Starting phenix.real_space_refine on Tue Jan 14 22:13:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx4_37900/01_2025/8wx4_37900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx4_37900/01_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_37900/01_2025/8wx4_37900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx4_37900/01_2025/8wx4_37900.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx4_37900/01_2025/8wx4_37900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx4_37900/01_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-5571/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: 6.09, per 1000 atoms: 0.81 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: 1.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.49 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: 1.91 Time building geometry restraints manager: 1.96 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: 0.410 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: 0.060 Process input model: 20.740 Find NCS groups from input model: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- 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 7696 Z= 0.244 Angle : 0.706 16.688 10464 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 *********************** 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 : 0.741 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: 0.1684 time to fit residues: 29.0892 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 : 0.813 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 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 7696 Z= 0.199 Angle : 0.526 6.783 10464 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 *********************** 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 : 0.763 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: 0.1648 time to fit residues: 19.9379 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 : 0.729 ------------------------------------------------------------------------------- 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 7696 Z= 0.140 Angle : 0.469 6.257 10464 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 *********************** 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 : 0.716 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: 0.1409 time to fit residues: 18.1293 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 : 0.699 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 4.9990 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: 0.6592 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.141483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.105642 restraints weight = 8092.744| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.60 r_work: 0.2976 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7696 Z= 0.202 Angle : 0.510 6.530 10464 Z= 0.255 Chirality : 0.040 0.260 1228 Planarity : 0.003 0.026 1288 Dihedral : 4.621 45.744 1044 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.04 % Allowed : 13.14 % Favored : 84.82 % 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: 0.78 (0.28), residues: 960 helix: 1.37 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.99 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 94 HIS 0.002 0.001 HIS A 559 PHE 0.011 0.001 PHE B 194 TYR 0.014 0.001 TYR A 113 ARG 0.002 0.000 ARG B 48 *********************** 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 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.749 Fit side-chains REVERT: B 226 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 253 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6465 (p0) REVERT: B 318 LEU cc_start: 0.8255 (tt) cc_final: 0.8047 (tt) REVERT: B 433 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7360 (tttt) REVERT: B 489 MET cc_start: 0.8297 (mmt) cc_final: 0.7767 (mmt) REVERT: A 226 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7417 (m-10) REVERT: A 253 ASP cc_start: 0.6982 (p0) cc_final: 0.6521 (p0) REVERT: A 318 LEU cc_start: 0.8320 (tt) cc_final: 0.8093 (tt) REVERT: A 433 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7329 (tttt) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.2424 time to fit residues: 28.8162 Evaluate side-chains 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 226 TYR 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: 0.6980 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.139675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103780 restraints weight = 8033.880| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.60 r_work: 0.2950 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7696 Z= 0.190 Angle : 0.496 6.127 10464 Z= 0.248 Chirality : 0.040 0.216 1228 Planarity : 0.003 0.021 1288 Dihedral : 4.312 43.629 1040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 (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: 1.00 (0.28), residues: 960 helix: 1.55 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.002 0.001 HIS A 395 PHE 0.010 0.001 PHE A 194 TYR 0.008 0.001 TYR A 113 ARG 0.002 0.000 ARG B 394 *********************** 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 86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.723 Fit side-chains REVERT: B 33 ARG cc_start: 0.7497 (ptp-170) cc_final: 0.7101 (ptm160) REVERT: B 186 ARG cc_start: 0.7612 (mtt90) cc_final: 0.6977 (mtt-85) REVERT: B 226 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 253 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6565 (p0) REVERT: B 318 LEU cc_start: 0.8316 (tt) cc_final: 0.8085 (tt) REVERT: B 433 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7357 (tttt) REVERT: A 33 ARG cc_start: 0.7478 (ptp-170) cc_final: 