Starting phenix.real_space_refine on Sun Apr 27 17:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrd_37774/04_2025/8wrd_37774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrd_37774/04_2025/8wrd_37774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrd_37774/04_2025/8wrd_37774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrd_37774/04_2025/8wrd_37774.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrd_37774/04_2025/8wrd_37774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrd_37774/04_2025/8wrd_37774.cif" } resolution = 3.05 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= 0.000 sd= 1.000 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 42 5.16 5 C 4078 2.51 5 N 1017 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6326 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2957 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 23, 'TRANS': 369} Chain breaks: 1 Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1702 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Time building chain proxies: 4.53, per 1000 atoms: 0.72 Number of scatterers: 6326 At special positions: 0 Unit cell: (84.48, 84.48, 132, 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 42 16.00 O 1189 8.00 N 1017 7.00 C 4078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 206 " distance=2.04 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: 1.59 Conformation dependent library (CDL) restraints added in 891.4 milliseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 46.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.733A pdb=" N TRP A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.807A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.815A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.707A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.731A pdb=" N ARG A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.549A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.714A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.295A pdb=" N ALA A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.860A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.777A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.610A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.518A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 4.924A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 3.939A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.975A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.522A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.548A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.847A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.767A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.514A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.676A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.583A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.589A pdb=" N SER H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.508A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.589A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 118 removed outlier: 3.862A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.593A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.693A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA H 110 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.627A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1041 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: 2.02 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1957 1.34 - 1.46: 1540 1.46 - 1.58: 2914 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6478 Sorted by residual: bond pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " ideal model delta sigma weight residual 1.533 1.546 -0.013 1.37e-02 5.33e+03 8.60e-01 bond pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.31e-01 bond pdb=" CB ASP H 103 " pdb=" CG ASP H 103 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.12e-01 bond pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.86e-01 bond pdb=" CB VAL L 146 " pdb=" CG2 VAL L 146 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.53e-01 ... (remaining 6473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8657 1.61 - 3.23: 121 3.23 - 4.84: 28 4.84 - 6.45: 9 6.45 - 8.06: 1 Bond angle restraints: 8816 Sorted by residual: angle pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.40 -5.59 2.21e+00 2.05e-01 6.41e+00 angle pdb=" N GLY A 436 " pdb=" CA GLY A 436 " pdb=" C GLY A 436 " ideal model delta sigma weight residual 112.34 117.07 -4.73 2.04e+00 2.40e-01 5.39e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.28 -2.58 1.22e+00 6.72e-01 4.48e+00 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.42 113.57 -3.15 1.49e+00 4.50e-01 4.47e+00 ... (remaining 8811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 3344 17.15 - 34.30: 374 34.30 - 51.45: 98 51.45 - 68.61: 18 68.61 - 85.76: 6 Dihedral angle restraints: 3840 sinusoidal: 1451 harmonic: 2389 Sorted by residual: dihedral