Starting phenix.real_space_refine on Thu Mar 6 05:39:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgp_43220/03_2025/8vgp_43220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgp_43220/03_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_43220/03_2025/8vgp_43220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgp_43220/03_2025/8vgp_43220.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgp_43220/03_2025/8vgp_43220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgp_43220/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.56, per 1000 atoms: 1.50 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.80 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: 3.17 Time building geometry restraints manager: 1.76 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: 137.990 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.940 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.070 ------------------------------------------------------------------------------- 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 : 0.550 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: 2.0977 time to fit residues: 200.3676 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 : 0.948 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.055178 restraints weight = 40368.400| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 5.26 r_work: 0.2537 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 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 = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- 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 : 1.322 Fit side-chains revert: symmetry clash REVERT: A 464 GLN cc_start: 0.8729 (mp10) cc_final: 0.8436 (mp10) REVERT: H 31 ASP cc_start: 0.9221 (m-30) cc_final: 0.8978 (m-30) REVERT: H 82 MET cc_start: 0.9188 (mtp) cc_final: 0.8970 (mtm) REVERT: L 123 GLU cc_start: 0.9225 (mp0) cc_final: 0.8782 (mp0) REVERT: L 125 LEU cc_start: 0.8543 (mm) cc_final: 0.8068 (mt) REVERT: L 167 ASP cc_start: 0.8673 (t0) cc_final: 0.8191 (t0) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 1.8473 time to fit residues: 136.6191 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 : 0.702 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 0.0870 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 = 0.3138 r_free = 0.3138 target = 0.073155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.054820 restraints weight = 34825.361| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.97 r_work: 0.2526 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- 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 = 0.42 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: 0.8564 moved from start: 0.2269 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 : 0.639 9.488 6959 Z= 0.337 Chirality : 0.045 0.165 750 Planarity : 0.004 0.046 890 Dihedral : 5.162 25.305 704 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.09 % Allowed : 12.16 % 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: 0.17 (0.34), residues: 646 helix: -1.43 (0.69), residues: 46 sheet: 0.76 (0.31), residues: 276 loop : -0.13 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 73 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8797 (mm110) cc_final: 0.8552 (mm-40) REVERT: A 458 MET cc_start: 0.8977 (mmm) cc_final: 0.8547 (mmp) REVERT: A 464 GLN cc_start: 0.8707 (mp10) cc_final: 0.8447 (mp10) REVERT: H 31 ASP cc_start: 0.9227 (m-30) cc_final: 0.8949 (m-30) REVERT: H 82 MET cc_start: 0.9226 (mtp) cc_final: 0.8848 (mtm) REVERT: L 123 GLU cc_start: 0.9221 (mp0) cc_final: 0.8790 (mp0) REVERT: L 142 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8574 (ttt-90) REVERT: L 167 ASP cc_start: 0.8686 (t0) cc_final: 0.8190 (t0) outliers start: 6 outliers final: 2 residues processed: 70 average time/residue: 2.0848 time to fit residues: 151.4187 Evaluate side-chains 64 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.072198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053264 restraints weight = 45943.680| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 5.51 r_work: 0.2491 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2496 r_free = 0.2496 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5128 Z= 0.315 Angle : 0.644 9.426 6959 Z= 0.339 Chirality : 0.046 0.146 750 Planarity : 0.004 0.043 890 Dihedral : 5.146 26.938 704 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.81 % Allowed : 13.79 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.35), residues: 646 helix: -1.40 (0.71), residues: 46 sheet: 0.82 (0.32), residues: 282 loop : -0.16 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.004 0.001 HIS H 35 PHE 0.018 0.002 PHE H 98 TYR 0.012 0.001 TYR H 91 ARG 0.007 0.001 ARG A 463 *********************** 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 : 1.027 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8824 (mm110) cc_final: 0.8570 (mm-40) REVERT: A 458 MET cc_start: 0.9045 (mmm) cc_final: 0.8743 (mmp) REVERT: H 31 ASP cc_start: 0.9258 (m-30) cc_final: 0.8980 (m-30) REVERT: H 211 LYS cc_start: 0.9480 (ttmm) cc_final: 0.9246 (ttmm) REVERT: L 142 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8661 (ttt-90) REVERT: L 167 ASP cc_start: 0.8644 (t0) cc_final: 0.8276 (t0) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 1.7536 time to fit residues: 129.0030 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 : 0.636 ------------------------------------------------------------------------------- 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 12 VAL 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: 5.