Starting phenix.real_space_refine on Sat Aug 3 15:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ene_19832/08_2024/9ene_19832.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ene_19832/08_2024/9ene_19832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ene_19832/08_2024/9ene_19832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ene_19832/08_2024/9ene_19832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ene_19832/08_2024/9ene_19832.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ene_19832/08_2024/9ene_19832.cif" } resolution = 3.15 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= -0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 144 5.49 5 S 36 5.16 5 C 4824 2.51 5 N 1494 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 181": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2686 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain breaks: 3 Chain: "B" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2686 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain breaks: 3 Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 61} Chain: "D" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 61} Time building chain proxies: 5.77, per 1000 atoms: 0.68 Number of scatterers: 8484 At special positions: 0 Unit cell: (102.34, 152.22, 68.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 144 15.00 O 1986 8.00 N 1494 7.00 C 4824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 34.5% alpha, 16.1% beta 44 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.590A pdb=" N ALA A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.513A pdb=" N SER A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN A 110 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.655A pdb=" N ARG A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 214 through 217 removed outlier: 3.505A pdb=" N VAL A 217 " --> pdb=" O GLN A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 277 through 291 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.625A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 370 removed outlier: 3.944A pdb=" N LYS A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.720A pdb=" N ALA B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 88 through 100 removed outlier: 4.230A pdb=" N LYS B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 4.321A pdb=" N ASN B 110 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.749A pdb=" N ARG B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 214 through 217 removed outlier: 3.758A pdb=" N VAL B 217 " --> pdb=" O GLN B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 214 through 217' Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.557A pdb=" N CYS B 281 " --> pdb=" O HIS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.610A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 368 removed outlier: 3.510A pdb=" N GLU B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 Processing helix chain 'B' and resid 398 through 402 removed outlier: 4.398A pdb=" N ALA B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.652A pdb=" N GLY A 61 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 6.413A pdb=" N TYR A 71 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE A 124 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 326 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN A 126 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N LYS A 328 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N CYS A 327 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 192 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 269 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLN A 266 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A 246 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A 268 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 244 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.714A pdb=" N GLY B 61 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 174 removed outlier: 6.511A pdb=" N TYR B 71 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE B 124 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP B 326 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN B 126 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS B 328 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N CYS B 327 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU B 192 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 269 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 243 " --> pdb=" O THR B 270 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1020 1.27 - 1.40: 2627 1.40 - 1.54: 4958 1.54 - 1.67: 315 1.67 - 1.81: 58 Bond restraints: 8978 Sorted by residual: bond pdb=" C CYS A 226 " pdb=" O CYS A 226 " ideal model delta sigma weight residual 1.234 1.133 0.102 1.20e-02 6.94e+03 7.19e+01 bond pdb=" C CYS A 226 " pdb=" N LYS A 227 " ideal model delta sigma weight residual 1.334 1.389 -0.056 1.79e-02 3.12e+03 9.62e+00 bond pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.57e+00 bond pdb=" N MET A 228 " pdb=" CA MET A 228 