Starting phenix.real_space_refine on Sat May 2 14:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvg_37867/05_2026/8wvg_37867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvg_37867/05_2026/8wvg_37867.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 { model { file = "/net/cci-nas-00/data/ceres_data/8wvg_37867/05_2026/8wvg_37867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvg_37867/05_2026/8wvg_37867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wvg_37867/05_2026/8wvg_37867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvg_37867/05_2026/8wvg_37867.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 4107 2.51 5 N 1019 2.21 5 O 1193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6361 Number of models: 1 Model: "" Number of chains: 4 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} Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2968 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 23, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'XEQ': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.26 Number of scatterers: 6361 At special positions: 0 Unit cell: (68.64, 82.72, 135.52, 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 1193 8.00 N 1019 7.00 C 4107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 365.1 milliseconds 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 45.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.772A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.767A 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: 3.608A 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 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.554A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.962A pdb=" N LEU A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 39 removed outlier: 3.905A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 Proline residue: A 45 - end of helix removed outlier: 3.515A pdb=" N LEU A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.701A pdb=" N VAL A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 removed outlier: 4.475A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.087A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.576A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 171 " --> pdb=" O CYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 211 removed outlier: 3.756A pdb=" N MET A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 247 removed outlier: 3.649A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.826A pdb=" N GLY A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.515A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.782A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.912A pdb=" N MET A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.341A pdb=" N MET A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 325 through 332 removed outlier: 4.198A pdb=" N GLN A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 4.291A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.642A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) 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 383 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.537A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.095A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.692A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.090A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 4.031A pdb=" N ILE A 455 " --> pdb=" O TRP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.440A pdb=" N GLU H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.440A pdb=" N GLU H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA H 110 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 135 Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 135 Processing sheet with id=AA6, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.208A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.391A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.796A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 145 through 150 removed outlier: 6.123A pdb=" N HIS L 198 " --> pdb=" O SER L 203 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER L 203 " --> pdb=" O HIS L 198 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.65 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: 1955 1.34 - 1.46: 1526 1.46 - 1.58: 2965 1.58 - 1.70: 2 1.70 - 1.81: 67 Bond restraints: 6515 Sorted by residual: bond pdb=" C05 XEQ A 601 " pdb=" C06 XEQ A 601 " ideal model delta sigma weight residual 1.520 1.586 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C11 XEQ A 601 " pdb=" C13 XEQ A 601 " ideal model delta sigma weight residual 1.543 1.601 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C15 XEQ A 601 " pdb=" C17 XEQ A 601 " ideal model delta sigma weight residual 1.429 1.382 0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C08 XEQ A 601 " pdb=" C10 XEQ A 601 " ideal model delta sigma weight residual 1.502 1.456 0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C10 XEQ A 601 " pdb=" O03 XEQ A 601 " ideal model delta sigma weight residual 1.222 1.262 -0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 6510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8686 1.87 - 3.73: 125 3.73 - 5.60: 43 5.60 - 7.46: 11 7.46 - 9.33: 4 Bond angle restraints: 8869 Sorted by residual: angle pdb=" CB GLU L 154 " pdb=" CG GLU L 154 " pdb=" CD GLU L 154 " ideal model delta sigma weight residual 112.60 119.85 -7.25 1.70e+00 3.46e-01 1.82e+01 angle pdb=" C16 XEQ A 601 " pdb=" C17 XEQ A 601 " pdb=" O02 XEQ A 601 " ideal model delta sigma weight residual 