Starting phenix.real_space_refine on Wed Aug 5 02:04:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21co_67574/08_2026/21co_67574.cif Found real_map, /net/cci-nas-00/data/ceres_data/21co_67574/08_2026/21co_67574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21co_67574/08_2026/21co_67574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21co_67574/08_2026/21co_67574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21co_67574/08_2026/21co_67574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21co_67574/08_2026/21co_67574.map" } resolution = 2.99 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= -0.001 sd= 0.186 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 16 5.16 5 C 4964 2.51 5 N 1316 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7850 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 192 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "B" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3924 Classifications: {'peptide': 513} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 476} Chain: "C" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3732 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 35, 'TRANS': 454} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.24 Number of scatterers: 7850 At special positions: 0 Unit cell: (153.36, 84.24, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 16 16.00 O 1552 8.00 N 1316 7.00 C 4964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.57 Conformation dependent library (CDL) restraints added in 430.2 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 19 sheets defined 14.4% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 168 through 173 removed outlier: 4.498A pdb=" N LEU B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.779A pdb=" N GLU B 318 " --> pdb=" O ASN B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 399 through 402 removed outlier: 3.669A pdb=" N PHE B 402 " --> pdb=" O LYS B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 402' Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.568A pdb=" N THR B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.518A pdb=" N GLY B 445 " --> pdb=" O PRO B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 311 through 316 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 382 through 386 removed outlier: 3.550A pdb=" N ASN C 385 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR C 386 " --> pdb=" O ARG C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 386' Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.673A pdb=" N VAL C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR C 440 " --> pdb=" O MET C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 440' Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 91 removed outlier: 7.130A pdb=" N VAL B 135 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 204 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 113 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 5.684A pdb=" N TYR B 63 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER A 558 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 65 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 559 " --> pdb=" O HIS B 488 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.813A pdb=" N ASP B 197 " --> pdb=" O ASN B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.830A pdb=" N TYR B 250 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR B 269 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 252 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.830A pdb=" N TYR B 250 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR B 269 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 252 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE B 273 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG B 392 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TRP B 275 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 390 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 277 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR B 388 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 280 through 281 removed outlier: 3.881A pdb=" N GLY B 280 " --> pdb=" O ASP B 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB2, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.672A pdb=" N VAL C 76 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 133 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLN C 206 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 135 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR C 233 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.672A pdb=" N VAL C 76 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 63 through 65 removed outlier: 5.741A pdb=" N TYR C 63 " --> pdb=" O SER B 558 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER B 558 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 65 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS B 557 " --> pdb=" O HIS C 488 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS C 490 " --> pdb=" O HIS B 557 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR B 559 " --> pdb=" O HIS C 490 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE C 489 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET C 242 " --> pdb=" O ILE C 489 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE C 491 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER C 244 " --> pdb=" O ILE C 491 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 163 through 165 Processing sheet with id=AB7, first strand: chain 'C' and resid 190 through 193 removed outlier: 3.739A pdb=" N ASP C 197 " --> pdb=" O ASN C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.702A pdb=" N TYR C 250 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR C 269 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 252 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.702A pdb=" N TYR C 250 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR C 269 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 252 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE C 273 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG C 392 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP C 275 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 390 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL C 277 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR C 388 " --> pdb=" O VAL C 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.509A pdb=" N PHE C 424 " --> pdb=" O TYR C 455 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 450 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: 1.36 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2578 1.34 - 1.46: 1464 1.46 - 1.57: 3969 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 8041 Sorted by residual: bond pdb=" C GLY C 53 " pdb=" N GLN C 54 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.25e-02 6.40e+03 1.30e+00 bond pdb=" N GLY C 65 " pdb=" CA GLY C 65 " ideal model delta sigma weight residual 1.447 1.457 -0.010 9.20e-03 1.18e+04 1.21e+00 bond pdb=" N PRO C 513 " pdb=" CA PRO C 513 " ideal model delta sigma weight residual 1.469 1.476 -0.008 7.40e-03 1.83e+04 1.07e+00 bond pdb=" CB TRP B 476 " pdb=" CG TRP B 476 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.50e-01 bond pdb=" CA TYR C 61 " pdb=" C TYR C 61 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.30e-01 ... (remaining 8036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 10509 1.28 - 2.56: 358 2.56 - 3.84: 100 3.84 - 5.12: 11 5.12 - 6.40: 3 Bond angle restraints: 10981 Sorted by residual: angle pdb=" C THR C 470 " pdb=" N THR C 471 " pdb=" CA THR C 471 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CA TRP C 476 " pdb=" CB TRP C 476 " pdb=" CG TRP C 476 " ideal model delta sigma weight residual 113.60 119.16 -5.56 1.90e+00 2.77e-01 8.57e+00 angle pdb=" N ASP B 55 " pdb=" CA ASP B 55 " pdb=" C ASP B 55 " ideal model delta sigma weight residual 114.09 109.61 4.48 1.55e+00 4.16e-01 8.35e+00 angle pdb=" C ASP B 423 " pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 122.36 118.66 3.70 1.60e+00 3.91e-01 5.36e+00 angle pdb=" C ALA C 278 " pdb=" N GLN C 279 " pdb=" CA GLN C 279 " ideal model delta sigma weight residual 122.63 125.73 -3.10 1.44e+00 4.82e-01 4.64e+00 ... (remaining 10976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4590 17.56 - 35.11: 168 35.11 - 52.67: 32 52.67 - 70.23: 20 70.23 - 87.78: 5 Dihedral angle restraints: 4815 sinusoidal: 1848 harmonic: 2967 Sorted by residual: dihedral pdb=" CA TYR C 61 " pdb=" C TYR C 61 " pdb=" N HIS C 62 " pdb=" CA HIS C 62 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PRO C 59 " pdb=" C PRO C 59 " pdb=" N ASP C 60 " pdb=" CA ASP C 60 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP B 52 " pdb=" CB ASP B 52 " pdb=" CG ASP B 52 " pdb=" OD1 ASP B 52 " ideal model delta sinusoidal sigma weight residual -30.00 -87.64 57.64 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 4812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 694 0.031 - 0.062: 325 0.062 - 0.093: 98 0.093 - 0.124: 97 0.124 - 0.154: 12 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CA THR C 471 " pdb=" N THR C 471 " pdb=" C THR C 471 " pdb=" CB THR C 471 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE B 491 " pdb=" N ILE B 491 " pdb=" C ILE B 491 " pdb=" CB ILE B 491 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA TYR C 61 " pdb=" N TYR C 61 " pdb=" C TYR C 61 " pdb=" CB TYR C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1223 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 476 " -0.029 2.00e-02 2.50e+03 2.42e-02 1.46e+01 pdb=" CG TRP C 476 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 476 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 476 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 476 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 476 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 476 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 476 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 476 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 476 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 58 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 59 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 58 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 59 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.024 5.00e-02 4.00e+02 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 911 2.75 - 3.29: 7058 3.29 - 3.83: 12451 3.83 - 4.36: 15435 4.36 - 4.90: 26949 Nonbonded interactions: 62804 Sorted by model distance: nonbonded pdb=" OD2 ASP C 423 " pdb=" NZ LYS C 454 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR B 463 " pdb=" OD1 ASN B 502 " model vdw 