Starting phenix.real_space_refine on Thu Mar 13 00:42:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kae_37008/03_2025/8kae_37008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kae_37008/03_2025/8kae_37008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kae_37008/03_2025/8kae_37008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kae_37008/03_2025/8kae_37008.map" model { file = "/net/cci-nas-00/data/ceres_data/8kae_37008/03_2025/8kae_37008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kae_37008/03_2025/8kae_37008.cif" } resolution = 3.18 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= -0.002 sd= 0.108 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5393 2.51 5 N 1412 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8440 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1732 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1619 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3183 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'YUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.63 Number of scatterers: 8440 At special positions: 0 Unit cell: (78.1, 89.1, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1594 8.00 N 1412 7.00 C 5393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 100 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.05 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: 2.07 Conformation dependent library (CDL) restraints added in 961.4 milliseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 37.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.841A pdb=" N TYR H 36 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.569A pdb=" N ASP H 94 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR H 95 " --> pdb=" O ALA H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 91 through 95' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 206 through 211 removed outlier: 4.211A pdb=" N THR H 210 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 123 through 130 removed outlier: 3.730A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.793A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 118 Processing helix chain 'R' and resid 122 through 124 No H-bonds generated for 'chain 'R' and resid 122 through 124' Processing helix chain 'R' and resid 125 through 134 removed outlier: 3.575A pdb=" N GLN R 130 " --> pdb=" O LEU R 126 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 165 removed outlier: 3.989A pdb=" N LEU R 142 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLN R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Proline residue: R 156 - end of helix removed outlier: 3.526A pdb=" N GLY R 162 " --> pdb=" O PHE R 158 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP R 163 " --> pdb=" O GLY R 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 185 Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 193 through 220 removed outlier: 3.557A pdb=" N VAL R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 226 through 236 Processing helix chain 'R' and resid 237 through 257 removed outlier: 3.627A pdb=" N GLY R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 removed outlier: 3.625A pdb=" N ARG R 264 " --> pdb=" O TRP R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 277 removed outlier: 4.221A pdb=" N LEU R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 310 removed outlier: 3.606A pdb=" N LYS R 307 " --> pdb=" O LEU R 303 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 347 removed outlier: 3.968A pdb=" N VAL R 325 " --> pdb=" O ALA R 321 " (cutoff:3.500A) Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 362 through 389 removed outlier: 3.936A pdb=" N PHE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 412 removed outlier: 3.791A pdb=" N LEU R 398 " --> pdb=" O ARG R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 422 through 438 removed outlier: 3.886A pdb=" N PHE R 437 " --> pdb=" O GLU R 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER R 438 " --> pdb=" O THR R 434 " (cutoff:3.500A) Processing helix chain 'R' and resid 442 through 448 Processing helix chain 'R' and resid 456 through 470 Processing helix chain 'R' and resid 474 through 488 removed outlier: 3.615A pdb=" N LEU R 478 " --> pdb=" O GLY R 474 " (cutoff:3.500A) Processing helix chain 'R' and resid 493 through 505 Processing helix chain 'R' and resid 506 through 541 removed outlier: 4.221A pdb=" N PHE R 510 " --> pdb=" O MET R 506 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA R 541 " --> pdb=" O VAL R 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.130A pdb=" N GLY H 14 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR H 54 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 40 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.955A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.955A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 169 through 173 Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.577A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.577A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.084A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.128A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 155 through 156 Processing sheet with id=AB5, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1281 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: 2.73 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2227 1.33 - 1.45: 2073 1.45 - 1.58: 4278 1.58 - 1.70: 0 1.70 - 1.83: 59 Bond restraints: 8637 Sorted by residual: bond pdb=" C07 YUX R 601 " pdb=" N06 YUX R 601 " ideal model delta sigma weight residual 1.367 1.440 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C07 YUX R 601 " pdb=" C08 YUX R 601 " ideal model delta sigma weight residual 1.460 1.520 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C04 