Starting phenix.real_space_refine on Thu Jul 2 16:13:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8exq_28659/07_2026/8exq_28659.cif" } resolution = 4.9 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= 0.003 sd= 0.045 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 Zn 2 6.06 5 S 38 5.16 5 C 6112 2.51 5 N 1534 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9304 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9304 At special positions: 0 Unit cell: (73.9927, 108.282, 135.353, 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) Zn 2 29.99 S 38 16.00 O 1618 8.00 N 1534 7.00 C 6112 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: 0.75 Conformation dependent library (CDL) restraints added in 304.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 57.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 99 through 133 removed outlier: 3.571A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 229 through 251 removed outlier: 3.969A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 253 No H-bonds generated for 'chain 'B' and resid 252 through 253' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.647A pdb=" N SER B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 402 removed outlier: 4.270A pdb=" N TYR B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'A' and resid 2 through 31 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.563A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 99 through 132 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.659A pdb=" N ASN A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.620A pdb=" N ASN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 5.426A pdb=" N ASN A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 272 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 402 removed outlier: 4.455A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY A 525 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 514 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.457A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY B 525 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU B 514 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR A 92 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 529 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 94 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 531 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 137 538 hydrogen bonds defined for protein. 1542 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: 1.52 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2085 1.32 - 1.46: 3022 1.46 - 1.59: 4346 1.59 - 1.73: 11 1.73 - 1.86: 68 Bond restraints: 9532 Sorted by residual: bond pdb=" CB HIS B 201 " pdb=" CG HIS B 201 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.14e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.418 0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" CB TYR B 552 " pdb=" CG TYR B 552 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB PHE A 90 " pdb=" CG PHE A 90 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.58e+01 bond pdb=" CG MET B 494 " pdb=" SD MET B 494 " ideal model delta sigma weight residual 1.803 1.678 0.125 2.50e-02 1.60e+03 2.52e+01 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10461 2.06 - 4.11: 1944 4.11 - 6.17: 331 6.17 - 8.22: 79 8.22 - 10.28: 21 Bond angle restraints: 12836 Sorted by residual: angle pdb=" CA PHE A 313 " pdb=" CB PHE A 313 " pdb=" CG PHE A 313 " ideal model delta sigma weight residual 113.80 105.83 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" CA ASP A 550 " pdb=" CB ASP A 550 " pdb=" CG ASP A 550 " ideal model delta sigma weight residual 112.60 120.57 -7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C SER B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.01e+00 9.80e-01 6.13e+01 angle pdb=" C TYR B 419 " pdb=" N PRO B 420 " pdb=" CA PRO B 420 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.02e+00 9.61e-01 6.11e+01 angle pdb=" C TYR A 419 " pdb=" N PRO A 420 " pdb=" CA PRO A 420 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.02e+00 9.61e-01 5.96e+01 ... (remaining 12831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5476 17.91 - 35.81: 176 35.81 - 53.72: 26 53.72 - 71.62: 9 71.62 - 89.53: 7 Dihedral angle restraints: 5694 sinusoidal: 2374 harmonic: 3320 Sorted by residual: dihedral pdb=" C ILE B 48 " pdb=" N ILE B 48 " pdb=" CA ILE B 48 " pdb=" CB ILE B 48 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C PHE B 501 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " pdb=" CB PHE B 501 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C TYR B 385 " pdb=" N TYR B 385 " pdb=" CA TYR B 385 " pdb=" CB TYR B 385 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 923 0.095 - 0.189: 364 0.189 - 0.284: 87 0.284 - 0.379: 13 0.379 - 0.473: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB ILE B 531 " pdb=" CA ILE B 531 " pdb=" CG1 ILE B 531 " pdb=" CG2 ILE B 531 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA PHE A 313 " pdb=" N PHE A 313 " pdb=" C PHE A 313 " pdb=" CB PHE A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ASN B 436 " pdb=" N ASN B 436 " pdb=" C ASN B 436 " pdb=" CB ASN B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1385 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 36 " -0.077 2.00e-02 2.50e+03 4.24e-02 3.60e+01 pdb=" CG TYR A 36 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 36 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 36 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 36 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 36 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 36 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 36 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 540 " -0.075 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP A 540 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 540 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 540 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 540 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 540 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 540 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 540 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 540 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 540 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 373 " 0.064 2.00e-02 2.50e+03 3.95e-02 3.12e+01 pdb=" CG TYR B 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 373 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 373 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 373 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR B 373 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B 373 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 373 " 0.068 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 67 2.58 - 3.16: 8618 3.16 - 3.74: 15153 3.74 - 4.32: 22622 4.32 - 4.90: 34188 Nonbonded interactions: 80648 Sorted by model distance: nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.002 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.033 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.044 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.061 2.230 nonbonded pdb=" CD GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.345 2.460 ... (remaining 80643 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.130 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.710 Find NCS groups from input model: 0.190 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 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 : 0.020 0.130 9536 Z= 1.094 Angle : 1.739 10.276 12836 Z= 1.191 Chirality : 0.104 0.473 1388 Planarity : 0.009 0.044 1574 Dihedral : 10.285 89.529 3554 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 0.34 (0.24), residues: 1100 helix: 0.79 (0.20), residues: 534 sheet: -0.15 (0.46), residues: 117 loop : -0.21 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 162 TYR 0.077 0.012 TYR A 36 PHE 0.037 0.007 PHE A 274 TRP 0.075 0.013 TRP A 540 HIS 0.009 0.002 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01975 / 1.09 ( 9532) covalent geometry : angle 1.73869 / 1.19 (12836) hydrogen bonds : bond 0.16429 / 10.54 ( 508) hydrogen bonds : angle 7.09006 / 5.16 ( 1542) metal coordination : bond 0.04009 / 2.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8886 (t80) cc_final: 0.7919 (t80) REVERT: A 131 LEU cc_start: 0.9043 (mt) cc_final: 0.8839 (mp) REVERT: A 143 LYS cc_start: 0.8863 (tttm) cc_final: 0.8445 (tmtt) REVERT: A 147 ASP cc_start: 0.8624 (m-30) cc_final: 0.8340 (m-30) REVERT: A 149 ILE cc_start: 0.9315 (mt) cc_final: 0.8812 (mm) REVERT: A 180 ILE cc_start: 0.8271 (mt) cc_final: 0.7615 (mt) REVERT: A 181 LEU cc_start: 0.9043 (mp) cc_final: 0.8751 (mp) REVERT: A 208 ASN cc_start: 0.9097 (m-40) cc_final: 0.7562 (m110) REVERT: A 215 ILE cc_start: 0.8958 (mt) cc_final: 0.8727 (mt) REVERT: A 216 ILE cc_start: 0.9672 (mt) cc_final: 0.9248 (mt) REVERT: A 220 PHE cc_start: 0.7931 (m-10) cc_final: 0.7512 (m-80) REVERT: A 227 ASN cc_start: 0.8976 (t0) cc_final: 0.8402 (t0) REVERT: A 248 PHE cc_start: 0.6596 (m-80) cc_final: 0.6072 (m-80) REVERT: A 292 LYS cc_start: 0.8466 (tptt) cc_final: 0.7860 (tttm) REVERT: A 296 ILE cc_start: 0.9503 (mt) cc_final: 0.9228 (mm) REVERT: A 297 ASN cc_start: 0.8595 (m-40) cc_final: 0.8230 (m110) REVERT: A 311 LEU cc_start: 0.9239 (pp) cc_final: 0.8839 (mp) REVERT: A 368 MET cc_start: -0.2060 (tpt) cc_final: -0.2607 (ttm) REVERT: A 462 ASN cc_start: 0.5872 (t0) cc_final: 0.5219 (m-40) REVERT: A 553 TYR cc_start: 0.3295 (m-80) cc_final: 0.1548 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0661 time to fit residues: 16.0936 Evaluate side-chains 114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 241 ASN A 567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.182762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.141619 restraints weight = 13168.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.146119 restraints weight = 8885.