0.7212 (ptm160) REVERT: A 226 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: A 253 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6593 (p0) REVERT: A 318 LEU cc_start: 0.8551 (tt) cc_final: 0.8316 (tt) REVERT: A 433 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7406 (tttt) REVERT: A 484 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7305 (mtt) outliers start: 17 outliers final: 11 residues processed: 80 average time/residue: 0.2246 time to fit residues: 24.0126 Evaluate side-chains 82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.137719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100610 restraints weight = 8075.469| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.69 r_work: 0.2905 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7696 Z= 0.212 Angle : 0.504 6.294 10464 Z= 0.253 Chirality : 0.040 0.200 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.305 42.167 1040 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 13.90 % Favored : 84.06 % 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: 1.11 (0.28), residues: 960 helix: 1.61 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.85 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.002 0.001 HIS B 395 PHE 0.011 0.001 PHE B 194 TYR 0.008 0.001 TYR A 113 ARG 0.004 0.000 ARG A 33 *********************** 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 80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.799 Fit side-chains REVERT: B 33 ARG cc_start: 0.7510 (ptp-170) cc_final: 0.7177 (ptm160) REVERT: B 117 MET cc_start: 0.8080 (mmm) cc_final: 0.7723 (mmt) REVERT: B 186 ARG cc_start: 0.7715 (mtt90) cc_final: 0.7340 (mtt-85) REVERT: B 207 ILE cc_start: 0.8046 (mm) cc_final: 0.7845 (mm) REVERT: B 226 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: B 253 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6689 (p0) REVERT: B 318 LEU cc_start: 0.8341 (tt) cc_final: 0.8100 (tt) REVERT: B 433 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7467 (tttt) REVERT: A 207 ILE cc_start: 0.8093 (mm) cc_final: 0.7886 (mm) REVERT: A 226 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: A 253 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6718 (p0) REVERT: A 318 LEU cc_start: 0.8347 (tt) cc_final: 0.8105 (tt) REVERT: A 433 LYS cc_start: 0.7716 (ttpt) cc_final: 0.7431 (tttt) REVERT: A 484 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7438 (mtt) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.2105 time to fit residues: 21.3586 Evaluate side-chains 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 253 ASP Chi-restraints excluded: chain B residue 483 SER 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 484 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.0030 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.137640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.100601 restraints weight = 8024.587| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.68 r_work: 0.2906 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7696 Z= 0.200 Angle : 0.500 6.212 10464 Z= 0.252 Chirality : 0.040 0.254 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.267 40.165 1040 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.30 % Allowed : 14.03 % Favored : 83.67 % 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: 1.24 (0.28), residues: 960 helix: 1.70 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.77 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.001 0.000 HIS A 348 PHE 0.010 0.001 PHE B 194 TYR 0.006 0.001 TYR A 52 ARG 0.002 0.000 ARG A 186 *********************** 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 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.725 Fit side-chains REVERT: B 33 ARG cc_start: 0.7453 (ptp-170) cc_final: 0.7139 (ptm160) REVERT: B 117 MET cc_start: 0.8155 (mmm) cc_final: 0.7824 (mmt) REVERT: B 186 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7360 (mtt-85) REVERT: B 226 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: B 253 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6782 (p0) REVERT: B 318 LEU cc_start: 0.8338 (tt) cc_final: 0.8099 (tt) REVERT: B 433 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7495 (tttt) REVERT: A 226 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: A 253 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 318 LEU cc_start: 0.8338 (tt) cc_final: 0.8095 (tt) REVERT: A 433 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7471 (tttt) outliers start: 18 outliers final: 12 residues processed: 71 average time/residue: 0.1992 time to fit residues: 19.5487 Evaluate side-chains 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 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 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 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 73 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.140429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104714 restraints weight = 8010.272| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.59 r_work: 0.2948 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7696 Z= 0.158 Angle : 0.477 6.145 10464 Z= 0.240 Chirality : 0.039 0.260 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.200 39.538 1040 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.66 % Allowed : 14.41 % 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 (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 : -1.79 (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 0.011 0.001 PHE A 198 TYR 0.005 0.001 TYR A 113 ARG 0.001 0.000 ARG B 186 *********************** 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 69 