Starting phenix.real_space_refine on Tue Jan 14 02:06:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgp_43220/01_2025/8vgp_43220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgp_43220/01_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_43220/01_2025/8vgp_43220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgp_43220/01_2025/8vgp_43220.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgp_43220/01_2025/8vgp_43220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgp_43220/01_2025/8vgp_43220.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.42, per 1000 atoms: 1.07 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: 1.13 Conformation dependent library (CDL) restraints added in 958.8 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: 0.92 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: 2.04 Time building geometry restraints manager: 1.36 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:17.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- 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 5128 Z= 0.631 Angle : 1.019 12.996 6959 Z= 0.548 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.32), 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 TRP 0.029 0.004 TRP H 33 HIS 0.013 0.003 HIS H 35 PHE 0.024 0.004 PHE H 98 TYR 0.022 0.005 TYR A 353 ARG 0.019 0.004 ARG A 327 *********************** 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 : 0.634 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: 1.5243 time to fit residues: 145.1784 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 : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 57 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: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.055176 restraints weight = 40368.401| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 5.26 r_work: 0.2539 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 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 = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5128 Z= 0.250 Angle : 0.684 9.496 6959 Z= 0.362 Chirality : 0.046 0.137 750 Planarity : 0.004 0.048 890 Dihedral : 5.476 26.440 704 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 10.53 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.34), residues: 646 helix: -1.90 (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 TRP 0.013 0.001 TRP H 33 HIS 0.006 0.001 HIS A 402 PHE 0.021 0.002 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.008 0.001 ARG L 142 *********************** 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 75 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 464 GLN cc_start: 0.8730 (mp10) cc_final: 0.8437 (mp10) REVERT: H 31 ASP cc_start: 0.9220 (m-30) cc_final: 0.8976 (m-30) REVERT: H 82 MET cc_start: 0.9187 (mtp) cc_final: 0.8969 (mtm) REVERT: L 123 GLU cc_start: 0.9223 (mp0) cc_final: 0.8779 (mp0) REVERT: L 125 LEU cc_start: 0.8544 (mm) cc_final: 0.8069 (mt) REVERT: L 167 ASP cc_start: 0.8678 (t0) cc_final: 0.8197 (t0) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 1.6284 time to fit residues: 119.8797 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 48 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.072581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.053988 restraints weight = 33960.776| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 4.93 r_work: 0.2511 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 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 = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5128 Z= 0.301 Angle : 0.653 9.501 6959 Z= 0.345 Chirality : 0.046 0.159 750 Planarity : 0.004 0.046 890 Dihedral : 5.227 25.753 704 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 11.80 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.34), residues: 646 helix: -1.48 (0.69), residues: 46 sheet: 0.76 (0.31), residues: 276 loop : -0.17 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.004 0.001 HIS A 402 PHE 0.022 0.002 PHE H 98 TYR 0.010 0.001 TYR A 353 ARG 0.007 0.001 ARG A 463 *********************** 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: 8 poor density : 67 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8808 (mm110) cc_final: 0.8570 (mm-40) REVERT: A 458 MET cc_start: 0.8994 (mmm) cc_final: 0.8568 (mmp) REVERT: A 464 GLN cc_start: 0.8746 (mp10) cc_final: 0.8494 (mp10) REVERT: H 31 ASP cc_start: 0.9258 (m-30) cc_final: 0.8989 (m-30) REVERT: H 82 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8817 (mtm) REVERT: L 123 GLU cc_start: 0.9219 (mp0) cc_final: 0.8776 (mp0) REVERT: L 142 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8589 (ttt-90) REVERT: L 167 ASP cc_start: 0.8708 (t0) cc_final: 0.8205 (t0) outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 1.5431 time to fit residues: 113.6122 Evaluate side-chains 66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.072690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.053592 restraints weight = 45790.798| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 5.58 r_work: 0.2508 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 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 = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5128 Z= 0.261 Angle : 