Starting phenix.real_space_refine on Thu Jul 2 01:07:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgp_43220/07_2026/8vgp_43220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgp_43220/07_2026/8vgp_43220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vgp_43220/07_2026/8vgp_43220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgp_43220/07_2026/8vgp_43220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vgp_43220/07_2026/8vgp_43220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgp_43220/07_2026/8vgp_43220.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.011 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 Ca 1 9.91 5 S 34 5.16 5 C 3157 2.51 5 N 838 2.21 5 O 1016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5046 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 210} Conformer: "B" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 210} bond proxies already assigned to first conformer: 1796 Chain: "H" Number of atoms: 1624 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1613 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1613 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1643 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1609 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 24 Ad-hoc single atom residues: {' CA': 1} Classifications: {'water': 24} Link IDs: {None: 23} Chain breaks: 1 Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 400 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 400 " occ=0.50 residue: pdb=" N AARG H 19 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 19 " occ=0.50 Time building chain proxies: 1.90, per 1000 atoms: 0.38 Number of scatterers: 5046 At special positions: 0 Unit cell: (115.875, 64.1452, 95.1832, 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) Ca 1 19.99 S 34 16.00 O 1016 8.00 N 838 7.00 C 3157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 313 " distance=2.02 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 435 " distance=2.04 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 450 " distance=2.02 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 126 " - pdb=" SG CYS L 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS L 116 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 165 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 309.5 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 13 sheets defined 13.6% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 316 through 320 removed outlier: 4.322A pdb=" N GLY A 319 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N PHE L 83 " --> pdb=" O CYS L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 301 removed outlier: 25.594A pdb=" N GLU A 308 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 20.837A pdb=" N ARG A 328 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 14.326A pdb=" N LYS A 310 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N GLN A 326 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A 312 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET A 489 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG A 327 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 487 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 369 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A 389 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.467A pdb=" N MET A 489 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG A 327 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 487 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 369 " --> pdb=" O HIS A 389 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A 389 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.715A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.052A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL H 96 " --> pdb=" O MET H 100C" (cutoff:3.500A) removed outlier: 5.906A pdb=" N MET H 100C" --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 131 removed outlier: 6.599A pdb=" N CYS H 141 " --> pdb=" O PRO H 130 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 131 removed outlier: 6.599A pdb=" N CYS H 141 " --> pdb=" O PRO H 130 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR H 181 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 159 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.525A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N LEU L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.058A pdb=" N SER L 65 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.321A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.761A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 225 hydrogen bonds defined for protein. 