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.735 Fit side-chains REVERT: B 117 MET cc_start: 0.8200 (mmm) cc_final: 0.7809 (mmt) REVERT: B 186 ARG cc_start: 0.7714 (mtt90) cc_final: 0.6664 (mtm110) REVERT: B 226 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 253 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6790 (p0) REVERT: B 318 LEU cc_start: 0.8332 (tt) cc_final: 0.8084 (tt) REVERT: B 433 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7512 (tttt) REVERT: B 489 MET cc_start: 0.8401 (mmt) cc_final: 0.7942 (mmt) REVERT: A 168 VAL cc_start: 0.8702 (t) cc_final: 0.8383 (t) REVERT: A 226 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: A 253 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6834 (p0) REVERT: A 318 LEU cc_start: 0.8543 (tt) cc_final: 0.8300 (tt) REVERT: A 433 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7564 (tttt) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.1630 time to fit residues: 15.8054 Evaluate side-chains 69 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.139563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.102852 restraints weight = 8088.917| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.69 r_work: 0.2939 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7696 Z= 0.161 Angle : 0.477 6.171 10464 Z= 0.240 Chirality : 0.039 0.263 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.163 38.399 1040 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.79 % Allowed : 14.16 % Favored : 84.06 % 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: 1.46 (0.28), residues: 960 helix: 1.87 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.75 (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 0.010 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.002 0.000 ARG B 186 *********************** 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: 14 poor density : 59 time to evaluate : 0.811 Fit side-chains REVERT: B 117 MET cc_start: 0.8193 (mmm) cc_final: 0.7821 (mmt) REVERT: B 186 ARG cc_start: 0.7714 (mtt90) cc_final: 0.6705 (mtm110) REVERT: B 226 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: B 253 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6813 (p0) REVERT: B 318 LEU cc_start: 0.8331 (tt) cc_final: 0.8084 (tt) REVERT: B 433 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7523 (tttt) REVERT: A 168 VAL cc_start: 0.8687 (t) cc_final: 0.8375 (t) REVERT: A 226 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: A 253 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6851 (p0) REVERT: A 318 LEU cc_start: 0.8544 (tt) cc_final: 0.8300 (tt) REVERT: A 433 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7522 (tttt) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1784 time to fit residues: 18.5053 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 : 0.809 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 0.0270 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.138524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.102470 restraints weight = 8062.957| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.62 r_work: 0.2939 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7696 Z= 0.175 Angle : 0.484 6.207 10464 Z= 0.244 Chirality : 0.040 0.253 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.138 36.815 1040 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.79 % Allowed : 14.67 % 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 (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: 1.48 (0.28), residues: 960 helix: 1.91 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.77 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.001 0.000 HIS B 395 PHE 0.010 0.001 PHE B 194 TYR 0.007 0.001 TYR A 52 ARG 0.002 0.000 ARG A 129 ********************** 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 72 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.744 Fit side-chains REVERT: B 97 ASP cc_start: 0.7780 (m-30) cc_final: 0.7354 (m-30) REVERT: B 117 MET cc_start: 0.8242 (mmm) cc_final: 0.7893 (mmt) REVERT: B 186 ARG cc_start: 0.7740 (mtt90) cc_final: 0.6770 (mtm110) REVERT: B 226 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: B 253 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6796 (p0) REVERT: B 318 LEU cc_start: 0.8346 (tt) cc_final: 0.8100 (tt) REVERT: B 433 LYS cc_start: 0.7833 (ttpt) cc_final: 0.7535 (tttt) REVERT: A 226 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: A 253 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6908 (p0) REVERT: A 318 LEU cc_start: 0.8556 (tt) cc_final: 0.8312 (tt) REVERT: A 433 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7575 (tttt) outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.1695 time to fit residues: 17.0315 Evaluate side-chains 72 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.136173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.099457 restraints weight = 8040.888| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.68 r_work: 0.2894 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7696 Z= 0.213 Angle : 0.505 6.264 10464 Z= 0.255 Chirality : 0.041 0.245 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.177 36.376 1040 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.79 % Allowed : 14.41 % 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: 1.39 (0.28), residues: 960 helix: 1.83 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.77 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.002 0.001 HIS A 395 PHE 0.011 0.001 PHE B 194 TYR 0.008 0.001 TYR B 113 ARG 0.002 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3579.66 seconds wall clock time: 65 minutes 8.95 seconds (3908.95 seconds total)