Starting phenix.real_space_refine on Thu Jul 2 04:51:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m71_23707/07_2026/7m71_23707.map" } resolution = 2.66 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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4212 2.51 5 N 1112 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s 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: 6646 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "B" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.44, per 1000 atoms: 0.22 Number of scatterers: 6646 At special positions: 0 Unit cell: (115.193, 92.6293, 129.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1293 8.00 N 1112 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 222 " - pdb=" SG CYS L 214 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 355.8 milliseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 20 sheets defined 14.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.941A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.606A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.446A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.860A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.715A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.504A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.268A pdb=" N GLY H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.906A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.703A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.761A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.776A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.893A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 137 through 138 removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.410A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 148 Processing sheet with id=AC2, first strand: chain 'L' and resid 161 through 164 removed outlier: 4.153A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 465 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: 1.03 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1616 1.33 - 1.45: 1469 1.45 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6810 Sorted by residual: bond pdb=" CA PHE L 118 " pdb=" C PHE L 118 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.06e-02 8.90e+03 1.55e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CZ ARG A 454 " pdb=" NH2 ARG A 454 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA PRO L 119 " pdb=" C PRO L 119 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.18e+01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6411 1.84 - 3.69: 2379 3.69 - 5.53: 420 5.53 - 7.38: 41 7.38 - 9.22: 7 Bond angle restraints: 9258 Sorted by residual: angle pdb=" CA PHE H 68 " pdb=" CB PHE H 68 " pdb=" CG PHE H 68 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 114.23 120.16 -5.93 8.80e-01 1.29e+00 4.54e+01 angle pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " pdb=" ND2 ASN A 331 " ideal model delta sigma weight residual 116.40 107.47 8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C LYS H 215 " pdb=" N LYS H 216 " pdb=" CA LYS H 216 " ideal model delta sigma weight residual 120.95 128.90 -7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" CA PHE L 209 " pdb=" CB PHE L 209 " pdb=" CG PHE L 209 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 9253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3705 17.69 - 35.37: 269 35.37 - 53.05: 43 53.05 - 70.74: 10 70.74 - 88.42: 4 Dihedral angle restraints: 4031 sinusoidal: 1558 harmonic: 2473 Sorted by residual: dihedral pdb=" CA THR L 178 " pdb=" C THR L 178 " pdb=" N LEU L 179 " pdb=" CA LEU L 179 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ARG H 72 " pdb=" C ARG H 72 " pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU L 104 " pdb=" C LEU L 104 " pdb=" N GLU L 105 " pdb=" CA GLU L 105 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 4028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 1010 0.274 - 0.548: 13 0.548 - 0.822: 0 0.822 - 1.096: 0 1.096 - 1.370: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.69e+01 chirality pdb=" CA ASP H 150 " pdb=" N ASP H 150 " pdb=" C ASP H 150 " pdb=" CB ASP H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN B 331 " pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CB ASN B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 1021 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.098 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" CG ASN A 331 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.153 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " 0.131 2.00e-02 2.50e+03 7.39e-02 1.09e+02 pdb=" CG TYR L 49 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.121 2.00e-02 2.50e+03 6.35e-02 1.01e+02 pdb=" CG TRP B 353 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.074 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3298 3.00 - 3.48: 6121 3.48 - 3.95: 11157 3.95 - 4.43: 12531 4.43 - 4.90: 20762 Nonbonded interactions: 53869 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.531 3.040 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.549 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.561 3.040 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.577 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.579 3.040 ... (remaining 53864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 6.