Starting phenix.real_space_refine on Wed Sep 17 05:22:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgp_43220/09_2025/8vgp_43220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgp_43220/09_2025/8vgp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgp_43220/09_2025/8vgp_43220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgp_43220/09_2025/8vgp_43220.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgp_43220/09_2025/8vgp_43220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgp_43220/09_2025/8vgp_43220.cif" } 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-2.0-5805/lib/python3.9/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, 25 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 24} Link IDs: {None: 24} 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: 1.96, per 1000 atoms: 0.39 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: 0.32 Conformation dependent library (CDL) restraints added in 254.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.19 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: 0.87 Time building geometry restraints manager: 0.43 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: 2.250 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.220 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: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 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 aren 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 covalent geometry : bond 0.00980 ( 5128) covalent geometry : angle 1.01941 ( 6959) SS BOND : bond 0.00749 ( 13) SS BOND : angle 1.62910 ( 26) hydrogen bonds : bond 0.17839 ( 188) hydrogen bonds : angle 8.68279 ( 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 : 0.187 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: 0.7144 time to fit residues: 67.8198 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 : 0.204 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3151 r_free = 0.3151 target = 0.073768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.055399 restraints weight = 33900.577| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.93 r_work: 0.2548 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 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 = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5141 Z= 0.160 Angle : 0.691 9.161 6985 Z= 0.365 Chirality : 0.046 0.138 750 Planarity : 0.004 0.048 890 Dihedral : 5.484 26.474 704 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 10.71 % 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 aren not related in a simple way. whole: 0.01 (0.34), residues: 646 helix: -1.91 (0.64), residues: 45 sheet: 0.71 (0.31), residues: 276 loop : -0.25 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 142 TYR 0.011 0.001 TYR A 391 PHE 0.021 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 covalent geometry : bond 0.00372 ( 5128) covalent geometry : angle 0.68580 ( 6959) SS BOND : bond 0.00521 ( 13) SS BOND : angle 1.59542 ( 26) hydrogen bonds : bond 0.04023 ( 188) hydrogen bonds : angle 6.06802 ( 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 74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 464 GLN cc_start: 0.8718 (mp10) cc_final: 0.8422 (mp10) REVERT: H 31 ASP cc_start: 0.9213 (m-30) cc_final: 0.8972 (m-30) REVERT: H 82 MET cc_start: 0.9179 (mtp) cc_final: 0.8959 (mtm) REVERT: L 123 GLU cc_start: 0.9229 (mp0) cc_final: 0.8803 (mp0) REVERT: L 167 ASP cc_start: 0.8670 (t0) cc_final: 0.8188 (t0) outliers start: 5 outliers final: 1 residues processed: 70 average time/residue: 0.7887 time to fit residues: 56.9580 Evaluate side-chains 63 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.056056 restraints weight = 23078.009| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.23 r_work: 0.2575 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5141 Z= 0.136 Angle : 0.626 9.575 6985 Z= 0.330 Chirality : 0.045 0.164 750 Planarity : 0.004 0.047 890 Dihedral : 5.061 25.784 704 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.09 % Allowed : 12.52 % Favored : 86.39 % 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 aren not related in a simple way. whole: 0.22 (0.34), residues: 646 helix: -1.46 (0.68), residues: 47 sheet: 0.78 (0.31), residues: 276 loop : -0.08 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 463 TYR 0.010 0.001 TYR A 391 PHE 0.023 0.002 PHE H 98 TRP 0.010 0.001 TRP H 33 HIS 0.004 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5128) covalent geometry : angle 0.62194 ( 6959) SS BOND : bond 0.00459 ( 13) SS BOND : angle 1.30978 ( 26) hydrogen bonds : bond 0.03503 ( 188) hydrogen bonds : angle 5.54428 ( 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 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8774 (mm110) cc_final: 0.8550 (mm-40) REVERT: A 458 MET cc_start: 0.8979 (mmm) cc_final: 0.8544 (mmp) REVERT: A 464 GLN cc_start: 