127.15 117.82 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" CA ASP H 89 " pdb=" CB ASP H 89 " pdb=" CG ASP H 89 " ideal model delta sigma weight residual 112.60 115.71 -3.11 1.00e+00 1.00e+00 9.67e+00 angle pdb=" CA GLU L 154 " pdb=" CB GLU L 154 " pdb=" CG GLU L 154 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.36e+00 angle pdb=" C ASP H 89 " pdb=" CA ASP H 89 " pdb=" CB ASP H 89 " ideal model delta sigma weight residual 110.42 116.31 -5.89 1.99e+00 2.53e-01 8.75e+00 ... (remaining 8864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.18: 3598 25.18 - 50.35: 257 50.35 - 75.53: 16 75.53 - 100.71: 5 100.71 - 125.89: 2 Dihedral angle restraints: 3878 sinusoidal: 1485 harmonic: 2393 Sorted by residual: dihedral pdb=" CA ARG A 17 " pdb=" C ARG A 17 " pdb=" N SER A 18 " pdb=" CA SER A 18 " ideal model delta harmonic sigma weight residual 180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" C05 XEQ A 601 " pdb=" C12 XEQ A 601 " pdb=" N04 XEQ A 601 " pdb=" C14 XEQ A 601 " ideal model delta sinusoidal sigma weight residual 68.37 -57.52 125.89 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -54.86 -31.14 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 840 0.057 - 0.113: 157 0.113 - 0.170: 23 0.170 - 0.227: 1 0.227 - 0.284: 1 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CB ILE L 150 " pdb=" CA ILE L 150 " pdb=" CG1 ILE L 150 " pdb=" CG2 ILE L 150 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA TYR L 94 " pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CB TYR L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C13 XEQ A 601 " pdb=" C10 XEQ A 601 " pdb=" C11 XEQ A 601 " pdb=" C18 XEQ A 601 " both_signs ideal model delta sigma weight residual False 2.61 2.77 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 1019 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 154 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C GLU L 154 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU L 154 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG L 155 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 89 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ASP H 89 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP H 89 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP H 90 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.029 5.00e-02 4.00e+02 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1050 2.76 - 3.29: 5853 3.29 - 3.83: 10033 3.83 - 4.36: 11855 4.36 - 4.90: 21814 Nonbonded interactions: 50605 Sorted by model distance: nonbonded pdb=" NH2 ARG H 98 " pdb=" OD2 ASP H 112 " model vdw 2.225 3.120 nonbonded pdb=" O PHE A 334 " pdb=" OG SER A 338 " model vdw 2.267 3.040 nonbonded pdb=" NZ LYS L 24 " pdb=" OD1 ASP L 70 " model vdw 2.286 3.120 nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.321 3.040 nonbonded pdb=" NE1 TRP L 148 " pdb=" OG SER L 177 " model vdw 2.346 3.120 ... (remaining 50600 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: 1.930 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.005 0.066 6519 Z= 0.221 Angle : 0.692 9.327 8877 Z= 0.340 Chirality : 0.045 0.284 1022 Planarity : 0.005 0.053 1106 Dihedral : 15.952 125.887 2336 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.43 % Allowed : 23.01 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.30), residues: 823 helix: 0.20 (0.30), residues: 318 sheet: 0.94 (0.37), residues: 212 loop : -1.28 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.018 0.002 TYR L 140 PHE 0.022 0.002 PHE A 348 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 6515) covalent geometry : angle 0.69137 ( 8869) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.92410 ( 8) hydrogen bonds : bond 0.14955 ( 323) hydrogen bonds : angle 7.10072 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.230 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.0582 time to fit residues: 5.2666 Evaluate side-chains 62 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain A residue 271 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109991 restraints weight = 7478.836| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.61 r_work: 0.3072 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6519 Z= 0.148 Angle : 0.612 9.446 8877 Z= 0.309 Chirality : 0.043 0.189 1022 Planarity : 0.005 0.054 1106 Dihedral : 8.184 103.357 923 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.56 % Allowed : 20.88 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.30), residues: 823 helix: 0.73 (0.31), residues: 322 sheet: 0.99 (0.37), residues: 209 loop : -1.42 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 155 TYR 0.012 0.001 TYR L 140 PHE 0.016 0.001 PHE A 348 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6515) covalent geometry : angle 0.61161 ( 8869) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.60236 ( 8) hydrogen bonds : bond 0.04367 ( 323) hydrogen bonds : angle 5.35762 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.231 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 0.0579 time to fit residues: 7.2986 Evaluate side-chains 73 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112898 restraints weight = 7391.567| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.33 r_work: 0.3167 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6519 Z= 0.141 Angle : 0.588 8.380 8877 Z= 0.296 Chirality : 0.043 0.205 1022 Planarity : 0.004 0.053 1106 Dihedral : 8.139 107.312 919 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.69 % Allowed : 20.45 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.30), residues: 823 helix: 