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.073 6827 Z= 0.752 Angle : 1.872 9.869 9296 Z= 1.236 Chirality : 0.112 1.370 1024 Planarity : 0.016 0.190 1193 Dihedral : 13.090 88.419 2418 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.41 % Allowed : 3.81 % Favored : 95.78 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 2.17 % 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: -0.93 (0.27), residues: 844 helix: -4.22 (0.28), residues: 79 sheet: 0.09 (0.32), residues: 253 loop : -0.31 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.131 0.019 TYR L 49 PHE 0.077 0.013 PHE L 118 TRP 0.121 0.024 TRP B 353 HIS 0.007 0.003 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.01282 / 0.75 ( 6810) covalent geometry : angle 1.86108 / 1.24 ( 9258) SS BOND : bond 0.02022 / 0.88 ( 13) SS BOND : angle 2.54002 / 1.69 ( 26) hydrogen bonds : bond 0.12603 / 7.89 ( 199) hydrogen bonds : angle 9.08133 / 6.25 ( 465) link_NAG-ASN : bond 0.00964 / 0.47 ( 4) link_NAG-ASN : angle 5.38630 / 3.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.316 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.7601 time to fit residues: 44.2178 Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN A 487 ASN B 354 ASN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.053803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.034349 restraints weight = 33251.301| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.47 r_work: 0.2735 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6827 Z= 0.139 Angle : 0.645 7.726 9296 Z= 0.336 Chirality : 0.045 0.149 1024 Planarity : 0.005 0.039 1193 Dihedral : 5.861 34.859 933 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.82 % Allowed : 7.21 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.42 (0.29), residues: 844 helix: -3.24 (0.55), residues: 65 sheet: 0.10 (0.30), residues: 288 loop : 0.03 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.024 0.001 TYR L 186 PHE 0.015 0.002 PHE H 29 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6810) covalent geometry : angle 0.63386 / 0.33 ( 9258) SS BOND : bond 0.00322 / 0.13 ( 13) SS BOND : angle 0.81882 / 0.58 ( 26) hydrogen bonds : bond 0.03672 / 2.23 ( 199) hydrogen bonds : angle 7.04702 / 4.81 ( 465) link_NAG-ASN : bond 0.00217 / 0.11 ( 4) link_NAG-ASN : angle 3.27858 / 2.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.269 Fit side-chains REVERT: A 406 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8548 (mt-10) REVERT: B 340 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8650 (mp0) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.7074 time to fit residues: 28.0876 Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.052272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.032957 restraints weight = 33464.257| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.44 r_work: 0.2693 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6827 Z= 0.225 Angle : 0.629 7.008 9296 Z= 0.328 Chirality : 0.045 0.145 1024 Planarity : 0.005 0.042 1193 Dihedral : 5.253 26.869 930 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.82 % Allowed : 8.57 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.49 (0.29), residues: 844 helix: -3.03 (0.52), residues: 72 sheet: 0.17 (0.30), residues: 275 loop : -0.08 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 346 TYR 0.021 0.002 TYR A 495 PHE 0.013 0.002 PHE H 29 TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 ( 6810) covalent geometry : angle 0.61948 / 0.33 ( 9258) SS BOND : bond 0.00417 / 0.17 ( 13) SS BOND : angle 0.91796 / 0.63 ( 26) hydrogen bonds : bond 0.03742 / 2.29 ( 199) hydrogen bonds : angle 6.74005 / 4.60 ( 465) link_NAG-ASN : bond 0.00302 / 0.15 ( 4) link_NAG-ASN : angle 2.92452 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8448 (mt-10) REVERT: B 340 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8711 (mp0) REVERT: B 516 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8105 (pp20) REVERT: L 143 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8170 (pm20) outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.8068 time to fit residues: 26.1350 Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN L 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.052301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033026 restraints weight = 33732.823| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.42 r_work: 0.2698 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6827 Z= 0.176 Angle : 0.581 6.388 9296 Z= 0.300 Chirality : 0.044 0.139 1024 Planarity : 0.004 0.044 1193 Dihedral : 4.940 25.682 930 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.09 % Allowed : 10.07 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.40 (0.29), residues: 844 helix: -3.10 (0.53), residues: 66 sheet: 0.17 (0.31), residues: 276 loop : -0.01 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 142 TYR 0.019 0.001 TYR L 186 PHE 0.014 0.001 PHE H 29 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 6810) covalent geometry : angle 0.57288 / 0.30 ( 9258) SS BOND : bond 0.00344 / 0.13 ( 13) SS BOND : angle 0.79928 / 0.57 ( 26) hydrogen bonds : bond 0.03402 / 2.08 ( 199) hydrogen bonds : angle 6.41351 / 4.34 ( 465) link_NAG-ASN : bond 0.00200 / 0.10 ( 4) link_NAG-ASN : angle 2.58401 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 340 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8653 (mp0) REVERT: B 516 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8115 (pp20) REVERT: H 203 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6227 (p0) REVERT: L 143 GLU cc_start: 0.8406 (pm20) cc_final: 0.8189 (pm20) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.7039 time to fit residues: 24.4267 Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN L 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.052351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033067 restraints weight = 34073.244| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.51 r_work: 0.2701 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6827 Z= 0.159 Angle : 0.570 7.317 9296 Z= 0.291 Chirality : 0.044 0.152 1024 Planarity : 0.004 0.045 1193 Dihedral : 4.722 25.744 930 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.04 % Allowed : 9.39 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.32 (0.29), residues: 844 helix: -3.07 (0.54), residues: 66 sheet: 0.28 (0.30), residues: 285 loop : 0.02 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 346 TYR 0.017 0.001 TYR L 186 PHE 0.013 0.001 PHE H 29 TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6810) covalent geometry : angle 0.56325 / 0.29 ( 9258) SS BOND : bond 0.00313 / 0.12 ( 13) SS BOND : angle 0.76893 / 0.55 ( 26) hydrogen bonds : bond 0.03254 / 1.98 ( 199) hydrogen bonds : angle 6.32017 / 4.30 ( 465) link_NAG-ASN : bond 0.00113 / 0.06 ( 4) link_NAG-ASN : angle 2.40213 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8689 (mp0) REVERT: B 516 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8160 (pp20) REVERT: H 201 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8851 (pp) REVERT: H 203 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.6157 (p0) outliers start: 15 outliers final: 4 residues processed: 39 average time/residue: 0.6329 time to fit residues: 26.0225 Evaluate side-chains 31 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.051550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032013 restraints weight = 34404.472| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.55 r_work: 0.2662 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6827 Z= 0.314 Angle : 0.656 6.722 9296 Z= 0.338 Chirality : 0.046 0.148 1024 Planarity : 0.005 0.047 1193 Dihedral : 5.119 24.965 930 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.63 % Allowed : 10.34 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.61 (0.29), residues: 844 helix: -3.13 (0.52), residues: 72 sheet: 0.12 (0.30), residues: 286 loop : -0.20 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 346 TYR 0.018 0.002 TYR L 186 PHE 0.014 0.002 PHE L 83 TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 ( 6810) covalent geometry : angle 0.64764 / 0.34 ( 9258) SS BOND : bond 0.00488 / 0.20 ( 13) SS BOND : angle 1.02817 / 0.70 ( 26) hydrogen bonds : bond 0.03767 / 2.29 ( 199) hydrogen bonds : angle 6.66960 / 4.55 ( 465) link_NAG-ASN : bond 0.00488 / 0.25 ( 4) link_NAG-ASN : angle 2.76546 / 1.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8626 (mt-10) REVERT: B 340 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8705 (mp0) REVERT: B 516 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: H 201 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8857 (pp) REVERT: H 203 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6245 (p0) outliers start: 12 outliers final: 5 residues processed: 33 average time/residue: 0.7144 time to fit residues: 24.8165 Evaluate side-chains 30 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 80 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.051932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.032516 restraints weight = 33829.588| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.47 r_work: 0.2684 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6827 Z= 0.216 Angle : 0.599 6.886 9296 Z= 0.308 Chirality : 0.045 0.143 1024 Planarity : 0.005 0.050 1193 Dihedral : 4.863 24.387 930 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.09 % Allowed : 10.48 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.29), residues: 844 helix: -3.13 (0.52), residues: 72 sheet: 0.06 (0.30), residues: 280 loop : -0.23 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 346 TYR 0.017 0.001 TYR L 186 PHE 0.015 0.001 PHE H 29 TRP 0.015 0.002 TRP L 148 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 ( 6810) covalent geometry : angle 0.59186 / 0.31 ( 9258) SS BOND : bond 0.00362 / 0.14 ( 13) SS BOND : angle 0.80533 / 0.56 ( 26) hydrogen bonds : bond 0.03412 / 2.09 ( 199) hydrogen bonds : angle 6.42596 / 4.36 ( 465) link_NAG-ASN : bond 0.00242 / 0.12 ( 4) link_NAG-ASN : angle 2.49073 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8605 (mt-10) REVERT: B 340 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8668 (mp0) REVERT: B 516 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8138 (pp20) REVERT: H 201 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8915 (pp) REVERT: H 203 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6309 (p0) REVERT: L 105 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7425 (mp0) outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.6976 time to fit residues: 23.4371 Evaluate side-chains 31 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 0.0070 chunk 59 optimal weight: 0.0770 chunk 17 optimal weight: 0.0050 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.053562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.034536 restraints weight = 33798.250| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.49 r_work: 0.2761 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6827 Z= 0.096 Angle : 0.547 6.893 9296 Z= 0.279 Chirality : 0.043 0.163 1024 Planarity : 