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.27e-02 6.20e+03 6.75e+00 bond pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.55e+00 ... (remaining 8973 not shown) Histogram of bond angle deviations from ideal: 80.18 - 91.26: 2 91.26 - 102.34: 195 102.34 - 113.42: 5810 113.42 - 124.50: 6171 124.50 - 135.58: 672 Bond angle restraints: 12850 Sorted by residual: angle pdb=" O CYS A 226 " pdb=" C CYS A 226 " pdb=" N LYS A 227 " ideal model delta sigma weight residual 122.92 109.61 13.31 1.17e+00 7.31e-01 1.29e+02 angle pdb=" O3' A D 38 " pdb=" P U D 39 " pdb=" OP1 U D 39 " ideal model delta sigma weight residual 108.00 80.18 27.82 3.00e+00 1.11e-01 8.60e+01 angle pdb=" O3' A D 38 " pdb=" P U D 39 " pdb=" OP2 U D 39 " ideal model delta sigma weight residual 108.00 85.94 22.06 3.00e+00 1.11e-01 5.41e+01 angle pdb=" CA CYS A 226 " pdb=" C CYS A 226 " pdb=" N LYS A 227 " ideal model delta sigma weight residual 115.67 106.99 8.68 1.36e+00 5.41e-01 4.08e+01 angle pdb=" O3' A D 38 " pdb=" P U D 39 " pdb=" O5' U D 39 " ideal model delta sigma weight residual 104.00 98.05 5.95 1.50e+00 4.44e-01 1.57e+01 ... (remaining 12845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.86: 4502 18.86 - 37.73: 603 37.73 - 56.59: 225 56.59 - 75.45: 239 75.45 - 94.32: 21 Dihedral angle restraints: 5590 sinusoidal: 3664 harmonic: 1926 Sorted by residual: dihedral pdb=" O4' U C 40 " pdb=" C1' U C 40 " pdb=" N1 U C 40 " pdb=" C2 U C 40 " ideal model delta sinusoidal sigma weight residual -128.00 -56.88 -71.12 1 1.70e+01 3.46e-03 2.25e+01 dihedral pdb=" O4' U D 40 " pdb=" C1' U D 40 " pdb=" N1 U D 40 " pdb=" C2 U D 40 " ideal model delta sinusoidal sigma weight residual -128.00 -60.45 -67.55 1 1.70e+01 3.46e-03 2.05e+01 dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N ILE B 69 " pdb=" CA ILE B 69 " ideal model delta harmonic sigma weight residual 180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 1519 0.401 - 0.801: 0 0.801 - 1.202: 0 1.202 - 1.602: 0 1.602 - 2.003: 1 Chirality restraints: 1520 Sorted by residual: chirality pdb=" P U D 39 " pdb=" OP1 U D 39 " pdb=" OP2 U D 39 " pdb=" O5' U D 39 " both_signs ideal model delta sigma weight residual True 2.41 0.41 2.00 2.00e-01 2.50e+01 1.00e+02 chirality pdb=" CA PHE A 320 " pdb=" N PHE A 320 " pdb=" C PHE A 320 " pdb=" CB PHE A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA PHE B 320 " pdb=" N PHE B 320 " pdb=" C PHE B 320 " pdb=" CB PHE B 320 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 1517 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 226 " 0.084 2.00e-02 2.50e+03 1.69e-01 2.87e+02 pdb=" C CYS A 226 " -0.292 2.00e-02 2.50e+03 pdb=" O CYS A 226 " 0.124 2.00e-02 2.50e+03 pdb=" N LYS A 227 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 18 " 0.025 2.00e-02 2.50e+03 1.07e-02 3.43e+00 pdb=" N9 G D 18 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G D 18 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G D 18 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G D 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G D 18 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G D 18 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G D 18 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G D 18 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G D 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 18 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G D 18 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 18 " -0.025 2.00e-02 2.50e+03 1.06e-02 3.40e+00 pdb=" N9 G C 18 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G C 18 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 18 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G C 18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G C 18 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C 18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G C 18 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G C 18 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 18 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 18 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G C 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1664 2.77 - 3.30: 7418 3.30 - 3.83: 15035 3.83 - 4.37: 17014 4.37 - 4.90: 26709 Nonbonded interactions: 67840 Sorted by model distance: nonbonded pdb=" N7 G D 22 " pdb=" N2 G D 46 " model vdw 2.233 2.560 nonbonded pdb=" N7 G C 22 " pdb=" N2 G C 46 " model vdw 2.233 2.560 nonbonded pdb=" OH TYR B 197 " pdb=" O VAL B 318 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 197 " pdb=" O VAL A 318 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU A 294 " pdb=" OH TYR A 411 " model vdw 2.236 3.040 ... (remaining 67835 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.920 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.880 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 0.102 8978 Z= 0.271 Angle : 0.642 27.822 12850 Z= 0.321 Chirality : 0.063 2.003 1520 Planarity : 0.006 0.169 1108 Dihedral : 22.563 94.318 4342 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.04 % Allowed : 