Starting phenix.real_space_refine on Tue Mar 11 22:23:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m71_23707/03_2025/7m71_23707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m71_23707/03_2025/7m71_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m71_23707/03_2025/7m71_23707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m71_23707/03_2025/7m71_23707.map" model { file = "/net/cci-nas-00/data/ceres_data/7m71_23707/03_2025/7m71_23707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m71_23707/03_2025/7m71_23707.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.53, per 1000 atoms: 0.98 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: 1.74 Conformation dependent library (CDL) restraints added in 996.9 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: 0.97 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: 1.83 Time building geometry restraints manager: 2.06 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: 3785 17.69 - 35.37: 271 35.37 - 53.05: 45 53.05 - 70.74: 10 70.74 - 88.42: 4 Dihedral angle restraints: 4115 sinusoidal: 1642 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 4112 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.030 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 6810 Z= 0.828 Angle : 1.861 9.223 9258 Z= 1.235 Chirality : 0.112 1.370 1024 Planarity : 0.016 0.190 1193 Dihedral : 12.979 88.419 2502 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.121 0.024 TRP B 353 HIS 0.007 0.003 HIS H 206 PHE 0.077 0.013 PHE L 118 TYR 0.131 0.019 TYR L 49 ARG 0.011 0.001 ARG A 403 *********************** 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 : 0.751 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 1.7670 time to fit residues: 103.1975 Evaluate side-chains 27 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 70 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 487 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.053828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.034315 restraints weight = 33177.698| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.46 r_work: 0.2736 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6810 Z= 0.201 Angle : 0.638 7.630 9258 Z= 0.336 Chirality : 0.045 0.175 1024 Planarity : 0.005 0.039 1193 Dihedral : 6.258 47.938 1017 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 844 helix: -3.27 (0.54), residues: 65 sheet: 0.09 (0.30), residues: 288 loop : 0.03 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.016 0.002 PHE H 29 TYR 0.024 0.001 TYR L 186 ARG 0.007 0.001 ARG A 346 *********************** 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 : 0.758 Fit side-chains REVERT: A 406 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8530 (mt-10) REVERT: B 340 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8653 (mp0) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 1.7400 time to fit residues: 69.6069 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 : 0.817 ------------------------------------------------------------------------------- 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 68 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.052682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.033348 restraints weight = 33644.412| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.48 r_work: 0.2708 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6810 Z= 0.248 Angle : 0.585 6.557 9258 Z= 0.306 Chirality : 0.044 0.150 1024 Planarity : 0.005 0.041 1193 Dihedral : 5.582 49.360 1014 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.54 % Allowed : 8.57 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 844 helix: -2.96 (0.58), residues: 65 sheet: 0.23 (0.31), residues: 277 loop : 0.05 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE H 29 TYR 0.021 0.001 TYR A 495 ARG 0.008 0.001 ARG B 346 *********************** 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 34 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 340 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8669 (mp0) REVERT: B 516 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: L 142 ARG cc_start: 0.9082 (ttp80) cc_final: 0.8580 (ttp80) outliers start: 4 outliers final: 3 residues processed: 33 average time/residue: 1.6222 time to fit residues: 56.3820 Evaluate side-chains 30 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain B residue 516 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 59 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.051316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.031903 restraints weight = 34361.751| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.54 r_work: 0.2654 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 6810 Z= 0.526 Angle : 0.667 6.347 9258 Z= 0.350 Chirality : 0.047 0.152 1024 Planarity : 0.005 0.045 1193 Dihedral : 6.341 47.492 1014 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.09 % Allowed : 9.66 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.29), residues: 844 helix: -3.17 (0.52), residues: 72 sheet: 0.02 (0.30), residues: 281 loop : -0.25 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.016 0.002 PHE L 83 TYR 0.020 0.002 TYR L 186 ARG 0.006 0.001 ARG A 346 *********************** 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 36 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: B 516 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8207 (pp20) REVERT: L 105 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7792 (mp0) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 1.5018 time to fit residues: 54.0020 Evaluate side-chains 27 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 50.0000 chunk 6 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.052448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.033261 restraints weight = 33726.781| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.48 r_work: 0.2711 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6810 Z= 0.172 Angle : 0.548 6.341 9258 Z= 0.283 Chirality : 0.043 0.148 1024 Planarity : 0.004 0.045 1193 Dihedral : 5.444 50.325 1014 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.22 % Allowed : 10.48 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 844 helix: -3.12 (0.55), residues: 66 sheet: 0.24 (0.31), residues: 278 loop : -0.09 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.001 0.000 HIS H 206 PHE 0.014 0.001 PHE H 29 TYR 0.017 0.001 TYR L 186 ARG 0.009 0.001 ARG A 346 *********************** 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 36 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 516 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8157 (pp20) REVERT: H 201 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8862 (pp) REVERT: H 203 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6130 (p0) outliers start: 9 outliers final: 3 residues processed: 35 average time/residue: 1.4390 time to fit residues: 53.4960 Evaluate side-chains 32 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.052143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.032831 restraints weight = 33805.515| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.41 r_work: 0.2692 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6810 Z= 0.267 Angle : 0.578 6.424 9258 Z= 0.298 Chirality : 0.044 0.146 1024 Planarity : 0.004 0.046 1193 Dihedral : 5.451 50.360 1014 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.63 % Allowed : 10.20 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 844 helix: -3.14 (0.51), residues: 72 sheet: 0.19 (0.30), residues: 285 loop : -0.18 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.013 0.001 PHE H 29 TYR 0.018 0.001 TYR L 186 ARG 0.010 0.001 ARG A 346 *********************** 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 40 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8634 (mt-10) REVERT: B 340 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8681 (mp0) REVERT: B 516 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8211 (pp20) REVERT: H 201 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8892 (pp) REVERT: H 203 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6297 (p0) outliers start: 12 outliers final: 6 residues processed: 38 average time/residue: 1.3073 time to fit residues: 52.8705 Evaluate side-chains 31 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.0070 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.052882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.033711 restraints weight = 33766.627| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.49 r_work: 0.2729 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6810 Z= 0.147 Angle : 0.541 6.793 9258 Z= 0.276 Chirality : 0.043 0.146 1024 Planarity : 0.004 0.045 1193 Dihedral : 5.027 51.685 1014 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.22 % Allowed : 10.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 844 helix: -3.00 (0.55), residues: 66 sheet: 0.42 (0.32), residues: 259 loop : -0.06 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.012 0.001 PHE H 29 TYR 0.016 0.001 TYR L 186 ARG 0.012 0.001 ARG B 346 *********************** 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 36 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8626 (mt-10) REVERT: B 340 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8649 (mp0) REVERT: B 516 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: H 201 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8906 (pp) REVERT: L 142 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8649 (ttp80) outliers start: 9 outliers final: 4 residues processed: 34 average time/residue: 1.5478 time to fit residues: 55.6848 Evaluate side-chains 32 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 516 GLU 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 L residue 134 CYS 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 23 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 15 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.052573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.033391 restraints weight = 33544.266| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.51 r_work: 0.2719 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6810 Z= 0.190 Angle : 0.552 6.483 9258 Z= 0.283 Chirality : 0.043 0.138 1024 Planarity : 0.004 0.047 1193 Dihedral : 5.010 51.437 1014 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.09 % Allowed : 11.29 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 844 helix: -2.98 (0.55), residues: 66 sheet: 0.45 (0.32), residues: 259 loop : -0.04 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.012 0.001 PHE H 29 TYR 0.016 0.001 TYR L 186 ARG 0.011 0.001 ARG A 346 *********************** 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 36 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8453 (mt-10) REVERT: B 340 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8638 (mp0) REVERT: B 516 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8190 (pp20) REVERT: H 194 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7502 (t) REVERT: L 142 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8644 (ttp80) outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 1.5983 time to fit residues: 59.2199 Evaluate side-chains 31 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain H residue 194 SER 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 75 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 53 optimal weight: 50.0000 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.051638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.032336 restraints weight = 34370.701| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.46 r_work: 0.2675 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 6810 Z= 0.423 Angle : 0.631 7.358 9258 Z= 0.327 Chirality : 0.045 0.139 1024 Planarity : 0.005 0.060 1193 Dihedral : 5.672 49.551 1014 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.95 % Allowed : 11.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.29), residues: 844 helix: -3.05 (0.53), residues: 72 sheet: 0.23 (0.32), residues: 264 loop : -0.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.013 0.001 PHE L 83 TYR 0.017 0.002 TYR L 186 ARG 0.013 0.001 ARG B 346 *********************** 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 29 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8585 (mt-10) REVERT: B 516 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: H 194 SER cc_start: 0.7764 (OUTLIER) cc_final: 0.7472 (t) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 1.3524 time to fit residues: 40.8038 Evaluate side-chains 27 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN L 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.052590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033252 restraints weight = 34159.391| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.52 r_work: 0.2716 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6810 Z= 0.185 Angle : 0.563 7.415 9258 Z= 0.290 Chirality : 0.044 0.141 1024 Planarity : 0.004 0.045 1193 Dihedral : 5.142 50.965 1014 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.82 % Allowed : 11.56 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 844 helix: -2.97 (0.56), residues: 66 sheet: 0.32 (0.32), residues: 254 loop : -0.11 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.001 0.000 HIS H 206 PHE 0.013 0.001 PHE H 29 TYR 0.016 0.001 TYR L 186 ARG 0.007 0.000 ARG A 346 ********************** 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 31 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 340 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8560 (mp0) REVERT: B 516 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8184 (pp20) REVERT: H 194 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7311 (t) REVERT: L 142 ARG cc_start: 0.9141 (ttp80) cc_final: 0.8745 (ttp80) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 1.4590 time to fit residues: 46.5844 Evaluate side-chains 30 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 25 optimal weight: 0.0570 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 30.0000 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.052438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.033325 restraints weight = 34063.434| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.48 r_work: 0.2713 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6810 Z= 0.204 Angle : 0.561 7.180 9258 Z= 0.289 Chirality : 0.043 0.140 1024 Planarity : 0.004 0.059 1193 Dihedral : 5.106 51.216 1014 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.82 % Allowed : 11.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 844 helix: -2.98 (0.55), residues: 66 sheet: 0.39 (0.33), residues: 254 loop : -0.10 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.013 0.001 PHE H 29 TYR 0.016 0.001 TYR L 186 ARG 0.014 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5682.43 seconds wall clock time: 97 minutes 35.35 seconds (5855.35 seconds total)