0.8665 (mp10) cc_final: 0.8427 (mp10) REVERT: H 31 ASP cc_start: 0.9210 (m-30) cc_final: 0.8951 (m-30) REVERT: H 46 GLU cc_start: 0.9118 (tt0) cc_final: 0.8903 (tt0) REVERT: H 82 MET cc_start: 0.9208 (mtp) cc_final: 0.8803 (mtm) REVERT: H 211 LYS cc_start: 0.9414 (ttmm) cc_final: 0.9151 (ttmm) REVERT: L 4 MET cc_start: 0.9207 (mmm) cc_final: 0.8987 (mmm) REVERT: L 123 GLU cc_start: 0.9197 (mp0) cc_final: 0.8782 (mp0) REVERT: L 167 ASP cc_start: 0.8693 (t0) cc_final: 0.8186 (t0) outliers start: 6 outliers final: 2 residues processed: 72 average time/residue: 0.6991 time to fit residues: 52.0092 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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: 0.9980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3143 r_free = 0.3143 target = 0.073344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.054457 restraints weight = 40734.736| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 5.30 r_work: 0.2533 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2542 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= 0.156 Angle : 0.626 9.552 6985 Z= 0.329 Chirality : 0.045 0.155 750 Planarity : 0.004 0.044 890 Dihedral : 4.967 28.089 704 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.81 % Allowed : 13.25 % Favored : 84.94 % 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 aren not related in a simple way. whole: 0.30 (0.35), residues: 646 helix: -1.35 (0.71), residues: 47 sheet: 0.86 (0.32), residues: 276 loop : -0.05 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 142 TYR 0.010 0.001 TYR H 91 PHE 0.020 0.001 PHE H 98 TRP 0.010 0.001 TRP H 33 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5128) covalent geometry : angle 0.62011 ( 6959) SS BOND : bond 0.00426 ( 13) SS BOND : angle 1.54233 ( 26) hydrogen bonds : bond 0.03449 ( 188) hydrogen bonds : angle 5.46525 ( 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 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8824 (mm110) cc_final: 0.8586 (mm-40) REVERT: A 458 MET cc_start: 0.9057 (mmm) cc_final: 0.8658 (mmp) REVERT: H 31 ASP cc_start: 0.9246 (m-30) cc_final: 0.8962 (m-30) REVERT: L 167 ASP cc_start: 0.8691 (t0) cc_final: 0.8207 (t0) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 0.7237 time to fit residues: 52.9956 Evaluate side-chains 69 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.073143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.054905 restraints weight = 29559.288| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 4.69 r_work: 0.2556 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5141 Z= 0.153 Angle : 0.623 9.389 6985 Z= 0.327 Chirality : 0.044 0.162 750 Planarity : 0.004 0.042 890 Dihedral : 4.923 30.478 704 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.45 % Allowed : 13.97 % Favored : 84.57 % 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 aren not related in a simple way. whole: 0.37 (0.35), residues: 646 helix: -1.37 (0.70), residues: 47 sheet: 0.94 (0.32), residues: 272 loop : -0.02 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.011 0.001 TYR H 91 PHE 0.020 0.001 PHE H 98 TRP 0.009 0.001 TRP H 33 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5128) covalent geometry : angle 0.61757 ( 6959) SS BOND : bond 0.00341 ( 13) SS BOND : angle 1.51531 ( 26) hydrogen bonds : bond 0.03359 ( 188) hydrogen bonds : angle 5.32633 ( 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 : 0.132 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8800 (mm110) cc_final: 0.8552 (mm-40) REVERT: A 458 MET cc_start: 0.8994 (mmm) cc_final: 0.8580 (mmp) REVERT: H 31 ASP cc_start: 0.9251 (m-30) cc_final: 0.8948 (m-30) REVERT: H 197 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8307 (tp-100) REVERT: L 142 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8542 (ttt-90) REVERT: L 167 ASP cc_start: 0.8629 (t0) cc_final: 0.8355 (t0) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.7355 time to fit residues: 52.4712 Evaluate side-chains 68 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 22 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3152 r_free = 0.3152 target = 0.073984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.055156 restraints weight = 40372.375| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 5.29 r_work: 0.2544 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5141 Z= 0.131 Angle : 0.610 9.353 6985 Z= 0.321 Chirality : 0.044 0.163 750 Planarity : 0.004 0.040 890 Dihedral : 4.830 32.525 704 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 1.63 % Allowed : 14.52 % Favored : 83.85 % 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 aren not related in a simple way. whole: 0.45 (0.35), residues: 646 helix: -1.27 (0.71), residues: 47 sheet: 1.01 (0.32), residues: 272 loop : 0.01 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 covalent geometry : bond 