Starting phenix.real_space_refine on Wed Mar 12 07:22:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx4_37900/03_2025/8wx4_37900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx4_37900/03_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_37900/03_2025/8wx4_37900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx4_37900/03_2025/8wx4_37900.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx4_37900/03_2025/8wx4_37900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx4_37900/03_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-5624/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: 1.68 Conformation dependent library (CDL) restraints added in 991.6 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: 0.63 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: 2.00 Time building geometry restraints manager: 2.03 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: 0.500 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.210 Find NCS groups from input model: 0.160 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- 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 : 0.704 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: 0.1597 time to fit residues: 27.8700 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 : 0.720 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111054 restraints weight = 8180.627| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.67 r_work: 0.3054 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.822 Fit side-chains REVERT: B 226 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 433 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7360 (tttt) REVERT: B 489 MET cc_start: 0.8246 (mmt) cc_final: 0.7837 (tpp) REVERT: A 226 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: A 433 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7328 (tttt) REVERT: A 489 MET cc_start: 0.8240 (mmt) cc_final: 0.7853 (tpp) outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 0.1755 time to fit residues: 20.9770 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 : 0.716 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 40 optimal weight: 0.0970 chunk 31 optimal weight: 0.0270 chunk 84 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.147704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111277 restraints weight = 8154.893| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.68 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7696 Z= 0.150 Angle : 0.475 6.261 10464 Z= 0.240 Chirality : 0.039 0.247 1228 Planarity : 0.003 0.029 1288 Dihedral : 5.036 46.701 1044 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.04 % Allowed : 12.50 % 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: 0.67 (0.28), residues: 960 helix: 1.27 (0.21), residues: 710 sheet: None (None), residues: 0 loop : -1.99 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.002 0.000 HIS B 559 PHE 0.009 0.001 PHE B 194 TYR 0.011 0.001 TYR B 113 ARG 0.004 0.000 ARG B 33 *********************** 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 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.766 Fit side-chains REVERT: B 226 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: B 253 ASP cc_start: 0.6582 (p0) cc_final: 0.6140 (p0) REVERT: B 433 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7389 (tttt) REVERT: B 489 MET cc_start: 0.8334 (mmt) cc_final: 0.7880 (mmt) REVERT: A 226 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: A 253 ASP cc_start: 0.6588 (p0) cc_final: 0.6147 (p0) REVERT: A 433 LYS cc_start: 0.7734 (ttpt) cc_final: 0.7353 (tttt) REVERT: A 489 MET cc_start: 0.8323 (mmt) cc_final: 0.7878 (mmt) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 0.1417 time to fit residues: 18.1325 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 : 0.770 ------------------------------------------------------------------------------- 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: 0.4980 chunk 10 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.142414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106468 restraints weight = 8066.304| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.61 r_work: 0.2987 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7696 Z= 0.179 Angle : 0.498 6.333 10464 Z= 0.249 Chirality : 0.040 0.256 1228 Planarity : 0.003 0.022 1288 Dihedral : 4.621 45.849 1044 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.17 % Allowed : 13.52 % 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: 0.86 (0.28), residues: 960 helix: 1.42 (0.21), residues: 710 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.001 0.000 HIS A 559 PHE 0.010 0.001 PHE B 194 TYR 0.013 0.001 TYR A 113 ARG 0.003 0.000 ARG A 186 *********************** 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 86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.699 Fit side-chains REVERT: B 226 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7578 (m-10) REVERT: B 253 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6429 (p0) REVERT: B 318 LEU cc_start: 0.8251 (tt) cc_final: 0.8041 (tt) REVERT: B 433 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7378 (tttt) REVERT: B 489 MET cc_start: 0.8394 (mmt) cc_final: 0.7874 (mmt) REVERT: A 226 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: A 253 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6494 (p0) REVERT: A 318 LEU cc_start: 0.8531 (tt) cc_final: 0.8300 (tt) REVERT: A 433 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7343 (tttt) REVERT: A 489 MET cc_start: 0.8392 (mmt) cc_final: 0.7888 (mmt) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.1415 time to fit residues: 17.6339 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 : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.138673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102588 restraints weight = 8044.238| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.61 r_work: 0.2938 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2364 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= 0.198 Angle : 0.505 6.378 10464 Z= 0.253 Chirality : 0.040 0.214 1228 Planarity : 0.003 0.022 1288 Dihedral : 4.368 42.843 1040 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.79 % Allowed : 13.90 % 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: 