YUX R 601 " pdb=" C05 YUX R 601 " ideal model delta sigma weight residual 1.481 1.536 -0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" CB VAL N 94 " pdb=" CG1 VAL N 94 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.43e+00 bond pdb=" C07 YUX R 601 " pdb=" N24 YUX R 601 " ideal model delta sigma weight residual 1.300 1.354 -0.054 2.00e-02 2.50e+03 7.37e+00 ... (remaining 8632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11267 2.38 - 4.77: 386 4.77 - 7.15: 67 7.15 - 9.53: 6 9.53 - 11.92: 4 Bond angle restraints: 11730 Sorted by residual: angle pdb=" CA TRP R 178 " pdb=" CB TRP R 178 " pdb=" CG TRP R 178 " ideal model delta sigma weight residual 113.60 123.37 -9.77 1.90e+00 2.77e-01 2.65e+01 angle pdb=" C SER L 95 " pdb=" N SER L 96 " pdb=" CA SER L 96 " ideal model delta sigma weight residual 121.54 112.30 9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C TYR H 104 " pdb=" N GLN H 105 " pdb=" CA GLN H 105 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" CA TYR N 32 " pdb=" CB TYR N 32 " pdb=" CG TYR N 32 " ideal model delta sigma weight residual 113.90 122.23 -8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" C THR N 34 " pdb=" CA THR N 34 " pdb=" CB THR N 34 " ideal model delta sigma weight residual 109.34 103.07 6.27 1.55e+00 4.16e-01 1.63e+01 ... (remaining 11725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 4875 26.56 - 53.13: 162 53.13 - 79.69: 11 79.69 - 106.26: 2 106.26 - 132.82: 3 Dihedral angle restraints: 5053 sinusoidal: 1890 harmonic: 3163 Sorted by residual: dihedral pdb=" CA THR N 34 " pdb=" C THR N 34 " pdb=" N LEU N 35 " pdb=" CA LEU N 35 " ideal model delta harmonic sigma weight residual 180.00 -143.57 -36.43 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.59 -59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CA LEU N 35 " pdb=" C LEU N 35 " pdb=" N GLY N 36 " pdb=" CA GLY N 36 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 915 0.056 - 0.113: 315 0.113 - 0.169: 74 0.169 - 0.226: 10 0.226 - 0.282: 3 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CB THR N 34 " pdb=" CA THR N 34 " pdb=" OG1 THR N 34 " pdb=" CG2 THR N 34 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA HIS H 110 " pdb=" N HIS H 110 " pdb=" C HIS H 110 " pdb=" CB HIS H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE R 519 " pdb=" N PHE R 519 " pdb=" C PHE R 519 " pdb=" CB PHE R 519 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1314 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 214 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO R 215 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 526 " -0.033 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE R 526 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE R 526 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 526 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 526 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 526 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 526 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 32 " -0.034 2.00e-02 2.50e+03 2.20e-02 9.70e+00 pdb=" CG TYR N 32 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR N 32 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR N 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR N 32 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR N 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR N 32 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR N 32 " -0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 358 2.70 - 3.25: 7885 3.25 - 3.80: 12282 3.80 - 4.35: 15294 4.35 - 4.90: 27145 Nonbonded interactions: 62964 Sorted by model distance: nonbonded pdb=" OD2 ASP N 74 " pdb=" NZ LYS N 77 " model vdw 2.147 3.120 nonbonded pdb=" OD1 ASP K 62 " pdb=" OG1 THR L 111 " model vdw 2.302 3.040 nonbonded pdb=" O THR R 284 " pdb=" OG1 THR R 284 " model vdw 2.313 3.040 nonbonded pdb=" OG SER H 21 " pdb=" O MET H 87 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP H 77 " pdb=" NZ LYS H 80 " model vdw 2.315 3.120 ... (remaining 62959 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.650 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.013 0.105 8637 Z= 0.849 Angle : 1.058 11.918 11730 Z= 0.585 Chirality : 0.060 0.282 1317 Planarity : 0.007 0.108 1478 Dihedral : 13.537 132.821 3025 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.16 (0.25), residues: 1091 helix: -0.39 (0.26), residues: 370 sheet: 0.20 (0.30), residues: 309 loop : -1.79 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP R 178 HIS 0.009 0.002 HIS H 110 PHE 0.062 0.004 PHE R 526 TYR 0.049 0.004 TYR N 32 ARG 0.011 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 163 ASP cc_start: 0.7809 (m-30) cc_final: 0.7579 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2443 time to fit residues: 31.9913 Evaluate side-chains 87 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.191753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137792 restraints weight = 10129.575| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.63 r_work: 0.3341 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8637 Z= 0.168 Angle : 0.573 5.986 11730 Z= 0.307 Chirality : 0.043 0.140 1317 Planarity : 0.005 0.071 1478 Dihedral : 6.828 90.659 1218 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.66 % Allowed : 6.27 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1091 helix: 1.00 (0.28), residues: 372 sheet: 0.74 (0.31), residues: 301 loop : -1.51 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.003 0.001 HIS H 219 PHE 0.016 0.001 PHE R 526 TYR 0.017 0.001 TYR R 160 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8392 (t) cc_final: 0.8151 (m) REVERT: L 8 GLN cc_start: 0.6877 (mt0) cc_final: 0.6586 (mt0) REVERT: L 190 