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.072623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.054135 restraints weight = 30053.815| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 4.75 r_work: 0.2534 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 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 = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2671 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= 0.266 Angle : 0.634 9.400 6959 Z= 0.334 Chirality : 0.045 0.155 750 Planarity : 0.004 0.040 890 Dihedral : 5.024 28.611 704 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.81 % Allowed : 13.43 % 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: -1.50 (0.68), residues: 47 sheet: 0.85 (0.32), residues: 282 loop : -0.13 (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 0.020 0.002 PHE H 98 TYR 0.011 0.001 TYR H 91 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 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 74 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.8668 (mmp) cc_final: 0.8138 (mmt) REVERT: A 366 GLN cc_start: 0.8809 (mm110) cc_final: 0.8564 (mm-40) REVERT: A 458 MET cc_start: 0.9038 (mmm) cc_final: 0.8729 (mmp) REVERT: H 31 ASP cc_start: 0.9272 (m-30) cc_final: 0.8975 (m-30) REVERT: H 211 LYS cc_start: 0.9478 (ttmm) cc_final: 0.9239 (ttmm) REVERT: L 123 GLU cc_start: 0.9293 (mp0) cc_final: 0.9092 (mp0) REVERT: L 142 ARG cc_start: 0.8833 (tpp80) cc_final: 0.8629 (ttt-90) REVERT: L 167 ASP cc_start: 0.8620 (t0) cc_final: 0.8232 (t0) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 1.5952 time to fit residues: 116.2660 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 : 0.463 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 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 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.073087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.054632 restraints weight = 32706.644| |-----------------------------------------------------------------------------| r_work (start): 0.2733 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: 0.2540 |-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: 0.8545 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 : 0.004 0.051 5128 Z= 0.245 Angle : 0.635 9.295 6959 Z= 0.331 Chirality : 0.044 0.159 750 Planarity : 0.004 0.040 890 Dihedral : 4.955 30.601 704 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 2.00 % Allowed : 13.79 % 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: 0.31 (0.35), residues: 646 helix: -1.47 (0.67), residues: 47 sheet: 0.90 (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 0.019 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.009 0.001 ARG L 24 *********************** 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 76 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8828 (mm110) cc_final: 0.8576 (mm-40) REVERT: A 458 MET cc_start: 0.8963 (mmm) cc_final: 0.8650 (mmp) REVERT: H 31 ASP cc_start: 0.9242 (m-30) cc_final: 0.8943 (m-30) REVERT: H 197 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8443 (tp-100) REVERT: L 3 GLN cc_start: 0.8639 (mp10) cc_final: 0.8177 (mp10) REVERT: L 142 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8649 (ttt-90) outliers start: 11 outliers final: 4 residues processed: 71 average time/residue: 1.9727 time to fit residues: 145.2277 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 : 0.588 ------------------------------------------------------------------------------- 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 142 ARG 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: 0.2980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.073438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.055352 restraints weight = 33432.541| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 4.86 r_work: 0.2545 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5128 Z= 0.228 Angle : 0.634 9.405 6959 Z= 0.332 Chirality : 0.044 0.139 750 Planarity : 0.004 0.044 890 Dihedral : 4.856 28.305 704 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.81 % Allowed : 14.16 % Favored : 84.03 % 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: 0.38 (0.35), residues: 646 helix: -1.49 (0.67), residues: 47 sheet: 0.97 (0.32), residues: 282 loop : -0.04 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.010 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: 10 poor density : 63 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8546 (mmt) cc_final: 0.8281 (mmt) REVERT: A 366 GLN cc_start: 0.8837 (mm110) cc_final: 0.8598 (mm-40) REVERT: A 458 MET cc_start: 0.8983 (mmm) cc_final: 0.8576 (mmp) REVERT: H 31 ASP cc_start: 0.9277 (m-30) cc_final: 0.8970 (m-30) REVERT: H 197 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8456 (tp-100) REVERT: L 3 GLN cc_start: 0.8664 (mp10) cc_final: 0.8168 (mp10) REVERT: L 142 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8075 (ttp80) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 1.8389 time to fit residues: 131.3629 Evaluate side-chains 65 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.960 ------------------------------------------------------------------------------- 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 142 ARG 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: 0.7980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 13 optimal weight: 0.0170 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.073847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.055648 restraints weight = 37697.532| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 