0.86 (0.31), residues: 322 sheet: 1.01 (0.37), residues: 209 loop : -1.41 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 155 TYR 0.012 0.001 TYR L 140 PHE 0.017 0.001 PHE A 348 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6515) covalent geometry : angle 0.58819 ( 8869) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.56029 ( 8) hydrogen bonds : bond 0.04082 ( 323) hydrogen bonds : angle 5.12208 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: L 175 MET cc_start: 0.9108 (ttp) cc_final: 0.8900 (ttm) REVERT: A 271 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7842 (tt0) outliers start: 26 outliers final: 16 residues processed: 92 average time/residue: 0.0558 time to fit residues: 7.7640 Evaluate side-chains 88 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 447 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.142714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111365 restraints weight = 7476.076| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.32 r_work: 0.3144 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6519 Z= 0.201 Angle : 0.648 8.571 8877 Z= 0.324 Chirality : 0.045 0.246 1022 Planarity : 0.005 0.055 1106 Dihedral : 8.424 110.259 919 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.40 % Allowed : 21.16 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.30), residues: 823 helix: 0.66 (0.30), residues: 329 sheet: 1.01 (0.37), residues: 209 loop : -1.43 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.014 0.002 TYR L 140 PHE 0.021 0.002 PHE A 348 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 6515) covalent geometry : angle 0.64774 ( 8869) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.68126 ( 8) hydrogen bonds : bond 0.04710 ( 323) hydrogen bonds : angle 5.21425 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 327 LYS cc_start: 0.5119 (OUTLIER) cc_final: 0.4516 (tttm) outliers start: 31 outliers final: 23 residues processed: 93 average time/residue: 0.0619 time to fit residues: 8.6515 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.142963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111920 restraints weight = 7561.836| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.33 r_work: 0.3169 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6519 Z= 0.151 Angle : 0.603 8.099 8877 Z= 0.302 Chirality : 0.043 0.191 1022 Planarity : 0.005 0.055 1106 Dihedral : 8.264 108.818 919 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.69 % Allowed : 21.02 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.30), residues: 823 helix: 0.85 (0.31), residues: 327 sheet: 1.06 (0.37), residues: 209 loop : -1.41 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.013 0.001 TYR L 140 PHE 0.017 0.001 PHE A 348 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6515) covalent geometry : angle 0.60312 ( 8869) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.55555 ( 8) hydrogen bonds : bond 0.04136 ( 323) hydrogen bonds : angle 5.06177 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: L 94 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6730 (t80) REVERT: L 175 MET cc_start: 0.9118 (ttp) cc_final: 0.8917 (ttm) REVERT: A 327 LYS cc_start: 0.5005 (OUTLIER) cc_final: 0.4382 (tttm) outliers start: 33 outliers final: 23 residues processed: 100 average time/residue: 0.0598 time to fit residues: 8.7750 Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 447 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.144873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113808 restraints weight = 7493.490| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.35 r_work: 0.3191 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6519 Z= 0.124 Angle : 0.579 8.140 8877 Z= 0.290 Chirality : 0.042 0.263 1022 Planarity : 0.004 0.054 1106 Dihedral : 8.206 109.982 919 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.12 % Allowed : 21.02 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 823 helix: 1.02 (0.31), residues: 322 sheet: 1.05 (0.37), residues: 209 loop : -1.36 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.011 0.001 TYR L 140 PHE 0.015 0.001 PHE A 348 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6515) covalent geometry : angle 0.57911 ( 8869) SS BOND : bond 0.00333 ( 4) SS BOND : angle 0.70693 ( 8) hydrogen bonds : bond 0.03709 ( 323) hydrogen bonds : angle 4.90439 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: L 94 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6443 (t80) REVERT: L 175 MET cc_start: 0.9108 (ttp) cc_final: 0.8902 (ttm) REVERT: A 327 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4496 (tttm) outliers start: 29 outliers final: 26 residues processed: 99 average time/residue: 0.0528 time to fit residues: 7.8687 Evaluate side-chains 99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110466 restraints weight = 7448.854| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.29 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6519 Z= 0.194 Angle : 0.639 7.932 8877 Z= 0.320 Chirality : 0.045 0.229 1022 Planarity : 0.005 0.053 1106 Dihedral : 8.450 111.294 919 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.97 % Allowed : 20.31 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.30), residues: 823 helix: 0.73 (0.30), residues: 329 sheet: 1.01 (0.37), residues: 209 loop : -1.39 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.015 0.002 TYR L 140 PHE 0.020 0.002 PHE A 348 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 6515) covalent geometry : angle 0.63856 ( 8869) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.77840 ( 8) hydrogen bonds : bond 0.04581 ( 323) hydrogen bonds : angle 5.11955 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: L 94 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6796 (t80) REVERT: A 184 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: A 327 LYS cc_start: 0.5053 (OUTLIER) cc_final: 0.4461 (tttm) outliers start: 35 outliers final: 28 residues processed: 96 average time/residue: 0.0543 time to fit residues: 7.8433 Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.142256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111455 restraints weight = 7418.456| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.31 r_work: 0.3165 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6519 Z= 0.161 Angle : 0.614 7.899 8877 Z= 0.308 Chirality : 0.044 0.299 1022 Planarity : 0.005 0.054 1106 Dihedral : 8.316 109.590 919 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.11 % Allowed : 20.88 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 823 helix: 0.82 (0.30), residues: 327 sheet: 1.04 (0.37), residues: 209 loop : -1.40 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.014 0.001 TYR L 140 PHE 0.018 0.002 PHE A 348 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6515) covalent geometry : angle 0.61390 ( 8869) SS BOND : bond 0.00292 ( 4) SS BOND : angle 0.67599 ( 8) hydrogen bonds : bond 0.04199 ( 323) hydrogen bonds : angle 5.04648 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: L 94 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 327 LYS cc_start: 0.5040 (OUTLIER) cc_final: 0.4419 (tttm) outliers start: 36 outliers final: 30 residues processed: 97 average time/residue: 0.0526 time to fit residues: 7.6349 Evaluate side-chains 97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.145793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114728 restraints weight = 7484.200| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.33 r_work: 0.3190 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6519 Z= 0.131 Angle : 0.589 8.168 8877 Z= 0.297 Chirality : 0.043 0.288 1022 Planarity : 0.004 0.054 1106 Dihedral : 8.202 109.614 919 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.26 % Allowed : 21.88 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.31), residues: 823 helix: 1.05 (0.31), residues: 321 sheet: 1.08 (0.37), residues: 208 loop : -1.30 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.012 0.001 TYR L 140 PHE 0.015 0.001 PHE A 348 TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6515) covalent geometry : angle 0.58897 ( 8869) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.60821 ( 8) hydrogen bonds : bond 0.03804 ( 323) hydrogen bonds : angle 4.92424 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8051 (t0) REVERT: L 94 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6443 (t80) outliers start: 30 outliers final: 26 residues processed: 99 average time/residue: 0.0549 time to fit residues: 8.0847 Evaluate side-chains 101 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 46 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.146094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115505 restraints weight = 7318.367| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.26 r_work: 0.3202 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6519 Z= 0.130 Angle : 0.585 7.959 8877 Z= 0.294 Chirality : 0.043 0.277 1022 Planarity : 0.004 0.054 1106 Dihedral : 8.202 110.396 919 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.40 % Allowed : 21.45 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.30), residues: 823 helix: 1.04 (0.31), residues: 322 sheet: 1.10 (0.37), residues: 208 loop : -1.36 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.012 0.001 TYR L 140 PHE 0.015 0.001 PHE A 348 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6515) covalent geometry : angle 0.58485 ( 8869) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.59485 ( 8) hydrogen bonds : bond 0.03772 ( 323) hydrogen bonds : angle 4.86868 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1646 Ramachandran restraints generated. 823 Oldfield, 0 Emsley, 823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8085 (t0) REVERT: L 94 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6312 (t80) outliers start: 31 outliers final: 28 residues processed: 101 average time/residue: 0.0521 time to fit residues: 7.8517 Evaluate side-chains 101 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 205 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.141014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110350 restraints weight = 7431.363| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.29 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6519 Z= 0.204 Angle : 0.654 8.067 8877 Z= 0.329 Chirality : 0.046 0.280 1022 Planarity : 0.005 0.052 1106 Dihedral : 8.435 110.161 919 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.55 % Allowed : 21.45 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.30), residues: 823 helix: 0.74 (0.30), residues: 329 sheet: 1.09 (0.37), residues: 207 loop : -1.42 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.016 0.002 TYR L 140 PHE 0.020 0.002 PHE L 139 TRP 0.011 0.001 TRP H 114 HIS 0.004 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 6515) covalent geometry : angle 0.65438 ( 8869) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.75377 ( 8) hydrogen bonds : bond 0.04699 ( 323) hydrogen bonds : angle 5.13207 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.60 seconds wall clock time: 27 minutes 35.37 seconds (1655.37 seconds total)