pdb=" CA LYS H 126 " pdb=" C LYS H 126 " pdb=" N THR H 127 " pdb=" CA THR H 127 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LEU L 136 " pdb=" C LEU L 136 " pdb=" N ASN L 137 " pdb=" CA ASN L 137 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 58.97 34.03 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 604 0.029 - 0.058: 260 0.058 - 0.087: 87 0.087 - 0.116: 59 0.116 - 0.145: 8 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE L 144 " pdb=" N ILE L 144 " pdb=" C ILE L 144 " pdb=" CB ILE L 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1015 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 126 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS H 126 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS H 126 " -0.014 2.00e-02 2.50e+03 pdb=" N THR H 127 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 386 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 387 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.023 5.00e-02 4.00e+02 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 265 2.72 - 3.27: 6059 3.27 - 3.81: 10078 3.81 - 4.36: 12165 4.36 - 4.90: 22210 Nonbonded interactions: 50777 Sorted by model distance: nonbonded pdb=" O ASN L 137 " pdb=" OG SER L 174 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR H 195 " pdb=" OG1 THR H 198 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 291 " pdb=" NE2 HIS A 414 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASP A 291 " pdb=" NH1 ARG A 413 " model vdw 2.310 3.120 nonbonded pdb=" O GLU L 123 " pdb=" OG1 THR L 126 " model vdw 2.316 3.040 ... (remaining 50772 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: 5.180 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.033 6482 Z= 0.146 Angle : 0.552 8.063 8824 Z= 0.285 Chirality : 0.042 0.145 1018 Planarity : 0.004 0.044 1103 Dihedral : 15.710 85.756 2300 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 22.33 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.84 (0.30), residues: 822 helix: 1.34 (0.30), residues: 329 sheet: 1.38 (0.36), residues: 221 loop : -1.13 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE L 87 TYR 0.012 0.001 TYR A 422 ARG 0.004 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.14359 ( 347) hydrogen bonds : angle 6.89795 ( 1041) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.87427 ( 8) covalent geometry : bond 0.00350 ( 6478) covalent geometry : angle 0.55189 ( 8816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.711 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2221 time to fit residues: 18.4916 Evaluate side-chains 61 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN L 77 ASN L 210 ASN H 5 GLN H 59 ASN H 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.095877 restraints weight = 8061.982| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.15 r_work: 0.3020 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6482 Z= 0.130 Angle : 0.548 6.099 8824 Z= 0.286 Chirality : 0.042 0.136 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.419 22.397 884 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.28 % Allowed : 21.19 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.90 (0.30), residues: 822 helix: 1.34 (0.30), residues: 334 sheet: 1.27 (0.36), residues: 217 loop : -0.90 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 347) hydrogen bonds : angle 5.18021 ( 1041) SS BOND : bond 0.00371 ( 4) SS BOND : angle 0.86251 ( 8) covalent geometry : bond 0.00307 ( 6478) covalent geometry : angle 0.54730 ( 8816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.827 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.2293 time to fit residues: 22.0299 Evaluate side-chains 65 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094631 restraints weight = 8134.095| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.19 r_work: 0.2995 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6482 Z= 0.154 Angle : 0.558 6.212 8824 Z= 0.288 Chirality : 0.042 0.135 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.499 24.067 884 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.56 % Allowed : 20.63 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.80 (0.30), residues: 822 helix: 1.29 (0.30), residues: 333 sheet: 1.20 (0.35), residues: 222 loop : -1.00 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 114 HIS 0.002 0.001 HIS A 414 PHE 0.012 0.001 PHE L 87 TYR 0.010 0.001 TYR L 140 ARG 0.001 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 347) hydrogen bonds : angle 5.00120 ( 1041) SS BOND : bond 0.00511 ( 4) SS BOND : angle 1.25357 ( 8) covalent geometry : bond 0.00378 ( 6478) covalent geometry : angle 0.55655 ( 8816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.736 Fit side-chains REVERT: L 6 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: H 89 ASP cc_start: 0.8648 (t0) cc_final: 0.8292 (t0) outliers start: 25 outliers final: 15 residues processed: 88 average time/residue: 0.2372 time to fit residues: 29.1785 Evaluate side-chains 79 