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.149614 restraints weight = 6420.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152325 restraints weight = 4812.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.154207 restraints weight = 3739.134| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 1.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9536 Z= 0.209 Angle : 0.794 11.126 12836 Z= 0.441 Chirality : 0.048 0.150 1388 Planarity : 0.005 0.036 1574 Dihedral : 5.628 27.397 1208 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.58 % Allowed : 3.67 % Favored : 95.75 % 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: 0.63 (0.25), residues: 1100 helix: 1.28 (0.21), residues: 562 sheet: 0.27 (0.47), residues: 126 loop : -0.67 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 293 TYR 0.030 0.003 TYR A 524 PHE 0.037 0.003 PHE A 14 TRP 0.035 0.003 TRP B 414 HIS 0.008 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 ( 9532) covalent geometry : angle 0.79350 / 0.44 (12836) hydrogen bonds : bond 0.07449 / 4.91 ( 508) hydrogen bonds : angle 5.44562 / 3.86 ( 1542) metal coordination : bond 0.00104 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8661 (pttp) cc_final: 0.8098 (pttt) REVERT: A 31 ASN cc_start: 0.9338 (m-40) cc_final: 0.8882 (p0) REVERT: A 54 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8944 (mmmt) REVERT: A 110 TRP cc_start: 0.8500 (t60) cc_final: 0.7703 (t60) REVERT: A 121 PHE cc_start: 0.9443 (t80) cc_final: 0.9059 (t80) REVERT: A 123 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8838 (ptpp) REVERT: A 126 LEU cc_start: 0.9436 (mt) cc_final: 0.9100 (mt) REVERT: A 127 TYR cc_start: 0.9004 (t80) cc_final: 0.8698 (t80) REVERT: A 147 ASP cc_start: 0.8592 (m-30) cc_final: 0.8371 (m-30) REVERT: A 202 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8748 (mt-10) REVERT: A 212 LEU cc_start: 0.9532 (tp) cc_final: 0.9230 (tp) REVERT: A 227 ASN cc_start: 0.8629 (t0) cc_final: 0.8145 (t0) REVERT: A 233 VAL cc_start: 0.8853 (m) cc_final: 0.8507 (m) REVERT: A 241 ASN cc_start: 0.9373 (m110) cc_final: 0.9108 (t0) REVERT: A 244 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 248 PHE cc_start: 0.8093 (m-80) cc_final: 0.7492 (m-80) REVERT: A 282 HIS cc_start: 0.7595 (m-70) cc_final: 0.7069 (m-70) REVERT: A 295 LEU cc_start: 0.9478 (mt) cc_final: 0.9181 (mt) REVERT: A 297 ASN cc_start: 0.9083 (m-40) cc_final: 0.8619 (m110) REVERT: A 320 LEU cc_start: 0.9415 (mt) cc_final: 0.9188 (mt) REVERT: A 494 MET cc_start: 0.6120 (ptt) cc_final: 0.5697 (ptt) REVERT: A 495 MET cc_start: 0.6791 (mmt) cc_final: 0.6361 (mmm) outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.0619 time to fit residues: 12.4300 Evaluate side-chains 120 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 51 optimal weight: 0.0170 chunk 77 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 500 HIS A 518 ASN A 557 HIS A 567 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.182652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.141973 restraints weight = 13674.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.146193 restraints weight = 9546.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.149294 restraints weight = 7004.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.151645 restraints weight = 5414.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.153359 restraints weight = 4323.542| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 1.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9536 Z= 0.151 Angle : 0.684 9.670 12836 Z= 0.378 Chirality : 0.044 0.146 1388 Planarity : 0.004 0.039 1574 Dihedral : 5.354 24.087 1208 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: 0.67 (0.25), residues: 1100 helix: 1.34 (0.22), residues: 564 sheet: 0.25 (0.45), residues: 126 loop : -0.70 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.024 0.002 TYR A 524 PHE 0.043 0.002 PHE A 14 TRP 0.025 0.002 TRP B 414 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 9532) covalent geometry : angle 0.68399 / 0.38 (12836) hydrogen bonds : bond 0.06046 / 3.94 ( 508) hydrogen bonds : angle 5.05491 / 3.58 ( 1542) metal coordination : bond 0.00171 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LEU cc_start: 0.9172 (mt) cc_final: 0.8623 (pp) REVERT: A 110 TRP cc_start: 0.8450 (t60) cc_final: 0.7694 (t60) REVERT: A 116 ILE cc_start: 0.9468 (mm) cc_final: 0.9179 (pt) REVERT: A 121 PHE cc_start: 0.9297 (t80) cc_final: 0.9026 (t80) REVERT: A 126 LEU cc_start: 0.9309 (mt) cc_final: 0.8949 (mt) REVERT: A 137 TYR cc_start: 0.8342 (p90) cc_final: 0.8130 (p90) REVERT: A 141 ASN cc_start: 0.9530 (m-40) cc_final: 0.9165 (m-40) REVERT: A 163 LYS cc_start: 0.5646 (pttt) cc_final: 0.5426 (tmmt) REVERT: A 174 TRP cc_start: 0.8637 (t60) cc_final: 0.8373 (t-100) REVERT: A 199 ILE cc_start: 0.9738 (mm) cc_final: 0.9475 (mm) REVERT: A 202 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8732 (mt-10) REVERT: A 208 ASN cc_start: 0.9088 (m110) cc_final: 0.8108 (m110) REVERT: A 213 HIS cc_start: 0.8970 (m90) cc_final: 0.8638 (m90) REVERT: A 215 ILE cc_start: 0.9113 (tp) cc_final: 0.8865 (pt) REVERT: A 218 ASN cc_start: 0.9318 (t0) cc_final: 0.8297 (t0) REVERT: A 227 ASN cc_start: 0.8544 (t0) cc_final: 0.7845 (t0) REVERT: A 233 VAL cc_start: 0.8902 (m) cc_final: 0.8524 (m) REVERT: A 237 ILE cc_start: 0.9519 (mt) cc_final: 0.9280 (mt) REVERT: A 241 ASN cc_start: 0.9534 (m110) cc_final: 0.9308 (t0) REVERT: A 244 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 247 ARG cc_start: 0.9395 (ttp-170) cc_final: 0.9067 (ttp-170) REVERT: A 248 PHE cc_start: 0.8011 (m-80) cc_final: 0.7352 (m-10) REVERT: A 295 LEU cc_start: 0.9423 (mt) cc_final: 0.9144 (mt) REVERT: A 297 ASN cc_start: 0.8893 (m-40) cc_final: 0.8514 (m110) REVERT: A 302 ASN cc_start: 0.9109 (t0) cc_final: 0.8796 (t0) REVERT: A 495 MET cc_start: 0.7325 (mmt) cc_final: 0.6788 (mmt) REVERT: A 553 TYR cc_start: 0.7140 (m-80) cc_final: 0.6515 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0541 time to fit residues: 10.3431 Evaluate side-chains 116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 49 optimal weight: 0.0770 chunk 5 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 68 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.186982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.146625 restraints weight = 13847.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.150693 restraints weight = 9839.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.153840 restraints weight = 7324.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.156073 restraints weight = 5649.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.157856 restraints weight = 4491.665| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 1.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9536 Z= 0.156 Angle : 0.732 18.568 12836 Z= 0.391 Chirality : 0.044 0.191 1388 Planarity : 0.004 0.031 1574 Dihedral : 5.204 28.173 1208 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 0.56 (0.25), residues: 1100 helix: 1.20 (0.22), residues: 566 sheet: 0.49 (0.43), residues: 136 loop : -0.83 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.023 0.002 TYR B 544 PHE 0.047 0.002 PHE A 14 TRP 0.019 0.002 TRP A 414 HIS 0.006 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 9532) covalent geometry : angle 0.73220 / 0.39 (12836) hydrogen bonds : bond 0.05571 / 3.58 ( 508) hydrogen bonds : angle 5.11858 / 3.62 ( 1542) metal coordination : bond 0.00020 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8175 (tpt90) cc_final: 0.7458 (tpt90) REVERT: A 34 LEU cc_start: 0.9003 (tp) cc_final: 0.8677 (pp) REVERT: A 110 TRP cc_start: 0.8379 (t60) cc_final: 0.7643 (t60) REVERT: A 116 ILE cc_start: 0.9409 (mm) cc_final: 0.9166 (pt) REVERT: A 121 PHE cc_start: 0.9374 (t80) cc_final: 0.8994 (t80) REVERT: A 126 LEU cc_start: 0.9255 (mt) cc_final: 0.8919 (mt) REVERT: A 141 ASN cc_start: 0.9371 (m-40) cc_final: 0.9015 (m-40) REVERT: A 153 HIS cc_start: 0.8690 (m90) cc_final: 0.8414 (m90) REVERT: A 180 ILE cc_start: 0.8796 (mp) cc_final: 0.7657 (mp) REVERT: A 208 ASN cc_start: 0.8908 (m110) cc_final: 0.8248 (m110) REVERT: A 213 HIS cc_start: 0.8840 (m90) cc_final: 0.8593 (m90) REVERT: A 215 ILE cc_start: 0.9046 (tp) cc_final: 0.8815 (pt) REVERT: A 218 ASN cc_start: 0.9284 (t0) cc_final: 0.8316 (t0) REVERT: A 227 ASN cc_start: 0.8468 (t0) cc_final: 0.7768 (t0) REVERT: A 233 VAL cc_start: 0.8817 (m) cc_final: 0.8454 (m) REVERT: A 237 ILE cc_start: 0.9550 (mt) cc_final: 0.9323 (mt) REVERT: A 239 HIS cc_start: 0.8978 (m90) cc_final: 0.8464 (m90) REVERT: A 244 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8365 (mm-30) REVERT: A 247 ARG cc_start: 0.9339 (ttp-170) cc_final: 0.8997 (tmm-80) REVERT: A 253 ILE cc_start: 0.9409 (mt) cc_final: 0.9157 (mt) REVERT: A 295 LEU cc_start: 0.9480 (mt) cc_final: 0.9251 (mt) REVERT: A 297 ASN cc_start: 0.8980 (m-40) cc_final: 0.8625 (m110) REVERT: A 302 ASN cc_start: 0.8822 (t0) cc_final: 0.8602 (t0) REVERT: A 412 MET cc_start: 0.2074 (mmt) cc_final: 0.1866 (mmt) REVERT: A 495 MET cc_start: 0.6445 (mmt) cc_final: 0.6026 (mmm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0582 time to fit residues: 10.6245 Evaluate side-chains 114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.2980 chunk 99 optimal weight: 0.0170 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.186483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.146187 restraints weight = 13769.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.150637 restraints weight = 9463.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.153916 restraints weight = 6888.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.156134 restraints weight = 5242.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.157918 restraints weight = 4154.584| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 1.