0.00319 ( 5128) covalent geometry : angle 0.60372 ( 6959) SS BOND : bond 0.00344 ( 13) SS BOND : angle 1.54296 ( 26) hydrogen bonds : bond 0.03229 ( 188) hydrogen bonds : angle 5.16917 ( 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: 9 poor density : 64 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8857 (mm110) cc_final: 0.8620 (mm-40) REVERT: A 458 MET cc_start: 0.8954 (mmm) cc_final: 0.8550 (mmp) REVERT: H 31 ASP cc_start: 0.9254 (m-30) cc_final: 0.8956 (m-30) REVERT: H 197 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8302 (tp-100) REVERT: L 142 ARG cc_start: 0.9016 (ttm-80) cc_final: 0.8586 (ttt-90) REVERT: L 167 ASP cc_start: 0.8770 (t0) cc_final: 0.8287 (t0) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.6907 time to fit residues: 49.9557 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 : 0.185 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 62 optimal weight: 0.0010 chunk 24 optimal weight: 0.6980 overall best weight: 0.3524 ------------------------------------------------------------------------------- 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 = 0.3156 r_free = 0.3156 target = 0.074166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.055202 restraints weight = 43691.614| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 5.46 r_work: 0.2557 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 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 = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2935 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= 0.125 Angle : 0.629 9.324 6985 Z= 0.327 Chirality : 0.044 0.158 750 Planarity : 0.004 0.045 890 Dihedral : 4.766 30.318 704 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.09 % Allowed : 14.52 % 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 aren not related in a simple way. whole: 0.52 (0.35), residues: 646 helix: -1.23 (0.71), residues: 47 sheet: 1.09 (0.32), residues: 272 loop : 0.03 (0.38), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 covalent geometry : bond 0.00304 ( 5128) covalent geometry : angle 0.61732 ( 6959) SS BOND : bond 0.00339 ( 13) SS BOND : angle 2.07741 ( 26) hydrogen bonds : bond 0.03076 ( 188) hydrogen bonds : angle 5.05542 ( 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 68 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8861 (mm110) cc_final: 0.8631 (mm-40) REVERT: A 458 MET cc_start: 0.8955 (mmm) cc_final: 0.8562 (mmp) REVERT: H 31 ASP cc_start: 0.9242 (m-30) cc_final: 0.8930 (m-30) REVERT: H 197 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8290 (tp-100) REVERT: L 142 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8572 (ttt-90) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 0.7265 time to fit residues: 49.5122 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 : 0.310 ------------------------------------------------------------------------------- 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 170 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.073334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.055131 restraints weight = 32784.036| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.86 r_work: 0.2554 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5141 Z= 0.151 Angle : 0.632 9.923 6985 Z= 0.330 Chirality : 0.044 0.153 750 Planarity : 0.004 0.048 890 Dihedral : 4.772 28.491 704 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.63 % Allowed : 14.52 % 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 aren not related in a simple way. whole: 0.51 (0.35), residues: 646 helix: -1.36 (0.69), residues: 47 sheet: 1.06 (0.33), residues: 278 loop : 0.04 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.010 0.001 TYR H 91 PHE 0.020 0.001 PHE H 98 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5128) covalent geometry : angle 0.62785 ( 6959) SS BOND : bond 0.00386 ( 13) SS BOND : angle 1.34655 ( 26) hydrogen bonds : bond 0.03209 ( 188) hydrogen bonds : angle 5.11963 ( 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 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8842 (mm110) cc_final: 0.8597 (mm-40) REVERT: A 458 MET cc_start: 0.8923 (mmm) cc_final: 0.8511 (mmp) REVERT: H 31 ASP cc_start: 0.9211 (m-30) cc_final: 0.8912 (m-30) REVERT: H 43 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8715 (mmtm) REVERT: H 197 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8320 (tp-100) REVERT: L 142 ARG cc_start: 0.9025 (ttm-80) cc_final: 0.8561 (ttt-90) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.7062 time to fit residues: 51.1121 Evaluate side-chains 69 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 124 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 62 optimal weight: 0.0770 chunk 37 optimal weight: 0.0040 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 overall best weight: 0.