5.10 r_work: 0.2556 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 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 = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5128 Z= 0.204 Angle : 0.652 10.433 6959 Z= 0.341 Chirality : 0.044 0.147 750 Planarity : 0.004 0.047 890 Dihedral : 4.791 30.856 704 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 1.45 % Allowed : 14.70 % 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 (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: 0.45 (0.35), residues: 646 helix: -1.41 (0.68), residues: 47 sheet: 1.03 (0.32), residues: 274 loop : 0.00 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 PHE 0.021 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.012 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 71 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8868 (mm110) cc_final: 0.8635 (mm-40) REVERT: A 458 MET cc_start: 0.8943 (mmm) cc_final: 0.8549 (mmp) REVERT: H 31 ASP cc_start: 0.9267 (m-30) cc_final: 0.8978 (m-30) REVERT: H 43 LYS cc_start: 0.9034 (mmtm) cc_final: 0.8783 (mmtm) REVERT: H 197 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8469 (tp-100) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 1.5528 time to fit residues: 107.7380 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 : 0.554 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN L 79 GLN L 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.055830 restraints weight = 35047.802| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.98 r_work: 0.2565 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 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 = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3134 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= 0.208 Angle : 0.653 10.142 6959 Z= 0.341 Chirality : 0.044 0.147 750 Planarity : 0.004 0.052 890 Dihedral : 4.746 28.997 704 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 1.81 % Allowed : 14.88 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.35), residues: 646 helix: -1.24 (0.70), residues: 47 sheet: 1.07 (0.32), residues: 275 loop : 0.02 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 402 PHE 0.022 0.001 PHE H 98 TYR 0.011 0.001 TYR A 391 ARG 0.012 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 72 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8875 (mm110) cc_final: 0.8623 (mm-40) REVERT: A 458 MET cc_start: 0.8965 (mmm) cc_final: 0.8578 (mmp) REVERT: H 43 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8819 (mmtm) REVERT: H 197 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8423 (tp-100) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 2.2020 time to fit residues: 152.9313 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 : 1.715 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN L 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054856 restraints weight = 40105.244| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 5.26 r_work: 0.2538 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 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 = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3122 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= 0.258 Angle : 0.670 10.425 6959 Z= 0.349 Chirality : 0.045 0.147 750 Planarity : 0.004 0.056 890 Dihedral : 4.790 28.604 704 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.63 % Allowed : 15.06 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.20 (0.71), residues: 47 sheet: 1.08 (0.32), residues: 275 loop : 0.01 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.021 0.001 PHE H 98 TYR 0.010 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: 9 poor density : 61 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 GLN cc_start: 0.8895 (mm110) cc_final: 0.8657 (mm-40) REVERT: A 458 MET cc_start: 0.8961 (mmm) cc_final: 0.8563 (mmp) REVERT: H 31 ASP cc_start: 0.9329 (m-30) cc_final: 0.9014 (m-30) REVERT: H 43 LYS cc_start: 0.9075 (mmtm) cc_final: 0.8810 (mmtm) REVERT: H 197 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8436 (tp-100) REVERT: L 18 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8737 (ptm-80) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 1.5452 time to fit residues: 102.6489 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 : 0.598 ------------------------------------------------------------------------------- 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 18 ARG Chi-restraints excluded: chain L residue 122 ASP 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: 0.4980 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN H 204 ASN L 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.054820 restraints weight = 47375.600| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 5.58 r_work: 0.2527 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 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 = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5128 Z= 0.245 Angle : 0.668 10.129 6959 Z= 0.349 Chirality : 0.044 0.143 750 Planarity : 0.004 0.056 890 Dihedral : 4.788 27.751 704 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.81 % Allowed : 15.06 % 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 (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: 0.49 (0.35), residues: 646 helix: -1.23 (0.69), residues: 47 sheet: 1.03 (0.32), residues: 279 loop : 0.02 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.021 0.001 PHE H 98 TYR 0.010 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: 5591.47 seconds wall clock time: 100 minutes 44.72 seconds (6044.72 seconds total)