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9536 Z= 0.137 Angle : 0.669 7.607 12836 Z= 0.368 Chirality : 0.042 0.137 1388 Planarity : 0.004 0.036 1574 Dihedral : 4.997 21.389 1208 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.19 % Allowed : 2.90 % Favored : 96.91 % 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: 0.53 (0.25), residues: 1100 helix: 1.19 (0.22), residues: 566 sheet: 0.46 (0.42), residues: 136 loop : -0.84 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.020 0.002 TYR B 544 PHE 0.031 0.002 PHE A 14 TRP 0.035 0.003 TRP B 414 HIS 0.007 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 9532) covalent geometry : angle 0.66946 / 0.37 (12836) hydrogen bonds : bond 0.05303 / 3.40 ( 508) hydrogen bonds : angle 5.00520 / 3.55 ( 1542) metal coordination : bond 0.00027 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8289 (tpt90) cc_final: 0.7804 (tpt90) REVERT: A 110 TRP cc_start: 0.8283 (t60) cc_final: 0.7530 (t60) REVERT: A 116 ILE cc_start: 0.9357 (mm) cc_final: 0.9112 (pt) REVERT: A 117 LEU cc_start: 0.9167 (mt) cc_final: 0.8925 (mt) REVERT: A 121 PHE cc_start: 0.9540 (t80) cc_final: 0.9049 (t80) REVERT: A 126 LEU cc_start: 0.9104 (mt) cc_final: 0.8850 (mt) REVERT: A 141 ASN cc_start: 0.9320 (m-40) cc_final: 0.8944 (m-40) REVERT: A 153 HIS cc_start: 0.8655 (m90) cc_final: 0.8427 (m90) REVERT: A 167 ILE cc_start: 0.9197 (mp) cc_final: 0.8956 (tt) REVERT: A 178 TYR cc_start: 0.7380 (m-80) cc_final: 0.7071 (m-10) REVERT: A 198 ILE cc_start: 0.9178 (pt) cc_final: 0.8883 (pt) REVERT: A 199 ILE cc_start: 0.9735 (mm) cc_final: 0.9470 (mm) REVERT: A 202 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8863 (mt-10) REVERT: A 208 ASN cc_start: 0.8895 (m110) cc_final: 0.8514 (m110) REVERT: A 213 HIS cc_start: 0.8886 (m90) cc_final: 0.8678 (m170) REVERT: A 215 ILE cc_start: 0.9076 (tp) cc_final: 0.8819 (pt) REVERT: A 218 ASN cc_start: 0.9260 (t0) cc_final: 0.8395 (t0) REVERT: A 227 ASN cc_start: 0.8577 (t0) cc_final: 0.8102 (t0) REVERT: A 233 VAL cc_start: 0.8729 (m) cc_final: 0.8332 (m) REVERT: A 239 HIS cc_start: 0.9056 (m90) cc_final: 0.8728 (m90) REVERT: A 244 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8592 (mm-30) REVERT: A 247 ARG cc_start: 0.9314 (ttp-170) cc_final: 0.9054 (ttp80) REVERT: A 275 PHE cc_start: 0.8622 (t80) cc_final: 0.8079 (t80) REVERT: A 295 LEU cc_start: 0.9382 (mt) cc_final: 0.9081 (mt) REVERT: A 297 ASN cc_start: 0.8975 (m-40) cc_final: 0.8644 (m110) REVERT: A 313 PHE cc_start: 0.9411 (m-80) cc_final: 0.9055 (m-80) REVERT: A 317 PHE cc_start: 0.9257 (m-80) cc_final: 0.8626 (m-80) REVERT: A 320 LEU cc_start: 0.9489 (mm) cc_final: 0.9140 (mm) REVERT: A 325 GLN cc_start: 0.9203 (pm20) cc_final: 0.8970 (pm20) REVERT: A 462 ASN cc_start: 0.5240 (m-40) cc_final: 0.4975 (t0) REVERT: A 495 MET cc_start: 0.6356 (mmt) cc_final: 0.6012 (mmm) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.0505 time to fit residues: 9.9221 Evaluate side-chains 117 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 65 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.185614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.143906 restraints weight = 13473.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.147976 restraints weight = 9488.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.151176 restraints weight = 7052.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153533 restraints weight = 5507.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.155350 restraints weight = 4443.268| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 1.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9536 Z= 0.133 Angle : 0.656 7.301 12836 Z= 0.358 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.030 1574 Dihedral : 4.927 18.358 1208 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.53 (0.25), residues: 1100 helix: 1.24 (0.21), residues: 566 sheet: 0.61 (0.43), residues: 136 loop : -1.01 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 194 TYR 0.017 0.002 TYR B 441 PHE 0.025 0.002 PHE A 16 TRP 0.033 0.003 TRP B 414 HIS 0.010 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9532) covalent geometry : angle 0.65587 / 0.36 (12836) hydrogen bonds : bond 0.04976 / 3.14 ( 508) hydrogen bonds : angle 4.92705 / 3.48 ( 1542) metal coordination : bond 0.00088 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9449 (t80) cc_final: 0.9025 (t80) REVERT: A 28 ARG cc_start: 0.8298 (tpt90) cc_final: 0.7845 (tpt90) REVERT: A 110 TRP cc_start: 0.8265 (t60) cc_final: 0.7535 (t60) REVERT: A 116 ILE cc_start: 0.9348 (mm) cc_final: 0.9121 (pt) REVERT: A 121 PHE cc_start: 0.9568 (t80) cc_final: 0.9108 (t80) REVERT: A 126 LEU cc_start: 0.9029 (mt) cc_final: 0.8754 (mt) REVERT: A 127 TYR cc_start: 0.8874 (t80) cc_final: 0.8462 (t80) REVERT: A 131 LEU cc_start: 0.9119 (mt) cc_final: 0.8787 (mt) REVERT: A 141 ASN cc_start: 0.9468 (m-40) cc_final: 0.8897 (p0) REVERT: A 153 HIS cc_start: 0.8810 (m90) cc_final: 0.8459 (m90) REVERT: A 167 ILE cc_start: 0.8986 (mp) cc_final: 0.8770 (tt) REVERT: A 178 TYR cc_start: 0.7501 (m-80) cc_final: 0.7201 (m-10) REVERT: A 198 ILE cc_start: 0.9233 (pt) cc_final: 