0.628 9.411 6959 Z= 0.329 Chirality : 0.045 0.148 750 Planarity : 0.004 0.044 890 Dihedral : 5.054 28.009 704 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 1.45 % Allowed : 13.79 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.35), residues: 646 helix: -1.44 (0.69), residues: 47 sheet: 0.81 (0.31), residues: 282 loop : -0.10 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.003 0.001 HIS A 402 PHE 0.020 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.007 0.001 ARG L 24 *********************** 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 71 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8824 (mm110) cc_final: 0.8572 (mm-40) REVERT: A 458 MET cc_start: 0.9038 (mmm) cc_final: 0.8637 (mmp) REVERT: H 31 ASP cc_start: 0.9282 (m-30) cc_final: 0.8999 (m-30) REVERT: L 123 GLU cc_start: 0.9218 (mp0) cc_final: 0.8743 (mp0) REVERT: L 167 ASP cc_start: 0.8629 (t0) cc_final: 0.8104 (t0) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 1.6042 time to fit residues: 114.6514 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 : 0.582 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3136 r_free = 0.3136 target = 0.072685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.054261 restraints weight = 30173.086| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 4.72 r_work: 0.2540 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5128 Z= 0.261 Angle : 0.625 9.436 6959 Z= 0.328 Chirality : 0.045 0.163 750 Planarity : 0.004 0.042 890 Dihedral : 4.984 29.462 704 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 13.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.35), residues: 646 helix: -1.41 (0.69), residues: 47 sheet: 0.88 (0.32), residues: 282 loop : -0.11 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS A 402 PHE 0.019 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.009 0.001 ARG L 142 *********************** 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 71 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.669 Fit side-chains REVERT: A 315 MET cc_start: 0.8669 (mmt) cc_final: 0.8191 (mmt) REVERT: A 366 GLN cc_start: 0.8815 (mm110) cc_final: 0.8569 (mm-40) REVERT: A 458 MET cc_start: 0.9036 (mmm) cc_final: 0.8738 (mmp) REVERT: H 31 ASP cc_start: 0.9262 (m-30) cc_final: 0.8959 (m-30) REVERT: L 167 ASP cc_start: 0.8631 (t0) cc_final: 0.8125 (t0) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 1.8463 time to fit residues: 128.1595 Evaluate side-chains 66 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 170 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.073166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.054729 restraints weight = 33015.864| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 4.91 r_work: 0.2534 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5128 Z= 0.240 Angle : 0.635 9.348 6959 Z= 0.331 Chirality : 0.044 0.163 750 Planarity : 0.004 0.040 890 Dihedral : 4.969 33.721 704 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 13.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.35), residues: 646 helix: -1.39 (0.69), residues: 47 sheet: 0.95 (0.32), residues: 282 loop : -0.08 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 PHE 0.020 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.009 0.001 ARG L 142 *********************** 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 74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8828 (mm110) cc_final: 0.8572 (mm-40) REVERT: A 458 MET cc_start: 0.8948 (mmm) cc_final: 0.8634 (mmp) REVERT: H 31 ASP cc_start: 0.9235 (m-30) cc_final: 0.8934 (m-30) REVERT: H 197 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8397 (tp-100) REVERT: L 167 ASP cc_start: 0.8519 (t0) cc_final: 0.8219 (t0) outliers start: 9 outliers final: 4 residues processed: 68 average time/residue: 1.6212 time to fit residues: 114.2884 Evaluate side-chains 67 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.072339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.053972 restraints weight = 33889.277| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.90 r_work: 0.2524 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 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 = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5128 Z= 0.288 Angle : 0.645 9.175 6959 Z= 0.337 Chirality : 0.045 0.146 750 Planarity : 0.004 0.044 890 Dihedral : 4.971 30.928 704 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 1.63 % Allowed : 14.