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095347 restraints weight = 8181.426| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.21 r_work: 0.3009 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6482 Z= 0.133 Angle : 0.540 6.311 8824 Z= 0.278 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.433 23.881 884 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.13 % Allowed : 21.48 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.87 (0.30), residues: 822 helix: 1.40 (0.30), residues: 332 sheet: 1.21 (0.35), residues: 222 loop : -1.01 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 347) hydrogen bonds : angle 4.84248 ( 1041) SS BOND : bond 0.00519 ( 4) SS BOND : angle 1.11315 ( 8) covalent geometry : bond 0.00322 ( 6478) covalent geometry : angle 0.53902 ( 8816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.842 Fit side-chains REVERT: L 6 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: H 89 ASP cc_start: 0.8616 (t0) cc_final: 0.8277 (t0) outliers start: 22 outliers final: 16 residues processed: 87 average time/residue: 0.2070 time to fit residues: 25.4675 Evaluate side-chains 83 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095552 restraints weight = 8102.236| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.20 r_work: 0.3010 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6482 Z= 0.136 Angle : 0.540 6.295 8824 Z= 0.278 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.419 23.419 884 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.98 % Allowed : 20.91 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.87 (0.30), residues: 822 helix: 1.39 (0.30), residues: 332 sheet: 1.19 (0.35), residues: 222 loop : -0.97 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 347) hydrogen bonds : angle 4.78927 ( 1041) SS BOND : bond 0.00514 ( 4) SS BOND : angle 1.03730 ( 8) covalent geometry : bond 0.00331 ( 6478) covalent geometry : angle 0.53962 ( 8816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.779 Fit side-chains REVERT: L 6 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: H 89 ASP cc_start: 0.8650 (t0) cc_final: 0.8336 (t0) outliers start: 28 outliers final: 22 residues processed: 92 average time/residue: 0.1798 time to fit residues: 22.7955 Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095944 restraints weight = 8061.837| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.19 r_work: 0.3020 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6482 Z= 0.125 Angle : 0.534 6.912 8824 Z= 0.276 Chirality : 0.041 0.135 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.374 24.395 884 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.41 % Allowed : 20.91 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.89 (0.30), residues: 822 helix: 1.45 (0.30), residues: 331 sheet: 1.17 (0.35), residues: 222 loop : -0.99 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 347) hydrogen bonds : angle 4.71086 ( 1041) SS BOND : bond 0.00477 ( 4) SS BOND : angle 0.92905 ( 8) covalent geometry : bond 0.00299 ( 6478) covalent geometry : angle 0.53395 ( 8816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.743 Fit side-chains REVERT: A 244 GLU cc_start: 0.7974 (pp20) cc_final: 0.7440 (tm-30) REVERT: L 6 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: H 89 ASP cc_start: 0.8643 (t0) cc_final: 0.8386 (t0) outliers start: 31 outliers final: 24 residues processed: 93 average time/residue: 0.2245 time to fit residues: 29.2843 Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095233 restraints weight = 8119.446| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.20 r_work: 0.3008 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6482 Z= 0.143 Angle : 0.548 7.102 8824 Z= 0.283 Chirality : 0.042 0.135 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.423 24.039 884 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.41 % Allowed : 20.91 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.86 (0.30), residues: 822 helix: 1.40 (0.30), residues: 331 sheet: 1.13 (0.35), residues: 224 loop : -0.97 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.001 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 347) hydrogen bonds : angle 4.74643 ( 1041) SS BOND : bond 0.00499 ( 4) SS BOND : angle 0.96595 ( 8) covalent geometry : bond 0.00350 ( 6478) covalent geometry : angle 0.54744 ( 8816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.778 Fit side-chains REVERT: A 244 GLU cc_start: 0.7969 (pp20) cc_final: 0.7470 (tm-30) REVERT: L 6 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: H 89 ASP cc_start: 0.8654 (t0) cc_final: 0.8388 (t0) outliers start: 31 outliers final: 27 residues processed: 94 average time/residue: 0.2413 time to fit residues: 30.8927 Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096850 restraints weight = 8126.076| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.20 r_work: 0.3036 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6482 Z= 0.117 Angle : 0.528 7.476 8824 Z= 0.273 Chirality : 0.041 0.140 