2.217 3.040 nonbonded pdb=" O SER B 167 " pdb=" NH1 ARG B 282 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR B 245 " pdb=" OH TYR B 250 " model vdw 2.247 3.040 nonbonded pdb=" OG SER C 303 " pdb=" O THR C 369 " model vdw 2.252 3.040 ... (remaining 62799 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 51 through 540 or resid 601)) selection = chain 'C' } 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: 6.200 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.730 Find NCS groups from input model: 0.160 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.003 0.029 8041 Z= 0.147 Angle : 0.603 6.396 10981 Z= 0.342 Chirality : 0.047 0.154 1226 Planarity : 0.005 0.048 1441 Dihedral : 11.165 87.784 2915 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.96 (0.24), residues: 1020 helix: -0.05 (0.57), residues: 83 sheet: 0.11 (0.36), residues: 187 loop : -0.95 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 240 TYR 0.016 0.002 TYR B 347 PHE 0.019 0.001 PHE B 424 TRP 0.064 0.002 TRP C 476 HIS 0.005 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8041) covalent geometry : angle 0.60339 / 0.34 (10981) hydrogen bonds : bond 0.19681 / 12.67 ( 168) hydrogen bonds : angle 6.89149 / 4.87 ( 450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.301 Fit side-chains REVERT: A 548 GLU cc_start: 0.7805 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 562 ASP cc_start: 0.7898 (p0) cc_final: 0.7621 (p0) REVERT: B 52 ASP cc_start: 0.7881 (m-30) cc_final: 0.7595 (m-30) REVERT: B 80 MET cc_start: 0.8415 (mtm) cc_final: 0.7945 (mtt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4360 time to fit residues: 39.1531 Evaluate side-chains 58 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.0536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109981 restraints weight = 10787.777| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.97 r_work: 0.3125 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8041 Z= 0.085 Angle : 0.476 5.325 10981 Z= 0.252 Chirality : 0.045 0.138 1226 Planarity : 0.004 0.046 1441 Dihedral : 4.619 50.746 1089 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.71 % Allowed : 4.49 % Favored : 94.80 % 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: -0.77 (0.24), residues: 1020 helix: -0.18 (0.56), residues: 87 sheet: 0.17 (0.35), residues: 204 loop : -0.78 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 236 TYR 0.012 0.001 TYR B 347 PHE 0.009 0.001 PHE B 424 TRP 0.031 0.001 TRP C 476 HIS 0.002 0.000 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.09 ( 8041) covalent geometry : angle 0.47619 / 0.25 (10981) hydrogen bonds : bond 0.02819 / 1.85 ( 168) hydrogen bonds : angle 5.31961 / 3.87 ( 450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.299 Fit side-chains REVERT: A 548 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 80 MET cc_start: 0.8828 (mtm) cc_final: 0.8364 (mtp) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 0.3795 time to fit residues: 28.5677 Evaluate side-chains 54 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN B 248 GLN C 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101559 restraints weight = 10934.644| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.98 r_work: 0.2992 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8041 Z= 0.206 Angle : 0.621 8.628 10981 Z= 0.332 Chirality : 0.051 0.158 1226 Planarity : 0.005 0.046 1441 Dihedral : 5.431 60.400 1089 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.54 % Allowed : 5.67 % Favored : 92.79 % 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: -1.09 (0.24), residues: 1020 helix: -0.56 (0.54), residues: 87 sheet: -0.02 (0.35), residues: 193 loop : -0.99 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 240 TYR 0.016 0.002 TYR B 347 PHE 0.022 0.002 PHE B 424 TRP 0.035 0.002 TRP C 476 HIS 0.006 0.002 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 8041) covalent geometry : angle 0.62085 / 0.33 (10981) hydrogen bonds : bond 0.04121 / 2.56 ( 168) hydrogen bonds : angle 5.42254 / 3.93 ( 450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.300 Fit side-chains REVERT: A 548 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 80 MET cc_start: 0.8946 (mtm) cc_final: 0.8489 (mtt) REVERT: B 93 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8583 (mt-10) REVERT: C 181 ASN cc_start: 0.8640 (m110) cc_final: 0.8369 (m-40) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.4215 time to fit residues: 32.3743 Evaluate side-chains 60 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 chunk 98 optimal weight: 0.0000 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN C 515 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105903 restraints weight = 11044.915| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.99 r_work: 0.3065 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8041 Z= 0.092 Angle : 0.496 8.640 10981 Z= 0.262 Chirality : 0.046 0.181 1226 Planarity : 0.005 0.048 1441 Dihedral : 4.798 54.686 1089 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.30 % Allowed : 7.21 % Favored : 91.49 % 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: -0.90 (0.24), residues: 1020 helix: -0.24 (0.57), residues: 87 sheet: 0.04 (0.35), residues: 193 loop : -0.84 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 282 TYR 0.014 0.001 TYR B 347 PHE 0.011 0.001 PHE B 395 TRP 0.023 0.001 TRP