562 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: 0.83 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1552 1.34 - 1.46: 1255 1.46 - 1.58: 2279 1.58 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 5128 Sorted by residual: bond pdb=" C THR H 170 " pdb=" N PHE H 171 " ideal model delta sigma weight residual 1.340 1.228 0.112 5.87e-02 2.90e+02 3.67e+00 bond pdb=" CG LEU A 375 " pdb=" CD1 LEU A 375 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 bond pdb=" CD LYS A 478 " pdb=" CE LYS A 478 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.23e+00 bond pdb=" CG LEU L 175 " pdb=" CD1 LEU L 175 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.52e+00 bond pdb=" CB BARG A 400 " pdb=" CG BARG A 400 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.47e+00 ... (remaining 5123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 6751 2.60 - 5.20: 182 5.20 - 7.80: 21 7.80 - 10.40: 4 10.40 - 13.00: 1 Bond angle restraints: 6959 Sorted by residual: angle pdb=" N PHE A 447 " pdb=" CA PHE A 447 " pdb=" C PHE A 447 " ideal model delta sigma weight residual 112.89 118.86 -5.97 1.24e+00 6.50e-01 2.32e+01 angle pdb=" CA LEU L 73 " pdb=" CB LEU L 73 " pdb=" CG LEU L 73 " ideal model delta sigma weight residual 116.30 129.30 -13.00 3.50e+00 8.16e-02 1.38e+01 angle pdb=" N GLN A 462 " pdb=" CA GLN A 462 " pdb=" C GLN A 462 " ideal model delta sigma weight residual 112.34 116.82 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" C GLU H 152 " pdb=" N CYS H 153 " pdb=" CA CYS H 153 " ideal model delta sigma weight residual 121.80 129.92 -8.12 2.44e+00 1.68e-01 1.11e+01 angle pdb=" CA CYS L 124 " pdb=" CB CYS L 124 " pdb=" SG CYS L 124 " ideal model delta sigma weight residual 114.40 107.12 7.28 2.30e+00 1.89e-01 1.00e+01 ... (remaining 6954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2790 17.67 - 35.35: 183 35.35 - 53.02: 37 53.02 - 70.69: 10 70.69 - 88.37: 15 Dihedral angle restraints: 3035 sinusoidal: 1174 harmonic: 1861 Sorted by residual: dihedral pdb=" CD BARG H 19 " pdb=" NE BARG H 19 " pdb=" CZ BARG H 19 " pdb=" NH1BARG H 19 " ideal model delta sinusoidal sigma weight residual 0.00 -74.63 74.63 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CD BARG A 400 " pdb=" NE BARG A 400 " pdb=" CZ BARG A 400 " pdb=" NH1BARG A 400 " ideal model delta sinusoidal sigma weight residual 0.00 71.95 -71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CA PHE H 98 " pdb=" C PHE H 98 " pdb=" N LEU H 99 " pdb=" CA LEU H 99 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 3032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 433 0.050 - 0.099: 226 0.099 - 0.149: 78 0.149 - 0.199: 11 0.199 - 0.248: 2 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA TYR A 476 " pdb=" N TYR A 476 " pdb=" C TYR A 476 " pdb=" CB TYR A 476 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA TYR H 100A" pdb=" N TYR H 100A" pdb=" C TYR H 100A" pdb=" CB TYR H 100A" both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 324 " pdb=" CA ILE A 324 " pdb=" CG1 ILE A 324 " pdb=" CG2 ILE A 324 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 747 not shown) Planarity restraints: 890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG H 19 " 0.904 9.50e-02 1.11e+02 4.06e-01 1.11e+02 pdb=" NE BARG H 19 " -0.075 2.00e-02 2.50e+03 pdb=" CZ BARG H 19 " 0.046 2.00e-02 2.50e+03 pdb=" NH1BARG H 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH2BARG H 19 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD BARG A 400 " 0.874 9.50e-02 1.11e+02 3.93e-01 1.05e+02 pdb=" NE BARG A 400 " -0.074 2.00e-02 2.50e+03 pdb=" CZ BARG A 400 " 0.048 2.00e-02 2.50e+03 pdb=" NH1BARG A 400 " -0.014 2.00e-02 2.50e+03 pdb=" NH2BARG A 400 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD AARG A 400 " 0.243 9.50e-02 1.11e+02 1.10e-01 9.11e+00 pdb=" NE AARG A 400 " -0.022 2.00e-02 2.50e+03 pdb=" CZ AARG A 400 " 0.020 2.00e-02 2.50e+03 pdb=" NH1AARG A 400 " -0.010 2.00e-02 2.50e+03 pdb=" NH2AARG A 400 " 0.001 2.00e-02 2.50e+03 ... (remaining 887 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 183 2.70 - 3.25: 4731 3.25 - 3.80: 7880 3.80 - 4.35: 11345 4.35 - 4.90: 18704 Nonbonded interactions: 42843 Sorted by model distance: nonbonded pdb=" O GLY A 451 " pdb=" O HOH A 701 " model vdw 2.148 3.040 nonbonded pdb=" O HOH A 714 " pdb=" O HOH A 722 " model vdw 2.176 3.040 nonbonded pdb=" OG SER L 7 " pdb=" O HOH L 301 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS L 190 " pdb=" OD1 ASN L 210 " model vdw 2.250 3.120 nonbonded pdb=" O HOH A 709 " pdb=" O HOH A 716 " model vdw 2.250 3.040 ... (remaining 42838 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 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 : 0.010 0.112 5141 Z= 0.394 Angle : 1.022 12.996 6985 Z= 0.549 Chirality : 0.063 0.248 750 Planarity : 0.021 0.406 890 Dihedral : 14.339 88.368 1818 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.00 % Favored : 94.84 % Rotamer: Outliers : 0.91 % Allowed : 5.99 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.32), residues: 646 helix: -2.77 (0.56), residues: 42 sheet: 0.45 (0.31), residues: 266 loop : -0.98 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.004 ARG A 327 TYR 0.022 0.005 TYR A 353 PHE 0.024 0.004 PHE H 98 TRP 0.029 0.004 TRP H 33 HIS 0.013 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.39 ( 5128) covalent geometry : angle 1.01941 / 0.55 ( 6959) SS BOND : bond 0.00749 / 0.40 ( 13) SS BOND : angle 1.62910 / 1.04 ( 26) hydrogen bonds : bond 0.17839 / 11.48 ( 188) hydrogen bonds : angle 8.68279 / 5.87 ( 562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: H 141 CYS cc_start: 0.7481 (m) cc_final: 0.6963 (m) outliers start: 4 outliers final: 0 residues processed: 92 average time/residue: 0.6880 time to fit residues: 65.4063 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 GLN A 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.055527 restraints weight = 32850.772| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.90 r_work: 0.2557 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5141 Z= 0.159 Angle : 0.687 9.465 6985 Z= 0.364 Chirality : 0.046 0.138 750 Planarity : 0.004 0.048 890 Dihedral : 5.439 26.159 704 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.27 % Allowed : 10.53 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.34), residues: 646 helix: -1.87 (0.65), residues: 45 sheet: 0.72 (0.31), residues: 276 loop : -0.23 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 142 TYR 0.011 0.001 TYR A 391 PHE 0.022 0.002 PHE H 98 TRP 0.013 0.001 TRP H 33 HIS 0.006 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 5128) covalent geometry : angle 0.68190 / 0.36 ( 6959) SS BOND : bond 0.00611 / 0.32 ( 13) SS BOND : angle 1.53484 / 0.98 ( 26) hydrogen bonds : bond 0.03958 / 2.63 ( 188) hydrogen bonds : angle 6.00522 / 4.10 ( 562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 458 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8445 (mmp) REVERT: A 464 GLN cc_start: 0.8708 (mp10) cc_final: 0.8418 (mp10) REVERT: H 31 ASP cc_start: 0.9210 (m-30) cc_final: 0.8963 (m-30) REVERT: H 82 MET cc_start: 0.9196 (mtp) cc_final: 0.8942 (mtm) REVERT: L 123 GLU cc_start: 0.9227 (mp0) cc_final: 0.8803 (mp0) REVERT: L 125 LEU cc_start: 0.8555 (mm) cc_final: 0.8037 (mt) REVERT: L 167 ASP cc_start: 0.8663 (t0) cc_final: 0.8179 (t0) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 0.7383 time to fit residues: 54.1186 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 46 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.074728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.056899 restraints weight = 23289.805| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.21 r_work: 0.2609 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5141 Z= 0.115 Angle : 0.622 9.467 6985 Z= 0.328 Chirality : 0.044 0.161 750 Planarity : 0.004 0.047 890 Dihedral : 5.019 24.060 704 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 1.27 % Allowed : 11.43 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.35), residues: 646 helix: -1.33 (0.71), residues: 46 sheet: 0.80 (0.31), residues: 276 loop : -0.03 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.011 0.001 TYR A 391 PHE 0.025 0.001 PHE H 98 TRP 0.010 0.001 TRP A 354 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 5128) covalent geometry : angle 0.61587 / 0.33 ( 6959) SS BOND : bond 0.00387 / 0.20 ( 13) SS BOND : angle 1.59819 / 0.94 ( 26) hydrogen bonds : bond 0.03390 / 2.22 ( 188) hydrogen bonds : angle 5.52798 / 3.78 ( 562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 458 MET cc_start: 0.8940 (mmm) cc_final: 0.8518 (mmp) REVERT: H 31 ASP cc_start: 0.9199 (m-30) cc_final: 0.8934 (m-30) REVERT: H 46 GLU cc_start: 0.9062 (tt0) cc_final: 0.8840 (tt0) REVERT: H 82 MET cc_start: 0.9235 (mtp) cc_final: 0.8906 (mtm) REVERT: L 123 GLU cc_start: 0.9160 (mp0) cc_final: 0.8636 (mp0) REVERT: L 167 ASP cc_start: 0.8709 (t0) cc_final: 0.8208 (t0) outliers start: 7 outliers final: 2 residues processed: 70 average time/residue: 0.6792 time to fit residues: 49.1698 Evaluate side-chains 63 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 25 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.054822 restraints weight = 41061.716| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 5.31 r_work: 0.2533 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5141 Z= 0.151 Angle : 0.624 9.601 6985 Z= 0.328 Chirality : 0.045 0.142 750 Planarity : 0.004 0.044 890 Dihedral : 4.961 27.158 704 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 13.25 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.35), residues: 646 helix: -1.33 (0.71), residues: 47 sheet: 0.83 (0.32), residues: 266 loop : -0.01 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 142 TYR 0.010 0.001 TYR H 91 PHE 0.021 0.002 PHE H 98 TRP 0.011 0.001 TRP H 33 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 5128) covalent geometry : angle 0.61829 / 0.33 ( 6959) SS BOND : bond 0.00370 / 0.18 ( 13) SS BOND : angle 1.49877 / 0.91 ( 26) hydrogen bonds : bond 0.03550 / 2.34 ( 188) hydrogen bonds : angle 5.45981 / 3.73 ( 562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 458 MET cc_start: 0.9040 (mmm) cc_final: 0.8646 (mmp) REVERT: H 31 ASP cc_start: 0.9230 (m-30) cc_final: 0.8939 (m-30) REVERT: H 82 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8912 (mtm) REVERT: H 211 LYS cc_start: 0.9482 (ttmm) cc_final: 0.9257 (ttmm) REVERT: L 167 ASP cc_start: 0.8661 (t0) cc_final: 0.8162 (t0) outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 0.7462 time to fit residues: 53.1052 Evaluate side-chains 66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.073217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.054752 restraints weight = 30457.836| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 4.75 r_work: 0.2546 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5141 Z= 0.161 Angle : 0.636 9.410 6985 Z= 0.334 Chirality : 0.045 0.152 750 Planarity : 0.004 0.042 890 Dihedral : 4.949 30.201 704 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 1.45 % Allowed : 13.25 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.35), residues: 646 helix: -1.03 (0.76), residues: 41 sheet: 0.93 (0.33), residues: 266 loop : -0.02 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 142 TYR 0.011 0.001 TYR H 91 PHE 0.020 0.002 PHE H 98 TRP 0.009 0.001 TRP H 33 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 5128) covalent geometry : angle 0.63013 / 0.33 ( 6959) SS BOND : bond 0.00349 / 0.18 ( 13) SS BOND : angle 1.51220 / 0.89 ( 26) hydrogen bonds : bond 0.03418 / 2.24 ( 188) hydrogen bonds : angle 5.33136 / 3.64 ( 562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.8588 (mmp) cc_final: 0.8134 (mmt) REVERT: A 458 MET cc_start: 0.9048 (mmm) cc_final: 0.8645 (mmp) REVERT: H 31 ASP cc_start: 0.9266 (m-30) cc_final: 0.8960 (m-30) REVERT: H 46 GLU cc_start: 0.9184 (tt0) cc_final: 0.8974 (tt0) REVERT: H 82 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8929 (mtm) REVERT: H 211 LYS cc_start: 0.9472 (ttmm) cc_final: 0.9231 (ttmm) REVERT: L 167 ASP cc_start: 0.8651 (t0) cc_final: 0.8366 (t0) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.7245 time to fit residues: 51.6596 Evaluate side-chains 67 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.054287 restraints weight = 40350.398| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 5.22 r_work: 0.2518 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5141 Z= 0.179 Angle : 0.647 9.124 6985 Z= 0.341 Chirality : 0.045 0.155 750 Planarity : 0.004 0.039 890 Dihedral : 4.982 30.798 704 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 2.00 % Allowed : 13.61 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.35), residues: 646 helix: -1.50 (0.69), residues: 47 sheet: 0.93 (0.32), residues: 282 loop : -0.08 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 142 TYR 0.012 0.001 TYR H 91 PHE 0.019 0.002 PHE H 98 TRP 0.010 0.001 TRP H 33 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 5128) covalent geometry : angle 0.64160 / 0.34 ( 6959) SS BOND : bond 0.00396 / 0.19 ( 13) SS BOND : angle 1.49954 / 0.88 ( 26) hydrogen bonds : bond 0.03448 / 2.25 ( 188) hydrogen bonds : angle 5.32842 / 3.63 ( 562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.212 Fit side-chains REVERT: A 458 MET cc_start: 0.9050 (mmm) cc_final: 0.8637 (mmp) REVERT: H 31 ASP cc_start: 0.9272 (m-30) cc_final: 0.8980 (m-30) REVERT: H 46 GLU cc_start: 0.9173 (tt0) cc_final: 0.8912 (tt0) REVERT: H 197 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8433 (tp-100) REVERT: L 142 ARG cc_start: 0.8787 (ttt-90) cc_final: 0.8552 (ttt-90) REVERT: L 167 ASP cc_start: 0.8737 (t0) cc_final: 0.8259 (t0) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.7110 time to fit residues: 49.9304 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.072918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.054264 restraints weight = 43728.028| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 5.38 r_work: 0.2515 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5141 Z= 0.177 Angle : 0.679 9.292 6985 Z= 0.353 Chirality : 0.045 0.179 750 Planarity : 0.004 0.042 890 Dihedral : 5.012 28.592 704 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.81 % Allowed : 14.34 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.35), residues: 646 helix: -1.48 (0.69), residues: 47 sheet: 0.97 (0.32), residues: 282 loop : -0.08 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 24 TYR 0.012 0.001 TYR H 91 PHE 0.019 0.002 PHE H 98 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 5128) covalent geometry : angle 0.66640 / 0.35 ( 6959) SS BOND : bond 0.00347 / 0.18 ( 13) SS BOND : angle 2.23913 / 1.42 ( 26) hydrogen bonds : bond 0.03462 / 2.26 ( 188) hydrogen bonds : angle 5.30068 / 3.60 ( 562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8567 (mmp) cc_final: 0.8177 (mmt) REVERT: A 458 MET cc_start: 0.9056 (mmm) cc_final: 0.8745 (mmp) REVERT: H 31 ASP cc_start: 0.9288 (m-30) cc_final: 0.8978 (m-30) REVERT: H 46 GLU cc_start: 0.9199 (tt0) cc_final: 0.8928 (tt0) REVERT: H 197 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8410 (tp-100) REVERT: L 142 ARG cc_start: 0.8830 (ttt-90) cc_final: 0.8577 (ttt-90) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 0.7240 time to fit residues: 49.3716 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.0970 chunk 62 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.056030 restraints weight = 30892.629| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.71 r_work: 0.2578 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5141 Z= 0.127 Angle : 0.663 10.331 6985 Z= 0.346 Chirality : 0.044 0.161 750 Planarity : 0.004 0.048 890 Dihedral : 4.868 31.531 704 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.09 % Allowed : 15.25 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.35), residues: 646 helix: -1.36 (0.69), residues: 47 sheet: 0.96 (0.32), residues: 280 loop : 0.06 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.011 0.001 TYR A 391 PHE 0.021 0.001 PHE H 98 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 5128) covalent geometry : angle 0.65779 / 0.34 ( 6959) SS BOND : bond 0.00552 / 0.37 ( 13) SS BOND : angle 1.45136 / 0.85 ( 26) hydrogen bonds : bond 0.03119 / 2.03 ( 188) hydrogen bonds : angle 5.13587 / 3.49 ( 562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.8509 (mmp) cc_final: 0.8137 (mmt) REVERT: A 458 MET cc_start: 0.8986 (mmm) cc_final: 0.8580 (mmp) REVERT: H 31 ASP cc_start: 0.9280 (m-30) cc_final: 0.8991 (m-30) REVERT: H 43 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8763 (mmtm) REVERT: H 46 GLU cc_start: 0.9180 (tt0) cc_final: 0.8912 (tt0) REVERT: H 197 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8358 (tp-100) REVERT: L 3 GLN cc_start: 0.8626 (mp10) cc_final: 0.8113 (mp10) REVERT: L 142 ARG cc_start: 0.8842 (ttt-90) cc_final: 0.8589 (ttt-90) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.7557 time