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8061 (mmtm) REVERT: N 91 ASP cc_start: 0.8787 (m-30) cc_final: 0.8207 (m-30) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2308 time to fit residues: 33.3151 Evaluate side-chains 95 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136189 restraints weight = 10445.372| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.56 r_work: 0.3323 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.190 Angle : 0.569 7.243 11730 Z= 0.301 Chirality : 0.043 0.140 1317 Planarity : 0.004 0.060 1478 Dihedral : 6.338 83.806 1218 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.21 % Allowed : 8.80 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1091 helix: 1.27 (0.29), residues: 374 sheet: 1.17 (0.32), residues: 280 loop : -1.43 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.017 0.001 PHE K 68 TYR 0.023 0.001 TYR N 32 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 SER cc_start: 0.8460 (t) cc_final: 0.8211 (m) REVERT: H 104 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.6352 (t80) REVERT: L 8 GLN cc_start: 0.6889 (mt0) cc_final: 0.6552 (mt0) REVERT: L 190 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8095 (mmtm) REVERT: N 91 ASP cc_start: 0.8806 (m-30) cc_final: 0.8195 (m-30) REVERT: R 192 TYR cc_start: 0.8167 (m-80) cc_final: 0.7870 (m-80) REVERT: R 537 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7050 (t) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.2262 time to fit residues: 32.1403 Evaluate side-chains 105 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 537 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.189073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133461 restraints weight = 10443.381| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.68 r_work: 0.3286 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8637 Z= 0.236 Angle : 0.583 6.715 11730 Z= 0.308 Chirality : 0.043 0.143 1317 Planarity : 0.004 0.056 1478 Dihedral : 6.149 76.322 1218 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.98 % Allowed : 9.35 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1091 helix: 1.27 (0.29), residues: 374 sheet: 1.17 (0.31), residues: 289 loop : -1.35 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.017 0.001 PHE R 526 TYR 0.028 0.001 TYR N 32 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8490 (t) cc_final: 0.8228 (m) REVERT: H 104 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.6482 (t80) REVERT: H 105 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: L 8 GLN cc_start: 0.6964 (mt0) cc_final: 0.6648 (mt0) REVERT: L 190 LYS cc_start: 0.8518 (mmmm) cc_final: 0.8122 (mmtm) REVERT: N 91 ASP cc_start: 0.8772 (m-30) cc_final: 0.8193 (m-30) REVERT: R 192 TYR cc_start: 0.8220 (m-80) cc_final: 0.7898 (m-80) REVERT: R 537 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.7113 (t) outliers start: 18 outliers final: 10 residues processed: 105 average time/residue: 0.2346 time to fit residues: 33.6466 Evaluate side-chains 106 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 537 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132940 restraints weight = 10378.082| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.43 r_work: 0.3272 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8637 Z= 0.251 Angle : 0.589 6.829 11730 Z= 0.310 Chirality : 0.044 0.145 1317 Planarity : 0.004 0.054 1478 Dihedral : 5.937 68.939 1218 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.20 % Allowed : 10.34 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1091 helix: 1.34 (0.29), residues: 368 sheet: 1.22 (0.32), residues: 289 loop : -1.33 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.018 0.002 PHE K 68 TYR 0.028 0.001 TYR N 32 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8433 (t) cc_final: 0.8179 (m) REVERT: H 104 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.6506 (t80) REVERT: H 105 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7780 (tp40) REVERT: K 68 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: L 8 GLN cc_start: 0.6811 (mt0) cc_final: 0.6438 (mt0) REVERT: N 91 ASP cc_start: 0.8774 (m-30) cc_final: 0.8168 (m-30) REVERT: R 192 TYR cc_start: 0.8201 (m-80) cc_final: 0.7883 (m-80) outliers start: 20 outliers final: 13 residues processed: 105 average time/residue: 0.2261 time to fit residues: 32.5980 Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.9990 chunk 96 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.191366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136227 restraints weight = 10289.186| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.63 r_work: 0.3327 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.177 Angle : 0.538 6.800 11730 Z= 0.283 Chirality : 0.042 0.140 1317 Planarity : 0.004 0.052 1478 Dihedral : 5.142 58.848 1218 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.09 % Allowed : 10.56 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.67 (0.27), residues: 1091 helix: 1.59 (0.30), residues: 362 sheet: 1.33 (0.32), residues: 277 loop : -1.12 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.015 0.001 PHE R 176 TYR 0.021 0.001 TYR R 160 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8437 (t) cc_final: 0.8196 (m) REVERT: H 104 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.6451 (t80) REVERT: H 105 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7605 (tp40) REVERT: L 8 GLN cc_start: 0.6922 (mt0) cc_final: 0.6562 (mt0) REVERT: N 91 ASP cc_start: 0.8777 (m-30) cc_final: 0.8190 (m-30) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.2307 time to fit residues: 32.6464 Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 0.0050 chunk 102 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.194102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139277 restraints