C 476 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 8041) covalent geometry : angle 0.49645 / 0.26 (10981) hydrogen bonds : bond 0.02727 / 1.74 ( 168) hydrogen bonds : angle 5.02234 / 3.63 ( 450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.314 Fit side-chains REVERT: A 548 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7451 (tm-30) REVERT: B 80 MET cc_start: 0.8816 (mtm) cc_final: 0.8192 (mtt) REVERT: C 181 ASN cc_start: 0.8583 (m110) cc_final: 0.8296 (m-40) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.3394 time to fit residues: 22.9246 Evaluate side-chains 55 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 56 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 77 optimal weight: 0.0170 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN C 515 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108188 restraints weight = 10881.206| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.94 r_work: 0.3106 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8041 Z= 0.084 Angle : 0.468 7.577 10981 Z= 0.245 Chirality : 0.045 0.166 1226 Planarity : 0.004 0.046 1441 Dihedral : 4.371 48.481 1089 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.77 % Allowed : 7.21 % Favored : 91.02 % 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: -0.72 (0.24), residues: 1020 helix: -0.04 (0.58), residues: 87 sheet: 0.12 (0.36), residues: 187 loop : -0.72 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 282 TYR 0.010 0.001 TYR B 347 PHE 0.010 0.001 PHE B 395 TRP 0.023 0.001 TRP C 476 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.08 ( 8041) covalent geometry : angle 0.46766 / 0.25 (10981) hydrogen bonds : bond 0.02493 / 1.58 ( 168) hydrogen bonds : angle 4.77350 / 3.44 ( 450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.315 Fit side-chains REVERT: A 548 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 80 MET cc_start: 0.8741 (mtm) cc_final: 0.8194 (mtt) REVERT: C 181 ASN cc_start: 0.8557 (m110) cc_final: 0.8258 (m-40) REVERT: C 253 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7853 (mmtt) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 0.3753 time to fit residues: 28.0243 Evaluate side-chains 58 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN B 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099041 restraints weight = 11012.034| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.96 r_work: 0.2952 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8041 Z= 0.292 Angle : 0.700 7.029 10981 Z= 0.376 Chirality : 0.054 0.170 1226 Planarity : 0.006 0.066 1441 Dihedral : 5.800 66.116 1089 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.89 % Allowed : 7.57 % Favored : 90.54 % 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: -1.39 (0.23), residues: 1020 helix: -1.06 (0.50), residues: 91 sheet: -0.29 (0.35), residues: 183 loop : -1.12 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 483 TYR 0.017 0.003 TYR B 347 PHE 0.028 0.003 PHE B 395 TRP 0.032 0.003 TRP C 476 HIS 0.006 0.002 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.29 ( 8041) covalent geometry : angle 0.70044 / 0.38 (10981) hydrogen bonds : bond 0.04443 / 2.75 ( 168) hydrogen bonds : angle 5.54426 / 4.00 ( 450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.309 Fit side-chains REVERT: A 548 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 80 MET cc_start: 0.8884 (mtm) cc_final: 0.8406 (mtt) REVERT: B 562 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6631 (t70) REVERT: C 181 ASN cc_start: 0.8683 (m110) cc_final: 0.8393 (m-40) outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.3373 time to fit residues: 23.6641 Evaluate side-chains 57 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 520 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101545 restraints weight = 10942.019| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.97 r_work: 0.3004 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8041 Z= 0.145 Angle : 0.556 6.978 10981 Z= 0.295 Chirality : 0.048 0.153 1226 Planarity : 0.005 0.057 1441 Dihedral : 5.294 63.481 1089 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.89 % Allowed : 8.39 % Favored : 89.72 % 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: -1.30 (0.24), residues: 1020 helix: -0.63 (0.55), residues: 87 sheet: -0.15 (0.35), residues: 193 loop : -1.15 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 483 TYR 0.020 0.002 TYR B 347 PHE 0.017 0.001 PHE B 424 TRP 0.025 0.002 TRP C 476 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 8041) covalent geometry : angle 0.55554 / 0.30 (10981) hydrogen bonds : bond 0.03313 / 2.06 ( 168) hydrogen bonds : angle 5.21252 / 3.76 ( 450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.297 Fit side-chains REVERT: A 548 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 80 MET cc_start: 0.8897 (mtm) cc_final: 0.8359 (mtt) REVERT: B 93 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8552 (mt-10) REVERT: B 256 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7980 (p) REVERT: C 181 ASN cc_start: 0.8677 (m110) cc_final: 0.8383 (m-40) outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 0.3719 time to fit residues: 25.8970 Evaluate side-chains 59 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102859 restraints weight = 10912.816| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.97 r_work: 0.3024 