0.8968 (pt) REVERT: A 199 ILE cc_start: 0.9753 (mm) cc_final: 0.9472 (mm) REVERT: A 202 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8922 (mt-10) REVERT: A 208 ASN cc_start: 0.8833 (m110) cc_final: 0.8392 (m110) REVERT: A 218 ASN cc_start: 0.9242 (t0) cc_final: 0.8436 (t0) REVERT: A 233 VAL cc_start: 0.8803 (m) cc_final: 0.8406 (m) REVERT: A 244 GLU cc_start: 0.9038 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 247 ARG cc_start: 0.9248 (ttp-170) cc_final: 0.8621 (ttp-170) REVERT: A 248 PHE cc_start: 0.7906 (m-80) cc_final: 0.7020 (m-10) REVERT: A 267 ASP cc_start: 0.9210 (m-30) cc_final: 0.8733 (m-30) REVERT: A 291 LEU cc_start: 0.8932 (tp) cc_final: 0.8476 (tp) REVERT: A 295 LEU cc_start: 0.9439 (mt) cc_final: 0.9077 (mt) REVERT: A 297 ASN cc_start: 0.8995 (m-40) cc_final: 0.8662 (m110) REVERT: A 320 LEU cc_start: 0.9540 (mm) cc_final: 0.9268 (mm) REVERT: A 462 ASN cc_start: 0.5453 (m-40) cc_final: 0.5207 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0476 time to fit residues: 8.2222 Evaluate side-chains 108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 92 optimal weight: 0.0670 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.185482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.143284 restraints weight = 13461.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.147605 restraints weight = 9495.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.150715 restraints weight = 7091.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.153044 restraints weight = 5543.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.154836 restraints weight = 4472.454| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 1.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9536 Z= 0.133 Angle : 0.630 6.260 12836 Z= 0.350 Chirality : 0.042 0.140 1388 Planarity : 0.004 0.039 1574 Dihedral : 4.740 17.000 1208 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 0.58 (0.25), residues: 1100 helix: 1.21 (0.21), residues: 570 sheet: 0.81 (0.44), residues: 136 loop : -0.95 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.020 0.001 TYR A 544 PHE 0.034 0.002 PHE B 14 TRP 0.030 0.002 TRP A 414 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9532) covalent geometry : angle 0.63037 / 0.35 (12836) hydrogen bonds : bond 0.04830 / 3.07 ( 508) hydrogen bonds : angle 5.04023 / 3.58 ( 1542) metal coordination : bond 0.00044 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9288 (t80) cc_final: 0.8893 (t80) REVERT: A 28 ARG cc_start: 0.8334 (tpt90) cc_final: 0.7806 (tpt90) REVERT: A 110 TRP cc_start: 0.8284 (t60) cc_final: 0.7497 (t60) REVERT: A 116 ILE cc_start: 0.9338 (mm) cc_final: 0.9092 (pt) REVERT: A 121 PHE cc_start: 0.9537 (t80) cc_final: 0.9154 (t80) REVERT: A 126 LEU cc_start: 0.9222 (mt) cc_final: 0.8980 (mt) REVERT: A 141 ASN cc_start: 0.9406 (m-40) cc_final: 0.8722 (p0) REVERT: A 153 HIS cc_start: 0.8841 (m90) cc_final: 0.8469 (m90) REVERT: A 167 ILE cc_start: 0.9101 (mp) cc_final: 0.8694 (tt) REVERT: A 178 TYR cc_start: 0.7499 (m-80) cc_final: 0.7228 (m-10) REVERT: A 180 ILE cc_start: 0.8885 (mp) cc_final: 0.8282 (mp) REVERT: A 208 ASN cc_start: 0.8802 (m110) cc_final: 0.8278 (m110) REVERT: A 215 ILE cc_start: 0.9175 (tp) cc_final: 0.8894 (pt) REVERT: A 218 ASN cc_start: 0.9252 (t0) cc_final: 0.8518 (t0) REVERT: A 233 VAL cc_start: 0.8821 (m) cc_final: 0.8466 (m) REVERT: A 244 GLU cc_start: 0.9102 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 247 ARG cc_start: 0.9285 (ttp-170) cc_final: 0.8965 (ttp-110) REVERT: A 248 PHE cc_start: 0.8034 (m-80) cc_final: 0.7328 (m-10) REVERT: A 255 LYS cc_start: 0.9541 (mtmt) cc_final: 0.9105 (mtmm) REVERT: A 275 PHE cc_start: 0.8568 (t80) cc_final: 0.8110 (t80) REVERT: A 291 LEU cc_start: 0.8868 (tp) cc_final: 0.8394 (tp) REVERT: A 295 LEU cc_start: 0.9455 (mt) cc_final: 0.9108 (mt) REVERT: A 297 ASN cc_start: 0.8995 (m-40) cc_final: 0.8677 (m110) REVERT: A 313 PHE cc_start: 0.9684 (m-80) cc_final: 0.9460 (m-80) REVERT: A 317 PHE cc_start: 0.9290 (m-80) cc_final: 0.8765 (m-80) REVERT: A 320 LEU cc_start: 0.9552 (mm) cc_final: 0.9200 (mm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0531 time to fit residues: 9.4757 Evaluate side-chains 106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.0870 chunk 47 optimal weight: 0.0470 chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.189219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.145861 restraints weight = 13357.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.150275 restraints weight = 9301.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153361 restraints weight = 6892.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.155705 restraints weight = 5355.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.157432 restraints weight = 4314.582| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 1.