weight = 10374.607| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.34 r_work: 0.3360 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8637 Z= 0.147 Angle : 0.509 6.821 11730 Z= 0.267 Chirality : 0.041 0.141 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.639 54.335 1218 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.76 % Allowed : 11.22 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.94 (0.27), residues: 1091 helix: 1.90 (0.30), residues: 356 sheet: 1.29 (0.32), residues: 283 loop : -0.89 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.025 0.001 PHE K 68 TYR 0.022 0.001 TYR R 160 ARG 0.007 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8372 (t) cc_final: 0.8101 (m) REVERT: H 104 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.6540 (t80) REVERT: H 105 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7422 (tp40) REVERT: L 211 PHE cc_start: 0.7070 (t80) cc_final: 0.6857 (t80) REVERT: N 91 ASP cc_start: 0.8773 (m-30) cc_final: 0.8142 (m-30) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 0.2724 time to fit residues: 39.9837 Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN L 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128815 restraints weight = 10663.074| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.65 r_work: 0.3168 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8637 Z= 0.451 Angle : 0.694 8.961 11730 Z= 0.365 Chirality : 0.047 0.166 1317 Planarity : 0.005 0.052 1478 Dihedral : 5.101 47.626 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.20 % Allowed : 11.66 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.43 (0.26), residues: 1091 helix: 1.14 (0.29), residues: 362 sheet: 1.22 (0.31), residues: 310 loop : -1.23 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 178 HIS 0.008 0.002 HIS H 110 PHE 0.036 0.002 PHE K 68 TYR 0.031 0.002 TYR N 32 ARG 0.008 0.001 ARG R 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: H 104 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.6631 (t80) REVERT: H 105 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: N 91 ASP cc_start: 0.8760 (m-30) cc_final: 0.8165 (m-30) REVERT: R 192 TYR cc_start: 0.8371 (m-80) cc_final: 0.8018 (m-80) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.2596 time to fit residues: 35.1135 Evaluate side-chains 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.0070 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.190513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134944 restraints weight = 10480.629| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.28 r_work: 0.3305 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.192 Angle : 0.553 7.367 11730 Z= 0.290 Chirality : 0.042 0.141 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.699 43.429 1218 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.87 % Allowed : 11.88 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.68 (0.27), residues: 1091 helix: 1.49 (0.29), residues: 363 sheet: 1.20 (0.31), residues: 300 loop : -1.03 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.018 0.001 PHE R 176 TYR 0.022 0.001 TYR R 160 ARG 0.006 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8396 (t) cc_final: 0.8153 (m) REVERT: H 104 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.6506 (t80) REVERT: H 105 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7463 (tp40) REVERT: N 91 ASP cc_start: 0.8762 (m-30) cc_final: 0.8168 (m-30) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.2505 time to fit residues: 34.3398 Evaluate side-chains 103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 95 optimal weight: 0.0010 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143538 restraints weight = 10013.274| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.89 r_work: 0.3205 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8637 Z= 0.150 Angle : 0.521 7.445 11730 Z= 0.273 Chirality : 0.042 0.139 1317 Planarity : 0.004 0.048 1478 Dihedral : 4.368 34.094 1218 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.32 % Allowed : 12.76 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.99 (0.27), residues: 1091 helix: 1.89 (0.30), residues: 355 sheet: 1.35 (0.33), residues: 273 loop : -0.77 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 107 HIS 0.009 0.001 HIS H 110 PHE 0.021 0.001 PHE R 176 TYR 0.022 0.001 TYR R 160 ARG 0.007 0.000 ARG N 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8293 (t) cc_final: 0.8021 (m) REVERT: H 104 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.6509 (t80) REVERT: H 105 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7498 (tp40) REVERT: N 91 ASP cc_start: 0.8824 (m-30) cc_final: 0.8250 (m-30) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.2120 time to fit residues: 28.8573 Evaluate side-chains 102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 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 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.193491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140932 restraints weight = 10162.601| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.80 r_work: 0.3224 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.170 Angle : 0.533 7.228 11730 Z= 0.278 Chirality : 0.042 0.141 1317 Planarity : 0.004 0.048 1478 Dihedral : 4.308 31.633 1218 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.87 % Allowed : 12.32 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.98 (0.27), residues: 1091 helix: 1.86 (0.30), residues: 357 sheet: 1.35 (0.32), residues: 273 loop : -0.78 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.026 0.001 PHE K 68 TYR 0.022 0.001 TYR R 160 ARG 0.008 0.000 ARG R 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5344.65 seconds wall clock time: 95 minutes 3.62 seconds (5703.62 seconds total)