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.327 23.640 884 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.98 % Allowed : 21.48 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.89 (0.30), residues: 822 helix: 1.49 (0.30), residues: 331 sheet: 1.05 (0.34), residues: 224 loop : -0.96 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.008 0.001 TYR L 49 ARG 0.001 0.000 ARG L 211 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 347) hydrogen bonds : angle 4.65159 ( 1041) SS BOND : bond 0.00446 ( 4) SS BOND : angle 0.73541 ( 8) covalent geometry : bond 0.00276 ( 6478) covalent geometry : angle 0.52805 ( 8816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.677 Fit side-chains REVERT: A 244 GLU cc_start: 0.7974 (pp20) cc_final: 0.7406 (tm-30) REVERT: H 89 ASP cc_start: 0.8684 (t0) cc_final: 0.8417 (t0) outliers start: 28 outliers final: 24 residues processed: 93 average time/residue: 0.1707 time to fit residues: 21.7869 Evaluate side-chains 91 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096485 restraints weight = 8183.521| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.21 r_work: 0.3027 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6482 Z= 0.124 Angle : 0.536 7.704 8824 Z= 0.277 Chirality : 0.041 0.139 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.320 22.906 884 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.27 % Allowed : 21.19 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.87 (0.30), residues: 822 helix: 1.47 (0.30), residues: 331 sheet: 1.04 (0.35), residues: 224 loop : -0.95 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.008 0.001 TYR L 49 ARG 0.001 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 347) hydrogen bonds : angle 4.67329 ( 1041) SS BOND : bond 0.00507 ( 4) SS BOND : angle 0.88399 ( 8) covalent geometry : bond 0.00297 ( 6478) covalent geometry : angle 0.53551 ( 8816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.664 Fit side-chains REVERT: A 244 GLU cc_start: 0.7978 (pp20) cc_final: 0.7421 (tm-30) REVERT: L 211 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7148 (mtm110) REVERT: H 84 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7870 (p) REVERT: H 89 ASP cc_start: 0.8677 (t0) cc_final: 0.8455 (t0) outliers start: 30 outliers final: 28 residues processed: 94 average time/residue: 0.1858 time to fit residues: 23.5772 Evaluate side-chains 94 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.0000 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097356 restraints weight = 8133.716| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.17 r_work: 0.3046 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6482 Z= 0.115 Angle : 0.526 6.669 8824 Z= 0.272 Chirality : 0.041 0.139 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.247 21.690 884 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.98 % Allowed : 21.19 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.91 (0.30), residues: 822 helix: 1.51 (0.30), residues: 331 sheet: 1.07 (0.35), residues: 224 loop : -0.94 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE L 87 TYR 0.008 0.001 TYR L 49 ARG 0.002 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 347) hydrogen bonds : angle 4.61497 ( 1041) SS BOND : bond 0.00460 ( 4) SS BOND : angle 0.81039 ( 8) covalent geometry : bond 0.00271 ( 6478) covalent geometry : angle 0.52552 ( 8816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.722 Fit side-chains REVERT: A 244 GLU cc_start: 0.7939 (pp20) cc_final: 0.7380 (tm-30) REVERT: L 211 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7124 (mtm110) REVERT: H 84 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7825 (p) REVERT: H 89 ASP cc_start: 0.8648 (t0) cc_final: 0.8419 (t0) outliers start: 28 outliers final: 27 residues processed: 93 average time/residue: 0.1733 time to fit residues: 21.9241 Evaluate side-chains 92 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096058 restraints weight = 8249.047| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.22 r_work: 0.3024 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6482 Z= 0.132 Angle : 0.541 6.417 8824 Z= 0.279 Chirality : 0.042 0.137 1018 Planarity : 0.004 0.043 1103 Dihedral : 4.318 21.789 884 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.55 % Allowed : 20.48 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % 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: 0.87 (0.30), residues: 822 helix: 1.45 (0.30), residues: 331 sheet: 1.11 (0.35), residues: 220 loop : -0.96 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE L 87 TYR 0.009 0.001 TYR L 140 ARG 0.004 0.000 ARG L 155 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 347) hydrogen bonds : angle 4.67595 ( 1041) SS BOND : bond 0.00482 ( 4) SS BOND : angle 0.91454 ( 8) covalent geometry : bond 0.00320 ( 6478) covalent geometry : angle 0.54075 ( 8816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3889.57 seconds wall clock time: 69 minutes 35.94 seconds (4175.94 seconds total)