to fit residues: 49.1286 Evaluate side-chains 62 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054152 restraints weight = 40245.314| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 5.27 r_work: 0.2523 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5141 Z= 0.170 Angle : 0.705 10.747 6985 Z= 0.368 Chirality : 0.046 0.232 750 Planarity : 0.004 0.053 890 Dihedral : 5.035 30.059 704 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.09 % Allowed : 15.61 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.35), residues: 646 helix: -0.81 (0.76), residues: 41 sheet: 0.93 (0.32), residues: 283 loop : -0.03 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.011 0.001 TYR H 91 PHE 0.020 0.001 PHE H 98 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 5128) covalent geometry : angle 0.69909 / 0.37 ( 6959) SS BOND : bond 0.00372 / 0.20 ( 13) SS BOND : angle 1.69533 / 1.02 ( 26) hydrogen bonds : bond 0.03353 / 2.19 ( 188) hydrogen bonds : angle 5.22207 / 3.54 ( 562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.9017 (mmm) cc_final: 0.8605 (mmp) REVERT: H 31 ASP cc_start: 0.9271 (m-30) cc_final: 0.8972 (m-30) REVERT: H 46 GLU cc_start: 0.9230 (tt0) cc_final: 0.8946 (tt0) REVERT: H 197 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8432 (tp-100) REVERT: L 142 ARG cc_start: 0.8931 (ttt-90) cc_final: 0.8659 (ttt-90) REVERT: L 167 ASP cc_start: 0.8887 (t0) cc_final: 0.8396 (t0) REVERT: L 170 ASP cc_start: 0.8855 (t0) cc_final: 0.8483 (t0) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.7002 time to fit residues: 47.8307 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 204 ASN L 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.054994 restraints weight = 34074.294| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.96 r_work: 0.2549 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 5141 Z= 0.142 Angle : 0.688 10.362 6985 Z= 0.359 Chirality : 0.045 0.189 750 Planarity : 0.004 0.056 890 Dihedral : 4.988 29.360 704 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.09 % Allowed : 15.61 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.35), residues: 646 helix: -1.25 (0.71), residues: 47 sheet: 0.96 (0.32), residues: 281 loop : 0.01 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.011 0.001 TYR A 391 PHE 0.020 0.001 PHE H 98 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 5128) covalent geometry : angle 0.68316 / 0.36 ( 6959) SS BOND : bond 0.00461 / 0.29 ( 13) SS BOND : angle 1.51779 / 0.90 ( 26) hydrogen bonds : bond 0.03195 / 2.08 ( 188) hydrogen bonds : angle 5.15700 / 3.50 ( 562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.9011 (mmm) cc_final: 0.8602 (mmp) REVERT: H 31 ASP cc_start: 0.9238 (m-30) cc_final: 0.8934 (m-30) REVERT: H 46 GLU cc_start: 0.9216 (tt0) cc_final: 0.8928 (tt0) REVERT: H 197 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8403 (tp-100) REVERT: L 142 ARG cc_start: 0.8919 (ttt-90) cc_final: 0.8649 (ttt-90) REVERT: L 167 ASP cc_start: 0.8874 (t0) cc_final: 0.8356 (t70) REVERT: L 170 ASP cc_start: 0.8792 (t0) cc_final: 0.8402 (t0) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.7590 time to fit residues: 47.8822 Evaluate side-chains 62 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 204 ASN L 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.054429 restraints weight = 34162.863| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.97 r_work: 0.2539 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5141 Z= 0.170 Angle : 0.695 10.327 6985 Z= 0.363 Chirality : 0.045 0.189 750 Planarity : 0.004 0.055 890 Dihedral : 4.998 28.905 704 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.09 % Allowed : 15.43 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.35), residues: 646 helix: -1.29 (0.70), residues: 47 sheet: 0.92 (0.31), residues: 295 loop : 0.00 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.011 0.001 TYR H 91 PHE 0.020 0.001 PHE H 98 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 5128) covalent geometry : angle 0.69048 / 0.36 ( 6959) SS BOND : bond 0.00466 / 0.29 ( 13) SS BOND : angle 1.51742 / 0.90 ( 26) hydrogen bonds : bond 0.03303 / 2.15 ( 188) hydrogen bonds : angle 5.20405 / 3.53 ( 562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.84 seconds wall clock time: 39 minutes 31.65 seconds (2371.65 seconds total)