Starting phenix.real_space_refine on Sat Dec 28 02:49:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx4_37900/12_2024/8wx4_37900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx4_37900/12_2024/8wx4_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_37900/12_2024/8wx4_37900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx4_37900/12_2024/8wx4_37900.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx4_37900/12_2024/8wx4_37900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx4_37900/12_2024/8wx4_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.68, per 1000 atoms: 0.89 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: 2.04 Conformation dependent library (CDL) restraints added in 1.4 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: 0.76 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: 2.18 Time building geometry restraints manager: 2.34 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: 0.00 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.890 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- 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 : 0.818 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: 0.1766 time to fit residues: 30.3220 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 : 0.823 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.880 Fit side-chains REVERT: B 226 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: B 433 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7740 (tttt) REVERT: B 489 MET cc_start: 0.8309 (mmt) cc_final: 0.7989 (tpp) REVERT: A 226 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: A 433 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7709 (tttt) REVERT: A 489 MET cc_start: 0.8297 (mmt) cc_final: 0.7999 (tpp) outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 0.1749 time to fit residues: 21.0674 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 : 0.803 ------------------------------------------------------------------------------- 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 48 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN A 219 ASN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7696 Z= 0.290 Angle : 0.576 6.608 10464 Z= 0.292 Chirality : 0.043 0.247 1228 Planarity : 0.004 0.028 1288 Dihedral : 5.083 44.099 1044 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.42 % Allowed : 12.76 % 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: 0.21 (0.28), residues: 960 helix: 0.92 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.21 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 94 HIS 0.003 0.001 HIS A 559 PHE 0.014 0.002 PHE B 372 TYR 0.021 0.002 TYR B 113 ARG 0.004 0.001 ARG A 186 *********************** 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 93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.863 Fit side-chains REVERT: B 133 CYS cc_start: 0.5541 (OUTLIER) cc_final: 0.5320 (p) REVERT: B 168 VAL cc_start: 0.8829 (t) cc_final: 0.8570 (t) REVERT: B 226 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: B 433 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7739 (tttt) REVERT: A 168 VAL cc_start: 0.8842 (t) cc_final: 0.8512 (t) REVERT: A 226 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: A 318 LEU cc_start: 0.8473 (tt) cc_final: 0.8270 (tt) REVERT: A 373 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7776 (p0) REVERT: A 433 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7759 (tttt) outliers start: 19 outliers final: 10 residues processed: 91 average time/residue: 0.2468 time to fit residues: 29.1940 Evaluate side-chains 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 133 CYS 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 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 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7696 Z= 0.204 Angle : 0.527 9.911 10464 Z= 0.260 Chirality : 0.040 0.213 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.753 43.185 1044 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 0.60 (0.28), residues: 960 helix: 1.27 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.002 0.001 HIS A 559 PHE 0.010 0.001 PHE B 194 TYR 0.007 0.001 TYR A 113 ARG 0.001 0.000 ARG A 129 *********************** 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 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.883 Fit side-chains REVERT: B 133 CYS cc_start: 0.5566 (OUTLIER) cc_final: 0.5343 (p) REVERT: B 168 VAL cc_start: 0.8873 (t) cc_final: 0.8504 (t) REVERT: B 207 ILE cc_start: 0.8256 (mm) cc_final: 0.8039 (mt) REVERT: B 226 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: B 253 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6738 (p0) REVERT: B 260 MET cc_start: 0.4625 (mmm) cc_final: 0.4412 (mmm) REVERT: B 433 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7763 (tttt) REVERT: A 168 VAL cc_start: 0.8883 (t) cc_final: 0.8520 (t) REVERT: A 207 ILE cc_start: 0.8226 (mm) cc_final: 0.8006 (mt) REVERT: A 226 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: A 253 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6753 (p0) REVERT: A 318 LEU cc_start: 0.8480 (tt) cc_final: 0.8267 (tt) REVERT: A 433 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7826 (tttt) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.2266 time to fit residues: 23.4981 Evaluate side-chains 77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 133 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7696 Z= 0.250 Angle : 0.539 6.791 10464 Z= 0.270 Chirality : 0.042 0.278 1228 Planarity : 0.003 0.026 1288 Dihedral : 4.453 40.823 1040 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.86 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: 0.76 (0.28), residues: 960 helix: 1.37 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -2.03 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.002 0.001 HIS B 559 PHE 0.012 0.001 PHE B 194 TYR 0.010 0.001 TYR B 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 71 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.001 Fit side-chains REVERT: B 133 CYS cc_start: 0.5866 (OUTLIER) cc_final: 0.5613 (p) REVERT: B 168 VAL cc_start: 0.8900 (t) cc_final: 0.8555 (t) REVERT: B 226 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: B 253 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6942 (p0) REVERT: A 226 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: A 253 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6957 (p0) REVERT: A 318 LEU cc_start: 0.8521 (tt) cc_final: 0.8295 (tt) outliers start: 18 outliers final: 13 residues processed: 67 average time/residue: 0.1937 time to fit residues: 18.7329 Evaluate side-chains 67 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 133 CYS 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 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 Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7696 Z= 0.163 Angle : 0.488 6.520 10464 Z= 0.244 Chirality : 0.039 0.242 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.325 39.746 1040 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.55 % Allowed : 13.90 % 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: 1.13 (0.28), residues: 960 helix: 1.64 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.86 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.005 0.001 TYR A 52 ARG 0.002 0.000 ARG B 186 *********************** 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 76 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.859 Fit side-chains REVERT: B 133 CYS cc_start: 0.5547 (OUTLIER) cc_final: 0.5114 (p) REVERT: B 168 VAL cc_start: 