25.43 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.32), residues: 642 helix: 1.27 (0.40), residues: 176 sheet: -0.57 (0.58), residues: 64 loop : -1.40 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE A 320 TYR 0.013 0.001 TYR A 276 ARG 0.001 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.778 Fit side-chains REVERT: B 293 MET cc_start: 0.8314 (ptp) cc_final: 0.8060 (ptp) REVERT: B 361 MET cc_start: 0.9179 (ttm) cc_final: 0.8937 (ttm) outliers start: 6 outliers final: 1 residues processed: 37 average time/residue: 0.2628 time to fit residues: 13.3696 Evaluate side-chains 31 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 266 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8978 Z= 0.173 Angle : 0.600 27.751 12850 Z= 0.278 Chirality : 0.062 2.026 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.420 95.482 3019 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.38 % Allowed : 25.43 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.33), residues: 642 helix: 1.16 (0.39), residues: 184 sheet: -0.47 (0.59), residues: 60 loop : -1.35 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE B 320 TYR 0.011 0.001 TYR B 276 ARG 0.004 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.726 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 39 average time/residue: 0.2241 time to fit residues: 12.3950 Evaluate side-chains 35 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8572 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8978 Z= 0.286 Angle : 0.637 27.901 12850 Z= 0.300 Chirality : 0.063 2.005 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.365 95.363 3018 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.60 % Allowed : 24.91 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.32), residues: 642 helix: 1.05 (0.39), residues: 184 sheet: -0.69 (0.59), residues: 60 loop : -1.42 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.020 0.002 TYR A 276 ARG 0.009 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 0.662 Fit side-chains REVERT: A 163 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9052 (mp) REVERT: B 257 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8265 (mmp80) outliers start: 15 outliers final: 8 residues processed: 43 average time/residue: 0.2407 time to fit residues: 14.3130 Evaluate side-chains 39 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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: 0.8580 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8978 Z= 0.304 Angle : 0.641 28.085 12850 Z= 0.302 Chirality : 0.063 2.018 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.329 95.086 3018 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.63 % Allowed : 24.39 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.32), residues: 642 helix: 1.03 (0.39), residues: 182 sheet: -0.65 (0.59), residues: 60 loop : -1.50 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.019 0.002 PHE A 320 TYR 0.017 0.002 TYR A 276 ARG 0.006 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 30 time to evaluate : 0.676 Fit side-chains REVERT: A 163 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9035 (mp) REVERT: B 293 MET cc_start: 0.8301 (ptp) cc_final: 0.8037 (ptp) outliers start: 21 outliers final: 13 residues processed: 50 average time/residue: 0.2180 time to fit residues: 15.1998 Evaluate side-chains 43 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.8566 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8978 Z= 0.248 Angle : 0.619 27.880 12850 Z= 0.289 Chirality : 0.062 2.017 1520 Planarity : 0.004 0.044 1108 Dihedral : 22.273 94.605 3018 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.77 % Allowed : 24.74 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 642 helix: 1.05 (0.39), residues: 182 sheet: -0.58 (0.60), residues: 60 loop : -1.46 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.019 0.001 PHE A 320 TYR 0.014 0.001 TYR A 276 ARG 0.006 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 0.680 Fit side-chains REVERT: A 163 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9026 (mp) REVERT: A 257 ARG cc_start: 0.8394 (tmt170) cc_final: 0.8142 (tmt170) REVERT: B 282 MET cc_start: 0.8527 (mtp) cc_final: 0.8273 (mtp) REVERT: B 293 MET cc_start: 0.8299 (ptp) cc_final: 0.8035 (ptp) outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.1957 time to fit residues: 12.9515 Evaluate side-chains 43 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 327 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8579 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8978 Z= 0.292 Angle : 0.636 27.861 12850 Z= 0.299 Chirality : 0.063 2.021 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.275 95.417 3018 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.84 % Allowed : 23.18 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.32), residues: 642 helix: 1.00 (0.39), residues: 182 sheet: -0.60 (0.60), residues: 60 loop : -1.50 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.019 0.001 PHE A 320 TYR 0.014 0.002 TYR A 276 ARG 0.005 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 