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9536 Z= 0.133 Angle : 0.645 9.190 12836 Z= 0.352 Chirality : 0.042 0.148 1388 Planarity : 0.004 0.052 1574 Dihedral : 4.641 17.710 1208 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 0.71 (0.25), residues: 1100 helix: 1.43 (0.21), residues: 568 sheet: 0.52 (0.45), residues: 136 loop : -0.93 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.016 0.001 TYR B 441 PHE 0.040 0.002 PHE B 14 TRP 0.031 0.002 TRP A 414 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9532) covalent geometry : angle 0.64548 / 0.35 (12836) hydrogen bonds : bond 0.04630 / 2.89 ( 508) hydrogen bonds : angle 4.85584 / 3.45 ( 1542) metal coordination : bond 0.00055 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9382 (t80) cc_final: 0.8848 (t80) REVERT: A 28 ARG cc_start: 0.8389 (tpt90) cc_final: 0.7932 (tpt90) REVERT: A 110 TRP cc_start: 0.8366 (t60) cc_final: 0.7655 (t60) REVERT: A 116 ILE cc_start: 0.9298 (mm) cc_final: 0.9060 (pt) REVERT: A 126 LEU cc_start: 0.9119 (mt) cc_final: 0.8919 (mt) REVERT: A 141 ASN cc_start: 0.9319 (m-40) cc_final: 0.8545 (p0) REVERT: A 153 HIS cc_start: 0.8663 (m90) cc_final: 0.8429 (m-70) REVERT: A 167 ILE cc_start: 0.9057 (mp) cc_final: 0.8745 (tt) REVERT: A 198 ILE cc_start: 0.9300 (pt) cc_final: 0.8989 (pt) REVERT: A 199 ILE cc_start: 0.9735 (mm) cc_final: 0.9414 (mm) REVERT: A 202 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8916 (mt-10) REVERT: A 208 ASN cc_start: 0.8701 (m110) cc_final: 0.8287 (m110) REVERT: A 213 HIS cc_start: 0.8868 (m90) cc_final: 0.8493 (m170) REVERT: A 233 VAL cc_start: 0.8781 (m) cc_final: 0.8421 (m) REVERT: A 240 ASP cc_start: 0.9197 (m-30) cc_final: 0.8946 (m-30) REVERT: A 247 ARG cc_start: 0.9262 (ttp-170) cc_final: 0.8818 (ttp-170) REVERT: A 248 PHE cc_start: 0.7984 (m-80) cc_final: 0.7388 (m-10) REVERT: A 275 PHE cc_start: 0.8775 (t80) cc_final: 0.8370 (t80) REVERT: A 291 LEU cc_start: 0.8847 (tp) cc_final: 0.8344 (tp) REVERT: A 295 LEU cc_start: 0.9418 (mt) cc_final: 0.9076 (mt) REVERT: A 297 ASN cc_start: 0.9022 (m-40) cc_final: 0.8703 (m110) REVERT: A 313 PHE cc_start: 0.9588 (m-80) cc_final: 0.9194 (m-80) REVERT: A 317 PHE cc_start: 0.9335 (m-80) cc_final: 0.8786 (m-80) REVERT: A 330 MET cc_start: 0.0629 (tpp) cc_final: 0.0344 (tpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0529 time to fit residues: 8.7821 Evaluate side-chains 107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 71 optimal weight: 0.3980 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 74 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.189228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.145695 restraints weight = 13574.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.150109 restraints weight = 9343.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.153127 restraints weight = 6833.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.155393 restraints weight = 5277.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156842 restraints weight = 4235.715| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 1.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9536 Z= 0.128 Angle : 0.639 9.995 12836 Z= 0.352 Chirality : 0.042 0.143 1388 Planarity : 0.004 0.042 1574 Dihedral : 4.557 17.039 1208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 0.71 (0.25), residues: 1100 helix: 1.42 (0.21), residues: 568 sheet: 0.55 (0.45), residues: 136 loop : -0.92 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.017 0.001 TYR B 441 PHE 0.041 0.002 PHE B 14 TRP 0.040 0.003 TRP A 414 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 9532) covalent geometry : angle 0.63913 / 0.35 (12836) hydrogen bonds : bond 0.04587 / 2.90 ( 508) hydrogen bonds : angle 4.89413 / 3.48 ( 1542) metal coordination : bond 0.00002 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9359 (t80) cc_final: 0.8834 (t80) REVERT: A 20 LEU cc_start: 0.9731 (mt) cc_final: 0.9309 (mt) REVERT: A 28 ARG cc_start: 0.8411 (tpt90) cc_final: 0.7921 (tpt90) REVERT: A 39 TRP cc_start: 0.8610 (m100) cc_final: 0.6925 (m-90) REVERT: A 110 TRP cc_start: 0.8369 (t60) cc_final: 0.7713 (t60) REVERT: A 116 ILE cc_start: 0.9268 (mm) cc_final: 0.9036 (pt) REVERT: A 121 PHE cc_start: 0.9478 (t80) cc_final: 0.9006 (t80) REVERT: A 126 LEU cc_start: 0.9094 (mt) cc_final: 0.8839 (mt) REVERT: A 141 ASN cc_start: 0.9286 (m-40) cc_final: 0.8717 (p0) REVERT: A 167 ILE cc_start: 0.9121 (mp) cc_final: 0.8710 (tt) REVERT: A 198 ILE cc_start: 0.9311 (pt) cc_final: 0.8985 (pt) REVERT: A 199 ILE cc_start: 0.9744 (mm) cc_final: 0.9430 (mm) REVERT: A 202 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8893 (mt-10) REVERT: A 208 ASN cc_start: 0.8687 (m110) cc_final: 0.8193 (m110) REVERT: A 213 HIS cc_start: 0.8831 (m90) cc_final: 0.8448 (m170) REVERT: A 218 ASN cc_start: 0.9293 (t0) cc_final: 0.8684 (t0) REVERT: A 233 VAL cc_start: 0.8787 (m) cc_final: 0.8296 (m) REVERT: A 240 ASP cc_start: 0.9172 (m-30) cc_final: 0.8494 (m-30) REVERT: A 247 ARG cc_start: 0.9217 (ttp-170) cc_final: 0.8780 (ttp-170) REVERT: A 248 PHE cc_start: 0.7969 (m-80) cc_final: 0.7458 (m-10) REVERT: A 267 ASP cc_start: 0.9178 (m-30) cc_final: 0.8633 (m-30) REVERT: A 275 PHE cc_start: 0.8666 (t80) cc_final: 0.8256 (t80) REVERT: A 291 LEU cc_start: 0.8806 (tp) cc_final: 0.8254 (tp) REVERT: A 295 LEU cc_start: 0.9388 (mt) cc_final: 0.9040 (mt) REVERT: A 297 ASN cc_start: 0.9019 (m-40) cc_final: 0.8713 (m110) REVERT: A 313 PHE cc_start: 0.9585 (m-80) cc_final: 0.9180 (m-80) REVERT: A 317 PHE cc_start: 0.9331 (m-80) cc_final: 0.8768 (m-80) REVERT: A 385 TYR cc_start: 0.6918 (m-80) cc_final: 0.6707 (m-80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0493 time to fit residues: 8.4130 Evaluate side-chains 108 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.184609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142594 restraints weight = 13754.