0.8867 (t) cc_final: 0.8495 (t) REVERT: B 226 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: B 253 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6889 (p0) REVERT: B 341 THR cc_start: 0.8158 (p) cc_final: 0.7794 (p) REVERT: A 226 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 253 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6900 (p0) REVERT: A 341 THR cc_start: 0.8152 (p) cc_final: 0.7786 (p) outliers start: 20 outliers final: 13 residues processed: 68 average time/residue: 0.1459 time to fit residues: 15.3645 Evaluate side-chains 73 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 133 CYS 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 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7696 Z= 0.213 Angle : 0.517 8.892 10464 Z= 0.256 Chirality : 0.040 0.219 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.311 38.743 1040 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.55 % Allowed : 14.03 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 960 helix: 1.63 (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 A 94 HIS 0.001 0.000 HIS B 348 PHE 0.011 0.001 PHE A 194 TYR 0.007 0.001 TYR B 113 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.846 Fit side-chains REVERT: B 133 CYS cc_start: 0.5628 (OUTLIER) cc_final: 0.5192 (p) REVERT: B 168 VAL cc_start: 0.8876 (t) cc_final: 0.8525 (t) REVERT: B 226 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 253 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7015 (p0) REVERT: B 341 THR cc_start: 0.8221 (p) cc_final: 0.7850 (p) REVERT: A 226 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: A 253 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6993 (p0) REVERT: A 341 THR cc_start: 0.8213 (p) cc_final: 0.7836 (p) outliers start: 20 outliers final: 15 residues processed: 69 average time/residue: 0.1443 time to fit residues: 15.3770 Evaluate side-chains 74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 133 CYS 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 54 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7696 Z= 0.225 Angle : 0.510 6.303 10464 Z= 0.256 Chirality : 0.040 0.212 1228 Planarity : 0.003 0.026 1288 Dihedral : 4.289 37.905 1040 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.68 % Allowed : 13.78 % 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: 1.13 (0.28), residues: 960 helix: 1.63 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.86 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 94 HIS 0.001 0.001 HIS B 395 PHE 0.011 0.001 PHE A 194 TYR 0.008 0.001 TYR B 113 ARG 0.002 0.000 ARG A 48 *********************** 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 70 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.769 Fit side-chains REVERT: B 133 CYS cc_start: 0.5763 (OUTLIER) cc_final: 0.5362 (p) REVERT: B 226 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 253 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7039 (p0) REVERT: A 226 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 253 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7057 (p0) outliers start: 21 outliers final: 14 residues processed: 65 average time/residue: 0.1375 time to fit residues: 14.0503 Evaluate side-chains 67 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 133 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 171 VAL 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 54 ILE 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 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.0010 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7696 Z= 0.163 Angle : 0.480 5.958 10464 Z= 0.240 Chirality : 0.039 0.205 1228 Planarity : 0.003 0.024 1288 Dihedral : 4.224 37.196 1040 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.17 % Allowed : 15.05 % Favored : 82.78 % 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: 1.35 (0.28), residues: 960 helix: 1.80 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.83 (0.36), 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 559 PHE 0.009 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG A 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 69 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.917 Fit side-chains REVERT: B 133 CYS cc_start: 0.5696 (OUTLIER) cc_final: 0.5299 (p) REVERT: B 226 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 253 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7001 (p0) REVERT: B 341 THR cc_start: 0.8134 (p) cc_final: 0.7767 (p) REVERT: A 117 MET cc_start: 0.8097 (mmt) cc_final: 0.7855 (mmm) REVERT: A 226 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: A 253 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7016 (p0) REVERT: A 341 THR cc_start: 0.8130 (p) cc_final: 0.7764 (p) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.1599 time to fit residues: 16.3419 Evaluate side-chains 67 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 133 CYS 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 132 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3066 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= 0.187 Angle : 0.494 6.650 10464 Z= 0.247 Chirality : 0.039 0.206 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.214 36.788 1040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 15.18 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 960 helix: 1.77 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.84 (0.36), 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 0.010 0.001 PHE B 194 TYR 0.007 0.001 TYR A 52 ARG 0.001 0.000 ARG B 48 ********************** 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 70 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.837 Fit side-chains REVERT: B 133 CYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5344 (p) REVERT: B 168 VAL cc_start: 0.8861 (t) cc_final: 0.8525 (t) REVERT: B 226 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: B 253 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7017 (p0) REVERT: B 341 THR cc_start: 0.8163 (p) cc_final: 0.7804 (p) REVERT: A 117 MET cc_start: 0.8140 (mmt) cc_final: 0.7859 (mmm) REVERT: A 168 VAL cc_start: 0.8806 (t) cc_final: 0.8499 (t) REVERT: A 226 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: A 253 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7029 (p0) REVERT: A 341 THR cc_start: 0.8158 (p) cc_final: 0.7791 (p) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.1575 time to fit residues: 16.2793 Evaluate side-chains 68 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 133 CYS 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 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 23 optimal weight: 0.0000 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.136656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.100512 restraints weight = 7937.415| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.65 r_work: 0.2911 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3138 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 : 0.491 5.751 10464 Z= 0.247 Chirality : 0.039 0.202 1228 Planarity : 0.003 0.025 1288 Dihedral : 4.187 36.601 1040 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.30 % Allowed : 14.67 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 960 helix: 1.79 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.82 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 94 HIS 0.001 0.000 HIS B 362 PHE 0.010 0.001 PHE B 198 TYR 0.007 0.001 TYR A 52 ARG 0.001 0.000 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.69 seconds wall clock time: 30 minutes 2.68 seconds (1802.68 seconds total)