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.35), residues: 646 helix: -1.31 (0.70), residues: 46 sheet: 0.96 (0.32), residues: 282 loop : -0.14 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.010 0.001 ARG L 24 *********************** 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 73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8832 (mm110) cc_final: 0.8574 (mm-40) REVERT: A 458 MET cc_start: 0.8956 (mmm) cc_final: 0.8637 (mmp) REVERT: H 31 ASP cc_start: 0.9261 (m-30) cc_final: 0.8945 (m-30) REVERT: H 197 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8393 (tp-100) REVERT: L 167 ASP cc_start: 0.8721 (t0) cc_final: 0.8242 (t0) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 1.5972 time to fit residues: 114.1264 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 : 0.562 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053665 restraints weight = 37560.997| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 5.10 r_work: 0.2505 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5128 Z= 0.297 Angle : 0.686 10.494 6959 Z= 0.357 Chirality : 0.045 0.159 750 Planarity : 0.004 0.048 890 Dihedral : 4.989 29.256 704 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.35), residues: 646 helix: -1.33 (0.69), residues: 46 sheet: 0.91 (0.31), residues: 288 loop : -0.09 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE H 98 TYR 0.012 0.001 TYR H 91 ARG 0.011 0.001 ARG L 24 *********************** 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 : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8834 (mm110) cc_final: 0.8570 (mm-40) REVERT: A 458 MET cc_start: 0.8957 (mmm) cc_final: 0.8639 (mmp) REVERT: H 31 ASP cc_start: 0.9295 (m-30) cc_final: 0.9003 (m-30) REVERT: L 142 ARG cc_start: 0.8823 (ttt-90) cc_final: 0.8596 (ttt-90) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 1.6444 time to fit residues: 107.2637 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 204 ASN L 79 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 = 0.073240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054998 restraints weight = 34343.232| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.96 r_work: 0.2553 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 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 = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5128 Z= 0.222 Angle : 0.652 11.010 6959 Z= 0.340 Chirality : 0.044 0.146 750 Planarity : 0.004 0.050 890 Dihedral : 4.806 27.219 704 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.81 % Allowed : 14.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.35), residues: 646 helix: -1.33 (0.69), residues: 47 sheet: 1.02 (0.32), residues: 284 loop : 0.01 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 PHE 0.020 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.013 0.001 ARG L 24 *********************** 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: 10 poor density : 60 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8833 (mm110) cc_final: 0.8590 (mm-40) REVERT: A 458 MET cc_start: 0.8983 (mmm) cc_final: 0.8577 (mmp) REVERT: H 31 ASP cc_start: 0.9266 (m-30) cc_final: 0.8971 (m-30) REVERT: H 215 LYS cc_start: 0.8987 (tttp) cc_final: 0.8629 (tmtt) REVERT: L 18 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8746 (ptm-80) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 1.5697 time to fit residues: 105.7674 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 18 ARG Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 124 CYS Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.072702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.054191 restraints weight = 40256.102| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 5.26 r_work: 0.2517 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 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 = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5128 Z= 0.288 Angle : 0.673 10.506 6959 Z= 0.351 Chirality : 0.045 0.147 750 Planarity : 0.004 0.055 890 Dihedral : 4.842 26.785 704 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.81 % Allowed : 14.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.35), residues: 646 helix: -1.22 (0.70), residues: 46 sheet: 0.99 (0.31), residues: 289 loop : -0.05 (0.39), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.013 0.001 ARG L 24 ********************** 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 70 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8864 (mm110) cc_final: 0.8622 (mm-40) REVERT: A 458 MET cc_start: 0.8996 (mmm) cc_final: 0.8690 (mmp) REVERT: H 31 ASP cc_start: 0.9291 (m-30) cc_final: 0.8990 (m-30) REVERT: L 18 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8772 (ptm-80) REVERT: L 142 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8677 (ttt-90) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 1.5119 time to fit residues: 101.9079 Evaluate side-chains 67 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 18 ARG Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3146 r_free = 0.3146 target = 0.073360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.054483 restraints weight = 47124.715| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 5.60 r_work: 0.2525 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 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 = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5128 Z= 0.236 Angle : 0.667 10.460 6959 Z= 0.346 Chirality : 0.044 0.142 750 Planarity : 0.004 0.056 890 Dihedral : 4.806 28.444 704 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 14.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.35), residues: 646 helix: -1.19 (0.72), residues: 46 sheet: 1.08 (0.32), residues: 284 loop : -0.03 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.020 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.013 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.71 seconds wall clock time: 81 minutes 9.03 seconds (4869.03 seconds total)