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.056460 restraints weight = 40046.166| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 5.21 r_work: 0.2574 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 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 = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5141 Z= 0.116 Angle : 0.658 10.612 6985 Z= 0.342 Chirality : 0.044 0.238 750 Planarity : 0.004 0.054 890 Dihedral : 4.788 26.855 704 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.45 % Allowed : 15.06 % 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 aren not related in a simple way. whole: 0.48 (0.35), residues: 646 helix: -1.27 (0.70), residues: 47 sheet: 1.02 (0.32), residues: 280 loop : 0.01 (0.39), residues: 319 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 0.022 0.001 PHE H 98 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.000 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5128) covalent geometry : angle 0.65137 ( 6959) SS BOND : bond 0.00448 ( 13) SS BOND : angle 1.64523 ( 26) hydrogen bonds : bond 0.02905 ( 188) hydrogen bonds : angle 4.94017 ( 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 70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8879 (mm110) cc_final: 0.8653 (mm-40) REVERT: A 458 MET cc_start: 0.8971 (mmm) cc_final: 0.8584 (mmp) REVERT: H 31 ASP cc_start: 0.9238 (m-30) cc_final: 0.8940 (m-30) REVERT: H 43 LYS cc_start: 0.9053 (mmtm) cc_final: 0.8786 (mmtm) REVERT: H 197 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8321 (tp-100) REVERT: L 167 ASP cc_start: 0.8901 (t0) cc_final: 0.8412 (t70) REVERT: L 170 ASP cc_start: 0.8808 (t0) cc_final: 0.8463 (t0) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.7554 time to fit residues: 52.2968 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 124 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3152 r_free = 0.3152 target = 0.073679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.055406 restraints weight = 34104.160| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 4.92 r_work: 0.2551 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- 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 = 0.41 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5141 Z= 0.188 Angle : 0.683 10.137 6985 Z= 0.356 Chirality : 0.045 0.193 750 Planarity : 0.004 0.056 890 Dihedral : 4.893 26.904 704 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.45 % Allowed : 15.43 % Favored : 83.12 % 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 aren not related in a simple way. whole: 0.44 (0.35), residues: 646 helix: -1.20 (0.70), residues: 47 sheet: 1.04 (0.32), residues: 279 loop : -0.08 (0.38), residues: 320 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 0.022 0.002 PHE H 98 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5128) covalent geometry : angle 0.67660 ( 6959) SS BOND : bond 0.00467 ( 13) SS BOND : angle 1.64222 ( 26) hydrogen bonds : bond 0.03229 ( 188) hydrogen bonds : angle 5.09054 ( 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 69 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8868 (mm110) cc_final: 0.8635 (mm-40) REVERT: A 458 MET cc_start: 0.8986 (mmm) cc_final: 0.8588 (mmp) REVERT: H 31 ASP cc_start: 0.9237 (m-30) cc_final: 0.8961 (m-30) REVERT: L 167 ASP cc_start: 0.8916 (t0) cc_final: 0.8415 (t70) REVERT: L 170 ASP cc_start: 0.8817 (t0) cc_final: 0.8402 (t0) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.6990 time to fit residues: 47.7684 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain L residue 40 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: 0.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3162 r_free = 0.3162 target = 0.074338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.055953 restraints weight = 36605.098| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 5.07 r_work: 0.2567 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 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 = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5141 Z= 0.128 Angle : 0.666 9.495 6985 Z= 0.348 Chirality : 0.044 0.179 750 Planarity : 0.004 0.057 890 Dihedral : 4.848 27.792 704 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.27 % Allowed : 16.15 % Favored : 82.58 % 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 aren not related in a simple way. whole: 0.46 (0.35), residues: 646 helix: -1.06 (0.72), residues: 47 sheet: 1.05 (0.32), residues: 279 loop : -0.08 (0.38), residues: 320 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 0.022 0.001 PHE H 98 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5128) covalent geometry : angle 0.66084 ( 6959) SS BOND : bond 0.00406 ( 13) SS BOND : angle 1.54446 ( 26) hydrogen bonds : bond 0.03004 ( 188) hydrogen bonds : angle 4.99123 ( 562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.62 seconds wall clock time: 40 minutes 5.51 seconds (2405.51 seconds total)