29 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 163 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9060 (mp) REVERT: B 293 MET cc_start: 0.8319 (ptp) cc_final: 0.8057 (ptp) outliers start: 28 outliers final: 21 residues processed: 55 average time/residue: 0.1968 time to fit residues: 15.6013 Evaluate side-chains 51 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 29 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8978 Z= 0.144 Angle : 0.575 27.640 12850 Z= 0.262 Chirality : 0.062 2.038 1520 Planarity : 0.004 0.040 1108 Dihedral : 22.136 93.704 3018 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.08 % Allowed : 26.30 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.33), residues: 642 helix: 1.17 (0.40), residues: 184 sheet: -0.20 (0.62), residues: 60 loop : -1.28 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE B 320 TYR 0.012 0.001 TYR B 276 ARG 0.005 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.713 Fit side-chains REVERT: A 116 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7510 (ptp-170) REVERT: A 163 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8970 (mp) outliers start: 12 outliers final: 7 residues processed: 42 average time/residue: 0.2450 time to fit residues: 14.1901 Evaluate side-chains 39 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8543 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8978 Z= 0.214 Angle : 0.597 27.669 12850 Z= 0.275 Chirality : 0.062 2.017 1520 Planarity : 0.004 0.044 1108 Dihedral : 22.142 94.415 3018 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.60 % Allowed : 25.61 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.33), residues: 642 helix: 1.18 (0.40), residues: 182 sheet: -0.21 (0.62), residues: 60 loop : -1.32 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.017 0.001 TYR B 276 ARG 0.005 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 31 time to evaluate : 0.629 Fit side-chains REVERT: A 116 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7422 (ptp-170) REVERT: A 163 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9023 (mp) outliers start: 15 outliers final: 11 residues processed: 45 average time/residue: 0.2400 time to fit residues: 14.8459 Evaluate side-chains 44 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.8553 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8978 Z= 0.240 Angle : 0.611 27.632 12850 Z= 0.284 Chirality : 0.062 2.022 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.147 95.024 3018 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.77 % Allowed : 25.61 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.33), residues: 642 helix: 1.05 (0.40), residues: 182 sheet: -0.30 (0.62), residues: 60 loop : -1.37 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.016 0.002 TYR B 276 ARG 0.005 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 0.762 Fit side-chains REVERT: A 116 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7427 (ptp-170) REVERT: A 163 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9036 (mp) outliers start: 16 outliers final: 11 residues processed: 45 average time/residue: 0.2122 time to fit residues: 13.6327 Evaluate side-chains 43 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 30 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8570 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8978 Z= 0.289 Angle : 0.635 27.742 12850 Z= 0.298 Chirality : 0.063 2.017 1520 Planarity : 0.004 0.044 1108 Dihedral : 22.187 95.769 3018 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.42 % Allowed : 25.78 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.33), residues: 642 helix: 0.95 (0.39), residues: 182 sheet: -0.44 (0.62), residues: 60 loop : -1.43 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.020 0.001 PHE A 320 TYR 0.016 0.002 TYR B 276 ARG 0.005 0.000 ARG B 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 163 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9052 (mp) outliers start: 14 outliers final: 12 residues processed: 43 average time/residue: 0.2158 time to fit residues: 13.3285 Evaluate side-chains 43 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 30 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.087918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061566 restraints weight = 22515.891| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.70 r_work: 0.2927 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8978 Z= 0.164 Angle : 0.582 27.545 12850 Z= 0.267 Chirality : 0.062 2.040 1520 Planarity : 0.004 0.040 1108 Dihedral : 22.080 93.915 3018 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.08 % Allowed : 26.30 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.33), residues: 642 helix: 1.07 (0.40), residues: 182 sheet: -0.48 (0.57), residues: 70 loop : -1.28 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE A 320 TYR 0.015 0.001 TYR B 276 ARG 0.004 0.000 ARG B 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.30 seconds wall clock time: 29 minutes 42.44 seconds (1782.44 seconds total)