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8041 Z= 0.127 Angle : 0.534 6.857 10981 Z= 0.283 Chirality : 0.047 0.150 1226 Planarity : 0.005 0.053 1441 Dihedral : 5.069 61.763 1089 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.42 % Allowed : 8.98 % Favored : 89.60 % 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: -1.20 (0.24), residues: 1020 helix: -0.50 (0.56), residues: 87 sheet: -0.15 (0.35), residues: 193 loop : -1.07 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 282 TYR 0.021 0.001 TYR B 347 PHE 0.016 0.001 PHE B 424 TRP 0.030 0.002 TRP C 476 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8041) covalent geometry : angle 0.53372 / 0.28 (10981) hydrogen bonds : bond 0.03109 / 1.93 ( 168) hydrogen bonds : angle 5.09723 / 3.67 ( 450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.245 Fit side-chains REVERT: A 548 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 80 MET cc_start: 0.8787 (mtm) cc_final: 0.8277 (mtt) REVERT: B 93 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8582 (mt-10) REVERT: B 256 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8015 (p) REVERT: B 562 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6630 (t70) REVERT: C 181 ASN cc_start: 0.8696 (m110) cc_final: 0.8411 (m-40) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.3466 time to fit residues: 22.6145 Evaluate side-chains 62 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 0.0470 chunk 28 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.105760 restraints weight = 10817.574| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.96 r_work: 0.3067 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8041 Z= 0.093 Angle : 0.488 6.713 10981 Z= 0.257 Chirality : 0.046 0.156 1226 Planarity : 0.005 0.050 1441 Dihedral : 4.609 56.197 1089 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.18 % Allowed : 9.22 % Favored : 89.60 % 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: -1.01 (0.24), residues: 1020 helix: -0.20 (0.58), residues: 87 sheet: -0.03 (0.36), residues: 187 loop : -0.94 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 282 TYR 0.020 0.001 TYR B 347 PHE 0.012 0.001 PHE B 424 TRP 0.023 0.001 TRP C 476 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 8041) covalent geometry : angle 0.48767 / 0.26 (10981) hydrogen bonds : bond 0.02647 / 1.66 ( 168) hydrogen bonds : angle 4.88180 / 3.52 ( 450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.312 Fit side-chains REVERT: A 548 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 80 MET cc_start: 0.8754 (mtm) cc_final: 0.8207 (mtt) REVERT: B 256 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 181 ASN cc_start: 0.8694 (m110) cc_final: 0.8403 (m-40) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.3069 time to fit residues: 19.9041 Evaluate side-chains 60 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103730 restraints weight = 10903.391| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.97 r_work: 0.3033 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8041 Z= 0.125 Angle : 0.524 6.702 10981 Z= 0.277 Chirality : 0.047 0.161 1226 Planarity : 0.005 0.050 1441 Dihedral : 4.777 57.726 1089 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.42 % Allowed : 9.10 % Favored : 89.48 % 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: -1.07 (0.24), residues: 1020 helix: -0.30 (0.57), residues: 87 sheet: -0.08 (0.35), residues: 193 loop : -0.98 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 483 TYR 0.020 0.001 TYR B 347 PHE 0.017 0.001 PHE B 424 TRP 0.026 0.002 TRP C 476 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 8041) covalent geometry : angle 0.52352 / 0.28 (10981) hydrogen bonds : bond 0.02985 / 1.85 ( 168) hydrogen bonds : angle 4.97184 / 3.58 ( 450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.398 Fit side-chains REVERT: A 548 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 80 MET cc_start: 0.8761 (mtm) cc_final: 0.8241 (mtt) REVERT: B 256 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8027 (p) REVERT: C 181 ASN cc_start: 0.8712 (m110) cc_final: 0.8426 (m-40) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.3240 time to fit residues: 20.4871 Evaluate side-chains 60 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.0070 chunk 2 optimal weight: 0.0570 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102898 restraints weight = 10880.086| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.97 r_work: 0.3019 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8041 Z= 0.130 Angle : 0.535 6.713 10981 Z= 0.284 Chirality : 0.047 0.163 1226 Planarity : 0.005 0.049 1441 Dihedral : 4.901 59.313 1089 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.54 % Allowed : 9.10 % Favored : 89.36 % 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: -1.07 (0.24), residues: 1020 helix: -0.39 (0.57), residues: 87 sheet: -0.05 (0.36), residues: 187 loop : -0.97 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 483 TYR 0.021 0.001 TYR B 347 PHE 0.017 0.001 PHE B 424 TRP 0.026 0.002 TRP C 476 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8041) covalent geometry : angle 0.53480 / 0.28 (10981) hydrogen bonds : bond 0.03070 / 1.90 ( 168) hydrogen bonds : angle 5.03886 / 3.63 ( 450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.29 seconds wall clock time: 42 minutes 16.80 seconds (2536.80 seconds total)