 ( 2) SS BOND : angle 0.40995 ( 4) covalent geometry : bond 0.00232 ( 7696) covalent geometry : angle 0.46992 (10464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.82 seconds wall clock time: 63 minutes 37.08 seconds (3817.08 seconds total)