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.146988 restraints weight = 9465.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.150015 restraints weight = 6899.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.152356 restraints weight = 5304.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.154038 restraints weight = 4253.020| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 1.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9536 Z= 0.149 Angle : 0.667 10.281 12836 Z= 0.365 Chirality : 0.043 0.225 1388 Planarity : 0.004 0.037 1574 Dihedral : 4.690 17.556 1208 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.66 (0.25), residues: 1100 helix: 1.35 (0.21), residues: 572 sheet: 0.61 (0.44), residues: 136 loop : -0.96 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 294 TYR 0.019 0.002 TYR A 441 PHE 0.043 0.002 PHE A 14 TRP 0.041 0.003 TRP B 414 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 9532) covalent geometry : angle 0.66691 / 0.36 (12836) hydrogen bonds : bond 0.04734 / 3.00 ( 508) hydrogen bonds : angle 5.09844 / 3.62 ( 1542) metal coordination : bond 0.00066 / 0.03 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9408 (t80) cc_final: 0.9051 (t80) REVERT: A 20 LEU cc_start: 0.9750 (mt) cc_final: 0.9352 (mt) REVERT: A 39 TRP cc_start: 0.8557 (m100) cc_final: 0.7372 (m-90) REVERT: A 110 TRP cc_start: 0.8328 (t60) cc_final: 0.7565 (t60) REVERT: A 116 ILE cc_start: 0.9279 (mm) cc_final: 0.8955 (pt) REVERT: A 121 PHE cc_start: 0.9449 (t80) cc_final: 0.8936 (t80) REVERT: A 127 TYR cc_start: 0.8182 (t80) cc_final: 0.7632 (t80) REVERT: A 141 ASN cc_start: 0.9262 (m-40) cc_final: 0.8731 (p0) REVERT: A 153 HIS cc_start: 0.8303 (m90) cc_final: 0.7982 (m90) REVERT: A 167 ILE cc_start: 0.9302 (mp) cc_final: 0.8628 (tt) REVERT: A 198 ILE cc_start: 0.9322 (pt) cc_final: 0.8989 (pt) REVERT: A 199 ILE cc_start: 0.9745 (mm) cc_final: 0.9467 (mm) REVERT: A 202 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8916 (mt-10) REVERT: A 208 ASN cc_start: 0.8736 (m110) cc_final: 0.8238 (m110) REVERT: A 213 HIS cc_start: 0.8877 (m90) cc_final: 0.8224 (m-70) REVERT: A 217 PHE cc_start: 0.9168 (m-80) cc_final: 0.8390 (m-80) REVERT: A 218 ASN cc_start: 0.9250 (t0) cc_final: 0.8524 (t0) REVERT: A 233 VAL cc_start: 0.8689 (m) cc_final: 0.8241 (m) REVERT: A 244 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8930 (mm-30) REVERT: A 248 PHE cc_start: 0.8265 (m-80) cc_final: 0.7768 (m-10) REVERT: A 295 LEU cc_start: 0.9418 (mt) cc_final: 0.9169 (mt) REVERT: A 317 PHE cc_start: 0.9232 (m-80) cc_final: 0.8709 (t80) REVERT: A 385 TYR cc_start: 0.7427 (m-80) cc_final: 0.7188 (m-10) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0552 time to fit residues: 9.6072 Evaluate side-chains 107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 0.0070 chunk 88 optimal weight: 0.1980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.186755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143831 restraints weight = 13600.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.148368 restraints weight = 9157.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.151528 restraints weight = 6593.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.153926 restraints weight = 5020.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.155613 restraints weight = 3998.459| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 1.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9536 Z= 0.127 Angle : 0.632 10.190 12836 Z= 0.351 Chirality : 0.042 0.148 1388 Planarity : 0.004 0.042 1574 Dihedral : 4.695 20.743 1208 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 0.66 (0.25), residues: 1100 helix: 1.32 (0.21), residues: 584 sheet: 0.63 (0.44), residues: 136 loop : -1.00 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.018 0.001 TYR B 441 PHE 0.043 0.002 PHE B 14 TRP 0.038 0.002 TRP B 414 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 9532) covalent geometry : angle 0.63158 / 0.35 (12836) hydrogen bonds : bond 0.04531 / 2.84 ( 508) hydrogen bonds : angle 4.90956 / 3.49 ( 1542) metal coordination : bond 0.00054 / 0.03 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1117.90 seconds wall clock time: 20 minutes 11.96 seconds (1211.96 seconds total)