1.00 (0.28), residues: 960 helix: 1.50 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.83 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 517 HIS 0.002 0.001 HIS A 348 PHE 0.012 0.001 PHE A 194 TYR 0.009 0.001 TYR A 113 ARG 0.002 0.000 ARG B 186 *********************** 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 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.729 Fit side-chains REVERT: B 168 VAL cc_start: 0.8744 (t) cc_final: 0.8428 (t) REVERT: B 226 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: B 318 LEU cc_start: 0.8331 (tt) cc_final: 0.8099 (tt) REVERT: B 433 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7490 (tttt) REVERT: A 226 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: A 318 LEU cc_start: 0.8562 (tt) cc_final: 0.8326 (tt) REVERT: A 433 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7521 (tttt) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.2548 time to fit residues: 26.1763 Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 483 SER 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: 0.0670 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.139096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103039 restraints weight = 8071.343| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.62 r_work: 0.2940 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2519 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= 0.177 Angle : 0.484 6.146 10464 Z= 0.243 Chirality : 0.039 0.265 1228 Planarity : 0.003 0.022 1288 Dihedral : 4.261 42.116 1040 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.66 % Allowed : 14.54 % 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: 1.21 (0.28), residues: 960 helix: 1.69 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.82 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 94 HIS 0.002 0.000 HIS A 395 PHE 0.010 0.001 PHE B 194 TYR 0.006 0.001 TYR B 113 ARG 0.001 0.000 ARG B 102 *********************** 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 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.722 Fit side-chains REVERT: B 33 ARG cc_start: 0.7540 (ptp-170) cc_final: 0.7219 (ptm160) REVERT: B 117 MET cc_start: 0.7935 (mmm) cc_final: 0.7578 (mmm) REVERT: B 186 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7370 (mtt-85) REVERT: B 226 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: B 253 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6647 (p0) REVERT: B 318 LEU cc_start: 0.8325 (tt) cc_final: 0.8083 (tt) REVERT: B 433 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7516 (tttt) REVERT: B 484 MET cc_start: 0.7307 (mtp) cc_final: 0.7053 (mtt) REVERT: A 33 ARG cc_start: 0.7533 (ptp-170) cc_final: 0.7214 (ptm160) REVERT: A 186 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7389 (mtt-85) REVERT: A 226 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: A 253 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6665 (p0) REVERT: A 318 LEU cc_start: 0.8557 (tt) cc_final: 0.8317 (tt) REVERT: A 433 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7467 (tttt) REVERT: A 484 MET cc_start: 0.7319 (mtp) cc_final: 0.7072 (mtt) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.2100 time to fit residues: 21.0912 Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.0270 chunk 85 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.140326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103602 restraints weight = 7998.544| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.68 r_work: 0.2954 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7696 Z= 0.164 Angle : 0.476 6.080 10464 Z= 0.239 Chirality : 0.040 0.273 1228 Planarity : 0.003 0.022 1288 Dihedral : 4.172 40.052 1040 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.04 % Allowed : 14.29 % 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: 1.38 (0.28), residues: 960 helix: 1.81 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.76 (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 194 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG B 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 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.783 Fit side-chains REVERT: B 117 MET cc_start: 0.8038 (mmm) cc_final: 0.7613 (mmt) REVERT: B 186 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7398 (mtt-85) REVERT: B 226 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 253 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6691 (p0) REVERT: B 318 LEU cc_start: 0.8303 (tt) cc_final: 0.8060 (tt) REVERT: B 433 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7536 (tttt) REVERT: B 484 MET cc_start: 0.7160 (mtp) cc_final: 0.6934 (mtt) REVERT: A 186 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7470 (mtt-85) REVERT: A 226 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 253 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6712 (p0) REVERT: A 318 LEU cc_start: 0.8537 (tt) cc_final: 0.8296 (tt) REVERT: A 433 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7499 (tttt) REVERT: A 484 MET cc_start: 0.7147 (mtp) cc_final: 0.6934 (mtt) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.1706 time to fit residues: 18.1542 Evaluate side-chains 78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.138668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.101852 restraints weight = 8073.757| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.68 r_work: 0.2940 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2761 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= 0.185 Angle : 0.486 6.167 10464 Z= 0.244 Chirality : 0.040 0.247 1228 Planarity : 0.003 0.022 1288 Dihedral : 4.187 39.630 1040 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.04 % Allowed : 14.41 % 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: 1.36 (0.28), residues: 960 helix: 1.79 (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 B 194 TYR 0.007 0.001 TYR A 52 ARG 0.001 0.000 ARG A 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 80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.794 Fit side-chains REVERT: B 33 ARG cc_start: 0.7596 (ptp-170) cc_final: 0.7250 (ptm160) REVERT: B 117 MET cc_start: 0.8215 (mmm) cc_final: 0.7817 (mmt) REVERT: B 186 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7446 (mtt-85) REVERT: B 226 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: B 253 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6831 (p0) REVERT: B 318 LEU cc_start: 0.8399 (tt) cc_final: 0.8153 (tt) REVERT: B 433 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7684 (tttt) REVERT: A 33 ARG cc_start: 0.7547 (ptp-170) cc_final: 0.7148 (ptm160) REVERT: A 186 ARG cc_start: 0.7825 (mtt90) cc_final: 0.6779 (mtm110) REVERT: A 226 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: A 253 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6848 (p0) REVERT: A 318 LEU cc_start: 0.8601 (tt) cc_final: 0.8361 (tt) REVERT: A 433 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7591 (tttt) REVERT: A 484 MET cc_start: 0.7404 (mtp) cc_final: 0.7184 (mtt) outliers start: 16 outliers final: 10 residues processed: 76 average time/residue: 0.2158 time to fit residues: 22.2306 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 : 0.693 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.140420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103603 restraints weight = 8064.968| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.70 r_work: 0.2962 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2802 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= 0.153 Angle : 0.467 5.943 10464 Z= 0.234 Chirality : 0.039 0.248 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.127 38.442 1040 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.66 % Allowed : 14.80 % 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: 1.52 (0.28), residues: 960 helix: 1.93 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.76 (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 395 PHE 0.010 0.001 PHE A 198 TYR 0.005 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 77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.735 Fit side-chains REVERT: B 117 MET cc_start: 0.8195 (mmm) cc_final: 0.7759 (mmt) REVERT: B 168 VAL cc_start: 0.8788 (t) cc_final: 0.8476 (t) REVERT: B 186 ARG cc_start: 0.7782 (mtt90) cc_final: 0.6786 (mtm110) REVERT: B 207 ILE cc_start: 0.8295 (mm) cc_final: 0.7980 (mt) REVERT: B 226 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: B 253 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6798 (p0) REVERT: B 318 LEU cc_start: 0.8578 (tt) cc_final: 0.8345 (tt) REVERT: B 320 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7113 (mmtt) REVERT: B 433 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7680 (tttt) REVERT: B 489 MET cc_start: 0.8551 (mmt) cc_final: 0.8062 (mmt) REVERT: A 168 VAL cc_start: 0.8789 (t) cc_final: 0.8462 (t) REVERT: A 186 ARG cc_start: 0.7791 (mtt90) cc_final: 0.6799 (mtm110) REVERT: A 226 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 253 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6807 (p0) REVERT: A 318 LEU cc_start: 0.8387 (tt) cc_final: 0.8148 (tt) REVERT: A 320 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7117 (mmtt) REVERT: A 433 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7693 (tttt) REVERT: A 489 MET cc_start: 0.8562 (mmt) cc_final: 0.8073 (mmt) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.1846 time to fit residues: 19.5746 Evaluate side-chains 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 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 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: 0.6980 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 80 optimal weight: 0.0270 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.105239 restraints weight = 8028.956| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.68 r_work: 0.2977 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7696 Z= 0.143 Angle : 0.459 5.709 10464 Z= 0.230 Chirality : 0.039 0.245 1228 Planarity : 0.003 0.022 1288 Dihedral : 4.069 37.803 1040 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.79 % Allowed : 14.54 % 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: 1.61 (0.28), residues: 960 helix: 2.00 (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 A 452 HIS 0.001 0.000 HIS A 395 PHE 0.010 0.001 PHE A 198 TYR 0.005 0.001 TYR A 52 ARG 0.001 0.000 ARG A 186 ********************** 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 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.709 Fit side-chains REVERT: B 117 MET cc_start: 0.8090 (mmm) cc_final: 0.7673 (mmt) REVERT: B 168 VAL cc_start: 0.8581 (t) cc_final: 0.8220 (t) REVERT: B 186 ARG cc_start: 0.7748 (mtt90) cc_final: 0.6737 (mtm110) REVERT: B 226 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 253 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6922 (p0) REVERT: B 318 LEU cc_start: 0.8297 (tt) cc_final: 0.8056 (tt) REVERT: B 320 LYS cc_start: 0.7971 (mtpp) cc_final: 0.6946 (mmtt) REVERT: B 433 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7515 (tttt) REVERT: A 168 VAL cc_start: 0.8564 (t) cc_final: 0.8288 (t) REVERT: A 186 ARG cc_start: 0.7758 (mtt90) cc_final: 0.6743 (mtm110) REVERT: A 226 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: A 253 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6924 (p0) REVERT: A 318 LEU cc_start: 0.8521 (tt) cc_final: 0.8289 (tt) REVERT: A 320 LYS cc_start: 0.7980 (mtpp) cc_final: 0.6962 (mmtt) REVERT: A 372 PHE cc_start: 0.6898 (t80) cc_final: 0.6627 (t80) REVERT: A 433 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7537 (tttt) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1772 time to fit residues: 20.2401 Evaluate side-chains 81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.138591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102772 restraints weight = 7993.615| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.60 r_work: 0.2937 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7696 Z= 0.185 Angle : 0.480 5.828 10464 Z= 0.241 Chirality : 0.040 0.241 1228 Planarity : 0.003 0.023 1288 Dihedral : 4.087 36.727 1040 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.54 (0.28), residues: 960 helix: 1.93 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.73 (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 395 PHE 0.011 0.001 PHE A 198 TYR 0.008 0.001 TYR A 52 ARG 0.001 0.000 ARG A 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.23 seconds wall clock time: 62 minutes 37.17 seconds (3757.17 seconds total)