0.004 0.047 1193 Dihedral : 4.200 25.901 930 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 11.02 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.26 (0.29), residues: 844 helix: -2.97 (0.56), residues: 66 sheet: 0.58 (0.33), residues: 241 loop : -0.08 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 142 TYR 0.018 0.001 TYR A 369 PHE 0.013 0.001 PHE H 29 TRP 0.013 0.001 TRP A 436 HIS 0.001 0.000 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 6810) covalent geometry : angle 0.54328 / 0.28 ( 9258) SS BOND : bond 0.00154 / 0.08 ( 13) SS BOND : angle 0.56139 / 0.43 ( 26) hydrogen bonds : bond 0.02671 / 1.68 ( 199) hydrogen bonds : angle 5.81249 / 3.95 ( 465) link_NAG-ASN : bond 0.00234 / 0.12 ( 4) link_NAG-ASN : angle 1.83863 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8516 (mt-10) REVERT: B 340 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8654 (mp0) REVERT: H 201 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8890 (pp) REVERT: L 105 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7397 (mp0) outliers start: 7 outliers final: 3 residues processed: 33 average time/residue: 0.6284 time to fit residues: 21.9280 Evaluate side-chains 26 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.052980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.033736 restraints weight = 34444.825| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.53 r_work: 0.2731 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6827 Z= 0.114 Angle : 0.552 6.897 9296 Z= 0.283 Chirality : 0.043 0.145 1024 Planarity : 0.005 0.055 1193 Dihedral : 4.161 25.081 930 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.54 % Allowed : 11.56 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.21 (0.29), residues: 844 helix: -2.96 (0.55), residues: 66 sheet: 0.46 (0.33), residues: 259 loop : 0.03 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 346 TYR 0.015 0.001 TYR L 186 PHE 0.013 0.001 PHE H 29 TRP 0.009 0.001 TRP L 148 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6810) covalent geometry : angle 0.54800 / 0.28 ( 9258) SS BOND : bond 0.00218 / 0.09 ( 13) SS BOND : angle 0.63080 / 0.45 ( 26) hydrogen bonds : bond 0.02908 / 1.80 ( 199) hydrogen bonds : angle 5.79745 / 3.92 ( 465) link_NAG-ASN : bond 0.00098 / 0.05 ( 4) link_NAG-ASN : angle 1.87980 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8503 (mt-10) REVERT: B 340 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8642 (mp0) REVERT: L 105 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7410 (mp0) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.6009 time to fit residues: 17.8343 Evaluate side-chains 23 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.052986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.033669 restraints weight = 34038.487| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.54 r_work: 0.2728 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6827 Z= 0.116 Angle : 0.558 7.490 9296 Z= 0.287 Chirality : 0.043 0.143 1024 Planarity : 0.004 0.050 1193 Dihedral : 4.152 25.257 930 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.41 % Allowed : 11.56 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.29), residues: 844 helix: -2.96 (0.56), residues: 66 sheet: 0.49 (0.33), residues: 259 loop : 0.02 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 346 TYR 0.015 0.001 TYR L 186 PHE 0.013 0.001 PHE H 29 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6810) covalent geometry : angle 0.55339 / 0.29 ( 9258) SS BOND : bond 0.00232 / 0.10 ( 13) SS BOND : angle 0.61980 / 0.45 ( 26) hydrogen bonds : bond 0.02886 / 1.78 ( 199) hydrogen bonds : angle 5.75336 / 3.89 ( 465) link_NAG-ASN : bond 0.00140 / 0.07 ( 4) link_NAG-ASN : angle 1.93853 / 1.21 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8510 (mt-10) REVERT: B 340 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8655 (mp0) REVERT: H 194 SER cc_start: 0.7686 (OUTLIER) cc_final: 0.7452 (t) REVERT: L 105 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7493 (mp0) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.6306 time to fit residues: 18.7353 Evaluate side-chains 25 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 22 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 5 optimal weight: 0.6980 overall best weight: 1.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.052508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.033128 restraints weight = 34092.147| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.55 r_work: 0.2704 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6827 Z= 0.169 Angle : 0.579 7.210 9296 Z= 0.299 Chirality : 0.043 0.140 1024 Planarity : 0.005 0.056 1193 Dihedral : 4.371 24.868 930 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.41 % Allowed : 11.84 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 844 helix: -2.94 (0.56), residues: 66 sheet: 0.47 (0.33), residues: 259 loop : 0.01 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 346 TYR 0.015 0.001 TYR L 186 PHE 0.013 0.001 PHE H 29 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6810) covalent geometry : angle 0.57427 / 0.30 ( 9258) SS BOND : bond 0.00301 / 0.12 ( 13) SS BOND : angle 0.73515 / 0.51 ( 26) hydrogen bonds : bond 0.03138 / 1.92 ( 199) hydrogen bonds : angle 5.95059 / 4.02 ( 465) link_NAG-ASN : bond 0.00154 / 0.08 ( 4) link_NAG-ASN : angle 2.06876 / 1.31 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2597.63 seconds wall clock time: 45 minutes 11.11 seconds (2711.11 seconds total)